FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices

Abstract

Single-molecule FRET (smFRET) has become a mainstream technique for studying biomolecular structural dynamics. The rapid and wide adoption of smFRET experiments by an ever-increasing number of groups has generated significant progress in sample preparation, measurement procedures, data analysis, algorithms and documentation. Several labs that employ smFRET approaches have joined forces to inform the smFRET community about streamlining how to perform experiments and analyze results for obtaining quantitative information on biomolecular structure and dynamics. The recent efforts include blind tests to assess the accuracy and the precision of smFRET experiments among different labs using various procedures. These multi-lab studies have led to the development of smFRET procedures and documentation, which are important when submitting entries into the archiving system for integrative structure models, PDB-Dev. This position paper describes the current ‘state of the art’ from different perspectives, points to unresolved methodological issues for quantitative structural studies, provides a set of ‘soft recommendations’ about which an emerging consensus exists, and lists openly available resources for newcomers and seasoned practitioners. To make further progress, we strongly encourage ‘open science’ practices.

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    de Souza N, Picotti P. Mass spectrometry analysis of the structural proteome. Current Opinion in Structural Biology. 2020;60:57-65.

    Not in our library10.1016/j.sbi.2019.10.006

98. 98.

    Deniz AA, Dahan M, Grunwell JR, Ha T, Faulhaber AE, Chemla DS, Weiss S, Schultz PG. Single-pair fluorescence resonance energy transfer on freely diffusing molecules: observation of Förster distance dependence and subpopulations. PNAS. 1999;96:3670-3675.

    Not in our library10.1073/pnas.96.7.3670

99. 99.

    Deniz AA, Laurence TA, Beligere GS, Dahan M, Martin AB, Chemla DS, Dawson PE, Schultz PG, Weiss S. Single-molecule protein folding: diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. PNAS. 2000;97:5179-5184.

    Not in our library10.1073/pnas.090104997

100. 100.

     Deniz AA. Deciphering complexity in molecular biophysics with Single-Molecule resolution. Journal of Molecular Biology. 2016;428:301-307.

     Not in our library10.1016/j.jmb.2015.12.011

101. 101.

     Deplazes E, Jayatilaka D, Corry B. Testing the use of molecular dynamics to simulate fluorophore motions and FRET. Physical Chemistry Chemical Physics. 2011;13:11045-11054.

     Not in our library10.1039/c1cp20447e

102. 102.

     Dertinger T, Pacheco V, von der Hocht I, Hartmann R, Gregor I, Enderlein J. Two-focus fluorescence correlation spectroscopy: a new tool for accurate and absolute diffusion measurements. ChemPhysChem. 2007;8:433-443.

     Not in our library10.1002/cphc.200600638

103. 103.

     Dertinger T, Loman A, Ewers B, Müller CB, Krämer B, Enderlein J. The optics and performance of dual-focus fluorescence correlation spectroscopy. Optics Express. 2008;16:14353-14368.

     Not in our library10.1364/oe.16.014353

104. 104.

     Deußner-Helfmann NS, Auer A, Strauss MT, Malkusch S, Dietz MS, Barth HD, Jungmann R, Heilemann M. Correlative Single-Molecule FRET and DNA-PAINT imaging. Nano Letters. 2018;18:4626-4630.

     Not in our library10.1021/acs.nanolett.8b02185

105. 105.

     Dickson RM, Cubitt AB, Tsien RY, Moerner WE. On/off blinking and switching behaviour of single molecules of green fluorescent protein. Nature. 1997;388:355-358.

     Not in our library10.1038/41048

106. 106.

     Diez M, Zimmermann B, Börsch M, König M, Schweinberger E, Steigmiller S, Reuter R, Felekyan S, Kudryavtsev V, Seidel CA, Gräber P. Proton-powered subunit rotation in single membrane-bound F0F1-ATP synthase. Nature Structural & Molecular Biology. 2004;11:135-141.

     Not in our library10.1038/nsmb718

107. 107.

     Dimura M, Peulen TO, Hanke CA, Prakash A, Gohlke H, Seidel CA. Quantitative FRET studies and integrative modeling unravel the structure and dynamics of biomolecular systems. Current Opinion in Structural Biology. 2016;40:163-185.

     Not in our library10.1016/j.sbi.2016.11.012

108. 108.
     Automated and optimally FRET-assisted structural modeling · 2020

     Not checked
109. 109.

     Dingfelder F, Benke S, Nettels D, Schuler B. Mapping an equilibrium folding intermediate of the cytolytic pore toxin ClyA with single-molecule FRET. The Journal of Physical Chemistry B. 2018;122:11251-11261.

     Not in our library10.1021/acs.jpcb.8b07026

110. 110.

     Doose S, Neuweiler H, Sauer M. Fluorescence quenching by photoinduced electron transfer: a reporter for conformational dynamics of macromolecules. ChemPhysChem. 2009;10:1389-1398.

     Not in our library10.1002/cphc.200900238

111. 111.

     Dunkle JA, Wang L, Feldman MB, Pulk A, Chen VB, Kapral GJ, Noeske J, Richardson JS, Blanchard SC, Cate JH. Structures of the bacterial ribosome in classical and hybrid states of tRNA binding. Science. 2011;332:981-984.

     Not in our library10.1126/science.1202692

112. 112.

     Dupuis NF, Holmstrom ED, Nesbitt DJ. Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics. PNAS. 2014;111:8464-8469.

     Not in our library10.1073/pnas.1316039111

113. 113.

     Düser MG, Bi Y, Zarrabi N, Dunn SD, Börsch M. The proton-translocating a subunit of F0F1-ATP synthase is allocated asymmetrically to the peripheral stalk. Journal of Biological Chemistry. 2008;283:33602-33610.

     Not in our library10.1074/jbc.m805170200

114. 114.

     Dyla M, Terry DS, Kjaergaard M, Sørensen TL, Lauwring Andersen J, Andersen JP, Rohde Knudsen C, Altman RB, Nissen P, Blanchard SC. Dynamics of P-type ATPase transport revealed by single-molecule FRET. Nature. 2017;551:346-351.

     Not in our library10.1038/nature24296

115. 115.

     Ebbinghaus S, Dhar A, McDonald JD, Gruebele M. Protein folding stability and dynamics imaged in a living cell. Nature Methods. 2010;7:319-323.

     Not in our library10.1038/nmeth.1435

116. 116.

     Edman L, Földes-Papp Z, Wennmalm S, Rigler R. The fluctuating enzyme: a single molecule approach. Chemical Physics. 1999;247:11-22.

     Not in our library10.1016/s0301-0104(99)00098-1

117. 117.

     Eggeling C, Berger S, Brand L, Fries JR, Schaffer J, Volkmer A, Seidel CA. Data registration and selective single-molecule analysis using multi-parameter fluorescence detection. Journal of Biotechnology. 2001;86:163-180.

     Not in our library10.1016/s0168-1656(00)00412-0

118. 118.

     Eilert T, Beckers M, Drechsler F, Michaelis J. Fast-NPS—A Markov Chain Monte Carlo-based analysis tool to obtain structural information from single-molecule FRET measurements. Computer Physics Communications. 2017;219:377-389.

     Not in our library10.1016/j.cpc.2017.05.027

119. 119.

     Eilert T, Kallis E, Nagy J, Röcker C, Michaelis J. Complete kinetic theory of FRET. The Journal of Physical Chemistry B. 2018;122:11677-11694.

     Not in our library10.1021/acs.jpcb.8b07719

120. 120.

     Enderlein J, Robbins DL, Ambrose WP, Goodwin PM, Keller RA. Statistics of single-molecule detection. The Journal of Physical Chemistry B. 1997;101:3626-3632.

     Not in our library10.1021/jp963261x

121. 121.

     Enderlein J, Gregor I, Patra D, Dertinger T, Kaupp UB. Performance of fluorescence correlation spectroscopy for measuring diffusion and concentration. ChemPhysChem. 2005;6:2324-2336.

     Not in our library10.1002/cphc.200500414

122. 122.

     Ernst P, Zosel F, Reichen C, Nettels D, Schuler B, Plückthun A. Structure-guided design of a peptide lock for modular peptide binders. ACS Chemical Biology. 2020;15:457-468.

     Not in our library10.1021/acschembio.9b00928

123. 123.

     Farooq S, Hohlbein J. Camera-based single-molecule FRET detection with improved time resolution. Physical Chemistry Chemical Physics. 2015;17:27862-27872.

     Not in our library10.1039/c5cp04137f

124. 124.

     Fay JM, Zhu C, Proctor EA, Tao Y, Cui W, Ke H, Dokholyan NV. A phosphomimetic mutation stabilizes SOD1 and rescues cell viability in the context of an ALS-Associated mutation. Structure. 2016;24:1898-1906.

     Not in our library10.1016/j.str.2016.08.011

125. 125.

     Felekyan S, Kühnemuth R, Kudryavtsev V, Sandhagen C, Becker W, Seidel CAM. Full correlation from picoseconds to seconds by time-resolved and time-correlated single photon detection. Review of Scientific Instruments. 2005;76:083104-083114.

     Not in our library10.1063/1.1946088

126. 126.

     Felekyan S, Kalinin S, Sanabria H, Valeri A, Seidel CA. Filtered FCS: species auto- and cross-correlation functions highlight binding and dynamics in biomolecules. ChemPhysChem. 2012;13:1036-1053.

     Not in our library10.1002/cphc.201100897

127. 127.

     Felekyan S, Sanabria H, Kalinin S, Kühnemuth R, Seidel CAM, Tetin E. Analyzing Förster resonance energy transfer with fluctuation algorithms. Methods in Enzymology. 2013;39-85.

     Not in our library10.1016/b978-0-12-405539-1.00002-6

128. 128.

     Felekyan S, Eggeling C, Schaffer J, Antonik M, Haustein E, Kudryavtsev V, Kalinin S, Marawske S, Seidel CAM. HHU Düsseldorf. 2020.

     Not in our library

129. 129.

     Feng X, Fu Z, Kaledhonkar S, Jia Y, Shah B, Jin A, Liu Z, Sun M, Chen B, Grassucci RA, Ren Y, Jiang H, Frank J, Lin Q. A fast and effective microfluidic spraying-plunging method for high-resolution single-particle Cryo-EM. Structure. 2017;25:663-670.

     Not in our library10.1016/j.str.2017.02.005

130. 130.

     Ferguson A, Wang L, Altman RB, Terry DS, Juette MF, Burnett BJ, Alejo JL, Dass RA, Parks MM, Vincent CT, Blanchard SC. Functional dynamics within the human ribosome regulate the rate of active protein synthesis. Molecular Cell. 2015;60:475-486.

     Not in our library10.1016/j.molcel.2015.09.013

131. 131.

     Filius M, Kim SH, Severins I, Joo C. High-Resolution Single-Molecule FRET via DNA eXchange (FRET X). bioRxiv. 2020.

     Not in our library10.1101/2020.10.15.340885

132. 132.

     Fitzgerald GA, Terry DS, Warren AL, Quick M, Javitch JA, Blanchard SC. Quantifying secondary transport at single-molecule resolution. Nature. 2019;575:528-534.

     Not in our library10.1038/s41586-019-1747-5

133. 133.

     Fontana M, Fijen C, Lemay SG, Mathwig K, Hohlbein J. High-throughput, non-equilibrium studies of single biomolecules using glass-made nanofluidic devices. Lab on a Chip. 2019;19:79-86.

     Not in our library10.1039/c8lc01175c

134. 134.

     Förster T. Zwischenmolekulare Energiewanderung und Fluoreszenz. Annalen Der Physik. 1948;437:55-75.

     Not in our library10.1002/andp.19484370105

135. 135.

     Fries JR, Brand L, Eggeling C, Köllner M, Seidel CAM. Quantitative identification of different single molecules by selective time-resolved confocal fluorescence spectroscopy. The Journal of Physical Chemistry A. 1998;102:6601-6613.

     Not in our library10.1021/jp980965t

136. 136.

     Gaigalas AK, Wang L. Measurement of the fluorescence quantum yield using a spectrometer with an integrating sphere detector. Journal of Research of the National Institute of Standards and Technology. 2008;113:17-28.

     Not in our library10.6028/jres.113.004

137. 137.

     Gambin Y, VanDelinder V, Ferreon AC, Lemke EA, Groisman A, Deniz AA. Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing. Nature Methods. 2011;8:239-241.

     Not in our library10.1038/nmeth.1568

138. 138.

     Gansen A, Felekyan S, Kühnemuth R, Lehmann K, Tóth K, Seidel CAM, Langowski J. High precision FRET studies reveal reversible transitions in nucleosomes between microseconds and minutes. Nature Communications. 2018;9:4628.

     Not in our library10.1038/s41467-018-06758-1

139. 139.

     Gao M, Gnutt D, Orban A, Appel B, Righetti F, Winter R, Narberhaus F, Müller S, Ebbinghaus S. RNA hairpin folding in the crowded cell. Angewandte Chemie International Edition. 2016;55:3224-3228.

     Not in our library10.1002/anie.201510847

140. 140.

     Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen AC, Schmidt E, Kerfah R, Mas G, Colletier JP, Güntert P, Favier A, Schoehn G, Schanda P, Boisbouvier J. Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton enzyme complex. Nature Communications. 2019;10:2697.

     Not in our library10.1038/s41467-019-10490-9

141. 141.

     Geggier P, Dave R, Feldman MB, Terry DS, Altman RB, Munro JB, Blanchard SC. Conformational sampling of aminoacyl-tRNA during selection on the bacterial ribosome. Journal of Molecular Biology. 2010;399:576-595.

     Not in our library10.1016/j.jmb.2010.04.038

142. 142.

     Gidi Y, Payne L, Glembockyte V, Michie MS, Schnermann MJ, Cosa G. Unifying mechanism for thiol-induced photoswitching and photostability of cyanine dyes. Journal of the American Chemical Society. 2020;142:12681-12689.

     Not in our library10.1021/jacs.0c03786

143. 143.

     Gietl A, Holzmeister P, Grohmann D, Tinnefeld P. DNA origami as biocompatible surface to match single-molecule and ensemble experiments. Nucleic Acids Research. 2012;40:e110.

     Not in our library10.1093/nar/gks326

144. 144.

     Gilboa B, Jing B, Cui TJ, Sow M, Plochowietz A, Mazumder A, Kapanidis AN. Confinement-free wide-field ratiometric tracking of single fluorescent molecules. Biophysical Journal. 2019;117:2141-2153.

     Not in our library10.1016/j.bpj.2019.10.033

145. 145.

     Girodat D, Pati AK, Terry DS, Blanchard SC, Sanbonmatsu KY. Quantitative comparison between sub-millisecond time resolution single-molecule FRET measurements and 10-second molecular simulations of a biosensor protein. PLOS Computational Biology. 2020;16:e1008293.

     Not in our library10.1371/journal.pcbi.1008293

146. 146.

     Glembockyte V, Lincoln R, Cosa G. Cy3 photoprotection mediated by Ni2+ for extended single-molecule imaging: old tricks for new techniques. Journal of the American Chemical Society. 2015;137:1116-1122.

     Not in our library10.1021/ja509923e

147. 147.
     Excluded‐Volume Effects in Living Cells · 2014

     No notice
148. 148.

     Gomes GW, Krzeminski M, Namini A, Martin EW, Mittag T, Head-Gordon T, Forman-Kay JD, Gradinaru CC. Conformational ensembles of an intrinsically disordered protein consistent with NMR, SAXS, and Single-Molecule FRET. Journal of the American Chemical Society. 2020;142:15697-15710.

     Not in our library10.1021/jacs.0c02088

149. 149.

     Gomes GN, Gradinaru CC. Insights into the conformations and dynamics of intrinsically disordered proteins using single-molecule fluorescence. Biochimica Et Biophysica Acta (BBA) - Proteins and Proteomics. 2017;1865:1696-1706.

     Not in our library10.1016/j.bbapap.2017.06.008

150. 150.

     Gopich I, Szabo A. Theory of photon statistics in single-molecule Förster resonance energy transfer. The Journal of Chemical Physics. 2005a;122:14707.

     Not in our library10.1063/1.1812746

151. 151.

     Gopich IV, Szabo A. Photon counting histograms for diffusing fluorophores. The Journal of Physical Chemistry B. 2005b;109:17683-17688.

     Not in our library10.1021/jp052345f

152. 152.

     Gopich IV, Szabo A. Single-molecule FRET with diffusion and conformational dynamics. The Journal of Physical Chemistry B. 2007;111:12925-12932.

     Not in our library10.1021/jp075255e

153. 153.

     Gopich IV, Szabo A. Decoding the pattern of photon colors in single-molecule FRET. The Journal of Physical Chemistry B. 2009;113:10965-10973.

     Not in our library10.1021/jp903671p

154. 154.

     Gopich IV, Szabo A. Theory of the energy transfer efficiency and fluorescence lifetime distribution in single-molecule FRET. PNAS. 2012;109:7747-7752.

     Not in our library10.1073/pnas.1205120109

155. 155.

     Grabenhorst L, Trofymchuk K, Steiner F, Glembockyte V, Tinnefeld P. Fluorophore photostability and saturation in the hotspot of DNA origami nanoantennas. Methods and Applications in Fluorescence. 2020;8:24003.

     Not in our library10.1088/2050-6120/ab6ac8

156. 156.

     Graen T, Hoefling M, Grubmüller H. AMBER-DYES: characterization of charge fluctuations and force field parameterization of fluorescent dyes for molecular dynamics simulations. Journal of Chemical Theory and Computation. 2014;10:5505-5512.

     Not in our library10.1021/ct500869p

157. 157.

     Greenfeld M, van de Meent JW, Pavlichin DS, Mabuchi H, Wiggins CH, Gonzalez RL, Herschlag D. Single-molecule dataset (SMD): a generalized storage format for raw and processed single-molecule data. BMC Bioinformatics. 2015;16:3.

     Not in our library10.1186/s12859-014-0429-4

158. 158.

     Gregor I, Patra D, Enderlein J. Optical saturation in fluorescence correlation spectroscopy under continuous-wave and pulsed excitation. ChemPhysChem. 2005;6:164-170.

     Not in our library10.1002/cphc.200400319

159. 159.

     Gregorio GG, Masureel M, Hilger D, Terry DS, Juette M, Zhao H, Zhou Z, Perez-Aguilar JM, Hauge M, Mathiasen S, Javitch JA, Weinstein H, Kobilka BK, Blanchard SC. Single-molecule analysis of ligand efficacy in β2AR-G-protein activation. Nature. 2017;547:68-73.

     Not in our library10.1038/nature22354

160. 160.

     Greife A, Felekyan S, Ma Q, Gertzen CG, Spomer L, Dimura M, Peulen TO, Wöhler C, Häussinger D, Gohlke H, Keitel V, Seidel CA. Structural assemblies of the di- and oligomeric G-protein coupled receptor TGR5 in live cells: an MFIS-FRET and integrative modelling study. Scientific Reports. 2016;6:36792.

     Not in our library10.1038/srep36792

161. 161.

     Grimm JB, English BP, Chen J, Slaughter JP, Zhang Z, Revyakin A, Patel R, Macklin JJ, Normanno D, Singer RH, Lionnet T, Lavis LD. A general method to improve fluorophores for live-cell and single-molecule microscopy. Nature Methods. 2015;12:244-250.

     Not in our library10.1038/nmeth.3256

162. 162.

     Grimm JB, Muthusamy AK, Liang Y, Brown TA, Lemon WC, Patel R, Lu R, Macklin JJ, Keller PJ, Ji N, Lavis LD. A general method to fine-tune fluorophores for live-cell and in vivo imaging. Nature Methods. 2017;14:987-994.

     Not in our library10.1038/nmeth.4403

163. 163.

     Grinvald A, Haas E, Steinberg IZ. Evaluation of the distribution of distances between energy donors and acceptors by fluorescence decay. PNAS. 1972;69:2273-2277.

     Not in our library10.1073/pnas.69.8.2273

164. 164.

     Grotz KK, Nueesch MF, Holmstrom ED, Heinz M, Stelzl LS, Schuler B, Hummer G. Dispersion correction alleviates dye stacking of single-stranded DNA and RNA in simulations of single-molecule fluorescence experiments. The Journal of Physical Chemistry B. 2018;122:11626-11639.

     Not in our library10.1021/acs.jpcb.8b07537

165. 165.

     Guin D, Gruebele M. Weak chemical interactions that drive protein evolution: crowding, sticking, and quinary structure in folding and function. Chemical Reviews. 2019;119:10691-10717.

     Not in our library10.1021/acs.chemrev.8b00753

166. 166.

     Guo J, Qiu X, Mingoes C, Deschamps JR, Susumu K, Medintz IL, Hildebrandt N. Conformational details of quantum dot-DNA resolved by Förster resonance energy transfer lifetime nanoruler. ACS Nano. 2019;13:505-514.

     Not in our library10.1021/acsnano.8b07137

167. 167.

     Gurunathan K, Levitus M. FRET fluctuation spectroscopy of diffusing biopolymers: contributions of conformational dynamics and translational diffusion. The Journal of Physical Chemistry B. 2010;114:980-986.

     Not in our library10.1021/jp907390n

168. 168.

     Ha T, Enderle T, Ogletree DF, Chemla DS, Selvin PR, Weiss S. Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. PNAS. 1996;93:6264-6268.

     Not in our library10.1073/pnas.93.13.6264

169. 169.

     Ha T, Chemla DS, Enderle T, Weiss S. Single molecule spectroscopy with automated positioning. Applied Physics Letters. 1997;70:782-784.

     Not in our library10.1063/1.118259

170. 170.
     Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism · 1999

     Not checked
171. 171.

     Ha T, Tinnefeld P. Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. Annual Review of Physical Chemistry. 2012;63:595-617.

     Not in our library10.1146/annurev-physchem-032210-103340

172. 172.

     Haas E, Wilchek M, Katchalski-Katzir E, Steinberg IZ. Distribution of end-to-end distances of oligopeptides in solution as estimated by energy transfer. PNAS. 1975;72:1807-1811.

     Not in our library10.1073/pnas.72.5.1807

173. 173.

     Haas E, Katchalski-Katzir E, Steinberg IZ. Effect of the orientation of donor and acceptor on the probability of energy transfer involving electronic transitions of mixed polarization. Biochemistry. 1978;17:5064-5070.

     Not in our library10.1021/bi00616a032

174. 174.

     Haas E, Steinberg IZ. Intramolecular dynamics of chain molecules monitored by fluctuations in efficiency of excitation energy transfer. A theoretical study. Biophysical Journal. 1984;46:429-437.

     Not in our library10.1016/s0006-3495(84)84040-0

175. 175.

     Hadi-Alijanvand H, Proctor EA, Ding F, Dokholyan NV, Moosavi-Movahedi AA. A hidden aggregation-prone structure in the heart of hypoxia inducible factor prolyl hydroxylase. Proteins: Structure, Function, and Bioinformatics. 2016;84:611-623.

     Not in our library10.1002/prot.25011

176. 176.

     Hadzic M, Kowerko D, Börner R, Zelger-Paulus S, Sigel RKO. Detailed analysis of complex single molecule FRET data with the software MASH. 2016.

     Not in our library10.1117/12.2211191

177. 177.

     Hadzic M, Börner R, König SLB, Kowerko D, Sigel RKO. Reliable state identification and state transition detection in fluorescence intensity-based single-molecule Förster resonance energy-transfer data. The Journal of Physical Chemistry B. 2018;122:6134-6147.

     Not in our library10.1021/acs.jpcb.7b12483

178. 178.

     Hadzic M, Kowerko D, Börner R, Paulus S, Sigel R, König S, Ritter M. GitHub. 2019.

     Not in our library

179. 179.

     Haenni D, Zosel F, Reymond L, Nettels D, Schuler B. Intramolecular distances and dynamics from the combined photon statistics of single-molecule FRET and photoinduced electron transfer. The Journal of Physical Chemistry B. 2013;117:13015-13028.

     Not in our library10.1021/jp402352s

180. 180.
     Systematic Assessment of Burst Impurity in Confocal-Based Single-Molecule Fluorescence Detection Using Brownian Motion Simulations · 2019

     Not checked
181. 181.

     Hamadani KM, Weiss S. Nonequilibrium single molecule protein folding in a coaxial mixer. Biophysical Journal. 2008;95:352-365.

     Not in our library10.1529/biophysj.107.127431

182. 182.

     Hanson JA, Duderstadt K, Watkins LP, Bhattacharyya S, Brokaw J, Chu JW, Yang H. Illuminating the mechanistic roles of enzyme conformational dynamics. PNAS. 2007;104:18055-18060.

     Not in our library10.1073/pnas.0708600104

183. 183.

     Hanspach G, Trucks S, Hengesbach M. Strategic labelling approaches for RNA single-molecule spectroscopy. RNA Biology. 2019;16:1119-1132.

     Not in our library10.1080/15476286.2019.1593093

184. 184.

     Hartmann A, Krainer G, Keller S, Schlierf M. Quantification of millisecond protein-folding dynamics in membrane-mimetic environments by single-molecule Förster resonance energy transfer spectroscopy. Analytical Chemistry. 2015;87:11224-11232.

     Not in our library10.1021/acs.analchem.5b03207

185. 185.

     Haustein E, Jahnz M, Schwille P. Triple FRET: a tool for studying long-range molecular interactions. ChemPhysChem. 2003;4:745-748.

     Not in our library10.1002/cphc.200200634

186. 186.

     Hell SW, Sahl SJ, Bates M, Zhuang X, Heintzmann R, Booth MJ, Bewersdorf J, Shtengel G, Hess H, Tinnefeld P, Honigmann A, Jakobs S, Testa I, Cognet L, Lounis B, Ewers H, Davis SJ, Eggeling C, Klenerman D, Willig KI, Vicidomini G, Castello M, Diaspro A, Cordes T. The 2015 super-resolution microscopy roadmap. Journal of Physics D: Applied Physics. 2015;48:443001.

     Not in our library10.1088/0022-3727/48/44/443001

187. 187.

     Hellenkamp B, Wortmann P, Kandzia F, Zacharias M, Hugel T. Multidomain structure and correlated dynamics determined by self-consistent FRET networks. Nature Methods. 2017;14:174-180.

     Not in our library10.1038/nmeth.4081

188. 188.
     Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study · 2018

     Corrected
189. 189.

     Hellenkamp B, Thurn J, Stadlmeier M, Hugel T. Kinetics of transient protein complexes determined via diffusion-independent microfluidic mixing and fluorescence stoichiometry. The Journal of Physical Chemistry B. 2018b;122:11554-11560.

     Not in our library10.1021/acs.jpcb.8b07437

190. 190.

     Henzler-Wildman KA, Thai V, Lei M, Ott M, Wolf-Watz M, Fenn T, Pozharski E, Wilson MA, Petsko GA, Karplus M, Hübner CG, Kern D. Intrinsic motions along an enzymatic reaction trajectory. Nature. 2007;450:838-844.

     Not in our library10.1038/nature06410

191. 191.

     Henzler-Wildman K, Kern D. Dynamic personalities of proteins. Nature. 2007;450:964-972.

     Not in our library10.1038/nature06522

192. 192.

     Hildebrandt LL, Preus S, Birkedal V. Quantitative single molecule FRET efficiencies using TIRF microscopy. Faraday Discussions. 2015;184:131-142.

     Not in our library10.1039/c5fd00100e

193. 193.

     Hinde E, Digman MA, Welch C, Hahn KM, Gratton E. Biosensor Förster resonance energy transfer detection by the phasor approach to fluorescence lifetime imaging microscopy. Microscopy Research and Technique. 2012;75:271-281.

     Not in our library10.1002/jemt.21054

194. 194.

     Hochstrasser RA, Chen SM, Millar DP. Distance distribution in a dye-linked oligonucleotide determined by time-resolved fluorescence energy transfer. Biophysical Chemistry. 1992;45:133-141.

     Not in our library10.1016/0301-4622(92)87005-4

195. 195.
     Structural heterogeneity and quantitative FRET efficiency distributions of polyprolines through a hybrid atomistic simulation and Monte Carlo approach. · 2011

     Not checked
196. 196.

     Hoffmann A, Nettels D, Clark J, Borgia A, Radford SE, Clarke J, Schuler B. Quantifying heterogeneity and conformational dynamics from single molecule FRET of diffusing molecules: recurrence analysis of single particles (RASP). Physical Chemistry Chemical Physics. 2011;13:1857-1871.

     Not in our library10.1039/c0cp01911a

197. 197.

     Hofkens J, Cotlet M, Vosch T, Tinnefeld P, Weston KD, Ego C, Grimsdale A, Müllen K, Beljonne D, Brédas JL, Jordens S, Schweitzer G, Sauer M, De Schryver F. Revealing competitive Förster-type resonance energy-transfer pathways in single bichromophoric molecules. PNAS. 2003;100:13146-13151.

     Not in our library10.1073/pnas.2235805100

198. 198.

     Hohlbein J, Aigrain L, Craggs TD, Bermek O, Potapova O, Shoolizadeh P, Grindley ND, Joyce CM, Kapanidis AN. Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nature Communications. 2013;4:2131.

     Not in our library10.1038/ncomms3131

199. 199.

     Hohng S, Joo C, Ha T. Single-molecule three-color FRET. Biophysical Journal. 2004;87:1328-1337.

     Not in our library10.1529/biophysj.104.043935

200. 200.

     Hohng S, Zhou R, Nahas MK, Yu J, Schulten K, Lilley DM, Ha T. Fluorescence-force spectroscopy maps two-dimensional reaction landscape of the holliday junction. Science. 2007;318:279-283.

     Not in our library10.1126/science.1146113

201. 201.

     Holden SJ, Uphoff S, Hohlbein J, Yadin D, Le Reste L, Britton OJ, Kapanidis AN. Defining the limits of single-molecule FRET resolution in TIRF microscopy. Biophysical Journal. 2010;99:3102-3111.

     Not in our library10.1016/j.bpj.2010.09.005

202. 202.

     Holden SJ, Uphoff S, Kapanidis AN. DAOSTORM: an algorithm for high- density super-resolution microscopy. Nature Methods. 2011;8:279-280.

     Not in our library10.1038/nmeth0411-279

203. 203.

     Holmstrom ED, Dupuis NF, Nesbitt DJ. Pulsed IR heating studies of single-molecule DNA duplex dissociation kinetics and thermodynamics. Biophysical Journal. 2014;106:220-231.

     Not in our library10.1016/j.bpj.2013.11.008

204. 204.

     Holmstrom ED, Holla A, Zheng W, Nettels D, Best RB, Schuler B, Rhoades E. Accurate transfer efficiencies, distance distributions, and ensembles of unfolded and intrinsically disordered proteins from single-molecule FRET. Methods in Enzymology. 2018;287-325.

     Not in our library10.1016/bs.mie.2018.09.030

205. 205.

     Hon J, Gonzalez RL. Bayesian-estimated hierarchical HMMs enable robust analysis of single-molecule kinetic heterogeneity. Biophysical Journal. 2019;116:1790-1802.

     Not in our library10.1016/j.bpj.2019.02.031

206. 206.

     Hong Y, Lam JW, Tang BZ. Aggregation-induced emission. Chemical Society Reviews. 2011;40:5361-5388.

     Not in our library10.1039/c1cs15113d

207. 207.

     Horsey I, Furey WS, Harrison JG, Osborne MA, Balasubramanian S. Double fluorescence resonance energy transfer to explore multicomponent binding interactions: a case study of DNA mismatches. Chemical Communications. 2000;10:1043-1044.

     Not in our library10.1039/b002540m

208. 208.

     Hua B, Han KY, Zhou R, Kim H, Shi X, Abeysirigunawardena SC, Jain A, Singh D, Aggarwal V, Woodson SA, Ha T. An improved surface passivation method for single-molecule studies. Nature Methods. 2014;11:1233-1236.

     Not in our library10.1038/nmeth.3143

209. 209.

     Huang B, Perroud TD, Zare RN. Photon counting histogram: one-photon excitation. ChemPhysChem. 2004;5:1523-1531.

     Not in our library10.1002/cphc.200400176

210. 210.

     Husada F, Gouridis G, Vietrov R, Schuurman-Wolters GK, Ploetz E, de Boer M, Poolman B, Cordes T. Watching conformational dynamics of ABC transporters with single-molecule tools. Biochemical Society Transactions. 2015;43:1041-1047.

     Not in our library10.1042/bst20150140

211. 211.

     Husada F, Bountra K, Tassis K, de Boer M, Romano M, Rebuffat S, Beis K, Cordes T. Conformational dynamics of the ABC transporter McjD seen by single-molecule FRET. The EMBO Journal. 2018;37:e100056.

     Not in our library10.15252/embj.2018100056

212. 212.

     Hwang H, Kim H, Myong S. Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity. PNAS. 2011;108:7414-7418.

     Not in our library10.1073/pnas.1017672108

213. 213.

     Hwang H, Myong S. Protein induced fluorescence enhancement (PIFE) for probing protein-nucleic acid interactions. Chem. Soc. Rev. 2014;43:1221-1229.

     Not in our library10.1039/c3cs60201j

214. 214.

     Hyman AA, Weber CA, Jülicher F. Liquid-liquid phase separation in biology. Annual Review of Cell and Developmental Biology. 2014;30:39-58.

     Not in our library10.1146/annurev-cellbio-100913-013325

215. 215.

     Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A. First community-wide, comparative cross-linking mass spectrometry study. Analytical Chemistry. 2019;91:6953-6961.

     Not in our library10.1021/acs.analchem.9b00658

216. 216.

     Iljina M, Mazal H, Goloubinoff P, Riven I, Haran G. Single-molecule spectroscopy reveals dynamic allostery mediated by the substrate-binding domain of a AAA+ machine. bioRxiv. 2020.

     Not in our library10.1101/2020.09.13.295345

217. 217.

     Ingargiola A, Laurence T, Boutelle R, Weiss S, Michalet X. Photon-HDF5: an open file format for timestamp-based single-molecule fluorescence experiments. Biophysical Journal. 2016a;110:26-33.

     Not in our library10.1016/j.bpj.2015.11.013

218. 218.

     Ingargiola A, Lerner E, Chung S, Weiss S, Michalet X. FRETBursts: an open source toolkit for analysis of freely-diffusing single-molecule FRET. PLOS ONE. 2016b;11:e0160716.

     Not in our library10.1371/journal.pone.0160716

219. 219.

     Ingargiola A, Lerner E, Chung S, Panzeri F, Gulinatti A, Rech I, Ghioni M, Weiss S, Michalet X. Multispot single-molecule FRET: High-throughput analysis of freely diffusing molecules. PLOS ONE. 2017;12:e0175766.

     Not in our library10.1371/journal.pone.0175766

220. 220.

     Ingargiola A, Segal M, Gulinatti A, Rech I, Labanca I, Maccagnani P, Ghioni M, Weiss S, Michalet X. 48-spot single-molecule FRET setup with periodic acceptor excitation. The Journal of Chemical Physics. 2018a;148:123304.

     Not in our library10.1063/1.5000742

221. 221.

     Ingargiola A, Weiss S, Lerner E. Monte carlo diffusion-enhanced photon inference: distance distributions and conformational dynamics in single-molecule FRET. The Journal of Physical Chemistry B. 2018b;122:11598-11615.

     Not in our library10.1021/acs.jpcb.8b07608

222. 222.

     Iqbal A, Arslan S, Okumus B, Wilson TJ, Giraud G, Norman DG, Ha T, Lilley DMJ. Orientation dependence in fluorescent energy transfer between Cy3 and Cy5 terminally attached to double-stranded nucleic acids. PNAS. 2008;105:11176-11181.

     Not in our library10.1073/pnas.0801707105

223. 223.

     Isselstein M, Zhang L, Glembockyte V, Brix O, Cosa G, Tinnefeld P, Cordes T. Self-healing dyes-keeping the promise? The Journal of Physical Chemistry Letters. 2020;11:4462-4480.

     Not in our library10.1021/acs.jpclett.9b03833

224. 224.

     Ivanov V, Li M, Mizuuchi K. Impact of emission anisotropy on fluorescence spectroscopy and FRET distance measurements. Biophysical Journal. 2009;97:922-929.

     Not in our library10.1016/j.bpj.2009.05.025

225. 225.

     Jacob MH, Amir D, Ratner V, Gussakowsky E, Haas E. Predicting reactivities of protein surface cysteines as part of a strategy for selective multiple labeling. Biochemistry. 2005;44:13664-13672.

     Not in our library10.1021/bi051205t

226. 226.

     Jäger M, Michalet X, Weiss S. Protein-protein interactions as a tool for site-specific labeling of proteins. Protein Science. 2005;14:2059-2068.

     Not in our library10.1110/ps.051384705

227. 227.

     Jäger M, Nir E, Weiss S. Site-specific labeling of proteins for single-molecule FRET by combining chemical and enzymatic modification. Protein Science. 2006;15:640-646.

     Not in our library10.1110/ps.051851506

228. 228.

     Jamieson T, Bakhshi R, Petrova D, Pocock R, Imani M, Seifalian AM. Biological applications of quantum dots. Biomaterials. 2007;28:4717-4732.

     Not in our library10.1016/j.biomaterials.2007.07.014

229. 229.

     Jazi AA, Ploetz E, Arizki M, Dhandayuthapani B, Waclawska I, Krämer R, Ziegler C, Cordes T. Caging and photoactivation in single-molecule Förster resonance energy transfer experiments. Biochemistry. 2017;56:2031-2041.

     Not in our library10.1021/acs.biochem.6b00916

230. 230.

     Jeschke G. DEER distance measurements on proteins. Annual Review of Physical Chemistry. 2012;63:419-446.

     Not in our library10.1146/annurev-physchem-032511-143716

231. 231.

     Jeschke G. The contribution of modern EPR to structural biology. Emerging Topics in Life Sciences. 2018;2:9-18.

     Not in our library10.1042/etls20170143

232. 232.

     Joo C, Ha T. Single-molecule FRET with total internal reflection microscopy. Cold Spring Harbor Protocols. 2012;7:1223-1237.

     Not in our library10.1101/pdb.top072058

233. 233.

     Juette MF, Terry DS, Wasserman MR, Zhou Z, Altman RB, Zheng Q, Blanchard SC. The bright future of single-molecule fluorescence imaging. Current Opinion in Chemical Biology. 2014;20:103-111.

     Not in our library10.1016/j.cbpa.2014.05.010

234. 234.

     Juette MF, Terry DS, Wasserman MR, Altman RB, Zhou Z, Zhao H, Blanchard SC. Single-molecule imaging of non-equilibrium molecular ensembles on the millisecond timescale. Nature Methods. 2016;13:341-344.

     Not in our library10.1038/nmeth.3769

235. 235.

     Kaledhonkar S, Fu Z, White H, Frank J, Marsh J. A. Time-resolved cryo-electron microscopy using a microfluidic chip. Methods in Molecular Biology. 2018;59-71.

     Not in our library10.1007/978-1-4939-7759-8_4

236. 236.

     Kalinin S, Sisamakis E, Magennis SW, Felekyan S, Seidel CA. On the origin of broadening of single-molecule FRET efficiency distributions beyond shot noise limits. The Journal of Physical Chemistry B. 2010a;114:6197-6206.

     Not in our library10.1021/jp100025v

237. 237.

     Kalinin S, Valeri A, Antonik M, Felekyan S, Seidel CA. Detection of structural dynamics by FRET: a photon distribution and fluorescence lifetime analysis of systems with multiple states. The Journal of Physical Chemistry B. 2010b;114:7983-7995.

     Not in our library10.1021/jp102156t

238. 238.

     Kalinin S, Peulen T, Sindbert S, Rothwell PJ, Berger S, Restle T, Goody RS, Gohlke H, Seidel CAM. A toolkit and benchmark study for FRET-restrained high-precision structural modeling. Nature Methods. 2012;9:1218-1225.

     Not in our library10.1038/nmeth.2222

239. 239.

     Kapanidis AN, Lee NK, Laurence TA, Doose S, Margeat E, Weiss S. Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules. PNAS. 2004;101:8936-8941.

     Not in our library10.1073/pnas.0401690101

240. 240.

     Kapanidis AN, Laurence TA, Lee NK, Margeat E, Kong X, Weiss S. Alternating-laser excitation of single molecules. Accounts of Chemical Research. 2005;38:523-533.

     Not in our library10.1021/ar0401348

241. 241.

     Kapusta P, Wahl M, Benda A, Hof M, Enderlein J. Fluorescence lifetime correlation spectroscopy. Journal of Fluorescence. 2007;17:43-48.

     Not in our library10.1007/s10895-006-0145-1

242. 242.

     Karimi A, Börner R, Mata G, Luedtke NW. A highly fluorescent nucleobase molecular rotor. Journal of the American Chemical Society. 2020;142:14422-14426.

     Not in our library10.1021/jacs.0c05180

243. 243.

     Kask P, Palo K, Ullmann D, Gall K. Fluorescence-intensity distribution analysis and its application in biomolecular detection technology. PNAS. 1999;96:13756-13761.

     Not in our library10.1073/pnas.96.24.13756

244. 244.

     Keller BG, Kobitski A, Jäschke A, Nienhaus GU, Noé F. Complex RNA folding kinetics revealed by single-molecule FRET and hidden markov models. Journal of the American Chemical Society. 2014;136:4534-4543.

     Not in our library10.1021/ja4098719

245. 245.

     Khara DC, Schreck JS, Tomov TE, Berger Y, Ouldridge TE, Doye JPK, Nir E. DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size. Nucleic Acids Research. 2018;46:1553-1561.

     Not in our library10.1093/nar/gkx1282

246. 246.
     Single-molecule FRET reveals multiscale chromatin dynamics modulated by HP1α · 2018

     No notice
247. 247.

     Kim HD, Nienhaus GU, Ha T, Orr JW, Williamson JR, Chu S. Mg2+-dependent conformational change of RNA studied by fluorescence correlation and FRET on immobilized single molecules. PNAS. 2002;99:4284-4289.

     Not in our library10.1073/pnas.032077799

248. 248.

     Kim S, Streets AM, Lin RR, Quake SR, Weiss S, Majumdar DS. High-throughput single-molecule optofluidic analysis. Nature Methods. 2011;8:242-245.

     Not in our library10.1038/nmeth.1569

249. 249.

     Kim J-Y, Kim C, Lee NK. Real-time submillisecond single-molecule FRET dynamics of freely diffusing molecules with liposome tethering. Nature Communications. 2015a;6:6992.

     Not in our library10.1038/ncomms7992

250. 250.

     Kim SE, Lee IB, Hyeon C, Hong SC. Deciphering kinetic information from single-molecule FRET data that show slow transitions. The Journal of Physical Chemistry B. 2015b;119:6974-6978.

     Not in our library10.1021/acs.jpcb.5b03991

251. 251.

     Kim J-Y, Meng F, Yoo J, Chung HS. Diffusion-limited association of disordered protein by non-native electrostatic interactions. Nature Communications. 2018a;9:4707.

     Not in our library10.1038/s41467-018-06866-y

252. 252.

     Kim N, Kwon J, Lim Y, Kang J, Bae S, Kim SK. Incorporation of STED technique into single-molecule spectroscopy to break the concentration limit of diffusing molecules in single-molecule detection. Chemical Communications. 2018b;54:9667-9670.

     Not in our library10.1039/c8cc05726e

253. 253.

     Kim J, Li BX, Huang RY, Qiao JX, Ewing WR, MacMillan DWC. Site-Selective functionalization of methionine residues via photoredox catalysis. Journal of the American Chemical Society. 2020;142:21260-21266.

     Not in our library10.1021/jacs.0c09926

254. 254.

     Kim J-Y, Chung HS. Disordered proteins follow diverse transition paths as they fold and bind to a partner. Science. 2020;368:1253-1257.

     Not in our library10.1126/science.aba3854

255. 255.

     Kinz-Thompson CD, Gonzalez RL. Increasing the time resolution of single-molecule experiments with bayesian inference. Biophysical Journal. 2018;114:289-300.

     Not in our library10.1016/j.bpj.2017.11.3741

256. 256.

     Knox RS, van Amerongen H. Refractive index dependence of the Förster resonance excitation transfer rate. The Journal of Physical Chemistry B. 2002;106:5289-5293.

     Not in our library10.1021/jp013927+

257. 257.

     Köfinger J, Stelzl LS, Reuter K, Allande C, Reichel K, Hummer G. Efficient ensemble refinement by reweighting. Journal of Chemical Theory and Computation. 2019;15:3390-3401.

     Not in our library10.1021/acs.jctc.8b01231

258. 258.

     Kong X, Nir E, Hamadani K, Weiss S. Photobleaching pathways in single-molecule FRET experiments. Journal of the American Chemical Society. 2007;129:4643-4654.

     Not in our library10.1021/ja068002s

259. 259.

     König SL, Hadzic M, Fiorini E, Börner R, Kowerko D, Blanckenhorn WU, Sigel RK. BOBA FRET: bootstrap-based analysis of single-molecule FRET data. PLOS ONE. 2013;8:e84157.

     Not in our library10.1371/journal.pone.0084157

260. 260.

     König I, Zarrine-Afsar A, Aznauryan M, Soranno A, Wunderlich B, Dingfelder F, Stüber JC, Plückthun A, Nettels D, Schuler B. Single-molecule spectroscopy of protein conformational dynamics in live eukaryotic cells. Nature Methods. 2015;12:773-779.

     Not in our library10.1038/nmeth.3475

261. 261.

     Koukos PI, Bonvin A. Integrative modelling of biomolecular complexes. Journal of Molecular Biology. 2020;432:2861-2881.

     Not in our library10.1016/j.jmb.2019.11.009

262. 262.

     Krainer G, Hartmann A, Schlierf M. farFRET: extending the range in single-molecule FRET experiments beyond 10 nm. Nano Letters. 2015;15:5826-5829.

     Not in our library10.1021/acs.nanolett.5b01878

263. 263.
     Guanylate binding proteins directly attack Toxoplasma gondii via supramolecular complexes · 2016

     No notice
264. 264.

     Krstić I, Hänsel R, Romainczyk O, Engels JW, Dötsch V, Prisner TF. Long-range distance measurements on nucleic acids in cells by pulsed EPR spectroscopy. Angewandte Chemie. 2011;50:5070-5074.

     Not in our library10.1002/anie.201100886

265. 265.

     Kudryavtsev V, Felekyan S, Woźniak AK, König M, Sandhagen C, Kühnemuth R, Seidel CA, Oesterhelt F. Monitoring dynamic systems with multiparameter fluorescence imaging. Analytical and Bioanalytical Chemistry. 2007;387:71-82.

     Not in our library10.1007/s00216-006-0917-0

266. 266.

     Kudryavtsev V, Sikor M, Kalinin S, Mokranjac D, Seidel CA, Lamb DC. Combining MFD and PIE for accurate single-pair Förster resonance energy transfer measurements. ChemPhysChem. 2012;13:1060-1078.

     Not in our library10.1002/cphc.201100822

267. 267.

     Kühnemuth R, Seidel CAM. Principles of single molecule multiparameter fluorescence spectroscopy. Single Molecules. 2001;2:251-254.

     Not in our library10.1002/1438-5171(200112)2:4<251::aid-simo251>3.0.co;2-t

268. 268.

     Kupitz C, Basu S, Grotjohann I, Fromme R, Zatsepin NA, Rendek KN, Hunter MS, Shoeman RL, White TA, Wang D, James D, Yang J-H, Cobb DE, Reeder B, Sierra RG, Liu H, Barty A, Aquila AL, Deponte D, Kirian RA, Bari S, Bergkamp JJ, Beyerlein KR, Bogan MJ, Caleman C, Chao T-C, Conrad CE, Davis KM, Fleckenstein H, Galli L, Hau-Riege SP, Kassemeyer S, Laksmono H, Liang M, Lomb L, Marchesini S, Martin AV, Messerschmidt M, Milathianaki D, Nass K, Ros A, Roy-Chowdhury S, Schmidt K, Seibert M, Steinbrener J, Stellato F, Yan L, Yoon C, Moore TA, Moore AL, Pushkar Y, Williams GJ, Boutet S, Doak RB, Weierstall U, Frank M, Chapman HN, Spence JCH, Fromme P. Serial time-resolved crystallography of photosystem II using a femtosecond X-ray laser. Nature. 2014;513:261-265.

     Not in our library10.1038/nature13453

269. 269.

     Kuzmenkina EV, Heyes CD, Nienhaus GU. Single-molecule Förster resonance energy transfer study of protein dynamics under denaturing conditions. PNAS. 2005;102:15471-15476.

     Not in our library10.1073/pnas.0507728102

270. 270.

     Kuzmenkina EV, Heyes CD, Nienhaus GU. Single-molecule FRET study of denaturant induced unfolding of RNase H. Journal of Molecular Biology. 2006;357:313-324.

     Not in our library10.1016/j.jmb.2005.12.061

271. 271.
     What Macromolecular Crowding Can Do to a Protein · 2014

     No notice
272. 272.
     Ultrahigh-resolution multicolor colocalization of single fluorescent probes · 2000

     Not checked
273. 273.

     Lamichhane R, Solem A, Black W, Rueda D. Single-molecule FRET of protein-nucleic acid and protein-protein complexes: surface passivation and immobilization. Methods. 2010;52:192-200.

     Not in our library10.1016/j.ymeth.2010.06.010

274. 274.

     Larsen KP, Choi J, Prabhakar A, Puglisi EV, Puglisi JD. Relating structure and dynamics in RNA biology. Cold Spring Harbor Perspectives in Biology. 2019;11:a032474.

     Not in our library10.1101/cshperspect.a032474

275. 275.

     Larson J, Kirk M, Drier EA, O'Brien W, MacKay JF, Friedman LJ, Hoskins AA. Design and construction of a multiwavelength, micromirror total internal reflectance fluorescence microscope. Nature Protocols. 2014;9:2317-2328.

     Not in our library10.1038/nprot.2014.155

276. 276.

     Laurence TA, Kong X, Jager M, Weiss S. Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins. PNAS. 2005;102:17348-17353.

     Not in our library10.1073/pnas.0508584102

277. 277.

     Laurence TA, Kwon Y, Yin E, Hollars CW, Camarero JA, Barsky D. Correlation spectroscopy of minor fluorescent species: signal purification and distribution analysis. Biophysical Journal. 2007;92:2184-2198.

     Not in our library10.1529/biophysj.106.093591

278. 278.

     Laurence TA, Kwon Y, Johnson A, Hollars CW, O'Donnell M, Camarero JA, Barsky D. Motion of a DNA sliding clamp observed by single molecule fluorescence spectroscopy. Journal of Biological Chemistry. 2008;283:22895-22906.

     Not in our library10.1074/jbc.m800174200

279. 279.

     LeBlanc S, Kulkarni P, Weninger K. Single molecule FRET: a powerful tool to study intrinsically disordered proteins. Biomolecules. 2018;8:140.

     Not in our library10.3390/biom8040140

280. 280.

     Lee NK, Kapanidis AN, Wang Y, Michalet X, Mukhopadhyay J, Ebright RH, Weiss S. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophysical Journal. 2005;88:2939-2953.

     Not in our library10.1529/biophysj.104.054114

281. 281.

     Lee NK, Koh HR, Han KY, Kim SK. Folding of 8-17 deoxyribozyme studied by three-color alternating-laser excitation of single molecules. Journal of the American Chemical Society. 2007a;129:15526-15534.

     Not in our library10.1021/ja0725145

282. 282.

     Lee NK, Kapanidis AN, Koh HR, Korlann Y, Ho SO, Kim Y, Gassman N, Kim SK, Weiss S. Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances. Biophysical Journal. 2007b;92:303-312.

     Not in our library10.1529/biophysj.106.093211

283. 283.

     Lee M, Kim SH, Hong S-C. Minute negative superhelicity is sufficient to induce the B-Z transition in the presence of low tension. PNAS. 2010a;107:4985-4990.

     Not in our library10.1073/pnas.0911528107

284. 284.

     Lee S, Lee J, Hohng S. Single-molecule three-color FRET with both negligible spectral overlap and long observation time. PLOS ONE. 2010b;5:e12270.

     Not in our library10.1371/journal.pone.0012270

285. 285.

     Lee J, Lee S, Ragunathan K, Joo C, Ha T, Hohng S. Single-molecule four-color FRET. Angewandte Chemie International Edition. 2010c;49:9922-9925.

     Not in our library10.1002/anie.201005402

286. 286.

     Lee TC, Moran CR, Cistrone PA, Dawson PE, Deniz AA. Site-specific three-color labeling of α-synuclein via conjugation to uniquely reactive cysteines during assembly by native chemical ligation. Cell Chemical Biology. 2018;25:797-801.

     Not in our library10.1016/j.chembiol.2018.03.009

287. 287.

     Léger C, Yahia-Ammar A, Susumu K, Medintz IL, Urvoas A, Valerio-Lepiniec M, Minard P, Hildebrandt N. Picomolar biosensing and conformational analysis using artificial bidomain proteins and terbium-to-quantum dot Förster resonance energy transfer. ACS Nano. 2020;14:5956-5967.

     Not in our library10.1021/acsnano.0c01410

288. 288.

     Lehmann K, Felekyan S, Kühnemuth R, Dimura M, Tóth K, Seidel CAM, Langowski J. Dynamics of the nucleosomal histone H3 N-terminal tail revealed by high precision single-molecule FRET. Nucleic Acids Research. 2020;48:1551-1571.

     Not in our library10.1093/nar/gkz1186

289. 289.

     Lemke EA, Gambin Y, Vandelinder V, Brustad EM, Liu HW, Schultz PG, Groisman A, Deniz AA. Microfluidic device for single-molecule experiments with enhanced photostability. Journal of the American Chemical Society. 2009;131:13610-13612.

     Not in our library10.1021/ja9027023

290. 290.

     Lerner E, Hilzenrat G, Amir D, Tauber E, Garini Y, Haas E. Preparation of homogeneous samples of double-labelled protein suitable for single-molecule FRET measurements. Analytical and Bioanalytical Chemistry. 2013;405:5983-5991.

     Not in our library10.1007/s00216-013-7002-2

291. 291.

     Lerner E, Orevi T, Ben Ishay E, Amir D, Haas E. Kinetics of fast changing intramolecular distance distributions obtained by combined analysis of FRET efficiency kinetics and time-resolved FRET equilibrium measurements. Biophysical Journal. 2014;106:667-676.

     Not in our library10.1016/j.bpj.2013.11.4500

292. 292.

     Lerner E, Ploetz E, Hohlbein J, Cordes T, Weiss S. A quantitative theoretical framework for protein-induced fluorescence enhancement-Förster-type resonance energy transfer (PIFE-FRET). The Journal of Physical Chemistry B. 2016;120:6401-6410.

     Not in our library10.1021/acs.jpcb.6b03692

293. 293.

     Lerner E, Ingargiola A, Lee JJ, Borukhov S, Michalet X, Weiss S. Different types of pausing modes during transcription initiation. Transcription. 2017;8:242-253.

     Not in our library10.1080/21541264.2017.1308853

294. 294.

     Lerner E, Cordes T, Ingargiola A, Alhadid Y, Chung S, Michalet X, Weiss S. Toward dynamic structural biology: Two decades of single-molecule Förster resonance energy transferster resonance energy transfer. Science. 2018a;359:eaan1133.

     Not in our library10.1126/science.aan1133

295. 295.

     Lerner E, Ingargiola A, Weiss S. Characterizing highly dynamic conformational states: The transcription bubble in RNAP-promoter open complex as an example. The Journal of Chemical Physics. 2018b;148:123315.

     Not in our library10.1063/1.5004606

296. 296.

     Lerner E. Zenodo. 2019.

     Not in our library10.5281/zenodo.3630498

297. 297.

     Lerner E. Zenodo. 2020.

     Not in our library10.5281/zenodo.3630474

298. 298.

     Levitus M, Ranjit S. Cyanine dyes in biophysical research: the photophysics of polymethine fluorescent dyes in biomolecular environments. Quarterly Reviews of Biophysics. 2011;44:123-151.

     Not in our library10.1017/s0033583510000247

299. 299.

     Li J, Zhang L, Johnson-Buck A, Walter NG. Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning. Nature Communications. 2020a;11:5833.

     Not in our library10.1038/s41467-020-19673-1

300. 300.

     Li Z, Li W, Lu M, Bess J, Chao CW, Gorman J, Terry DS, Zhang B, Zhou T, Blanchard SC, Kwong PD, Lifson JD, Mothes W, Liu J. Subnanometer structures of HIV-1 envelope trimers on aldrithiol-2-inactivated virus particles. Nature Structural & Molecular Biology. 2020b;27:726-734.

     Not in our library10.1038/s41594-020-0452-2

301. 301.

     Lindhoud S, Pirchi M, Westphal AH, Haran G, van Mierlo CPM. Gradual folding of an off-pathway molten globule detected at the single-molecule level. Journal of Molecular Biology. 2015;427:3148-3157.

     Not in our library10.1016/j.jmb.2015.07.002

302. 302.

     Lipman EA, Schuler B, Bakajin O, Eaton WA. Single-molecule measurement of protein folding kinetics. Science. 2003;301:1233-1235.

     Not in our library10.1126/science.1085399

303. 303.

     Liput DJ, Nguyen TA, Augustin SM, Lee JO, Vogel SS. A guide to fluorescence lifetime microscopy and Förster's Resonance Energy Transfer in Neuroscience. Current Protocols in Neuroscience. 2020;94:e108.

     Not in our library10.1002/cpns.108

304. 304.

     Liu Z, Gong Z, Cao Y, Ding YH, Dong MQ, Lu YB, Zhang WP, Tang C. Characterizing protein dynamics with integrative use of bulk and single-molecule techniques. Biochemistry. 2018;57:305-313.

     Not in our library10.1021/acs.biochem.7b00817

305. 305.

     Liu Z, Dong X, Yi HW, Yang J, Gong Z, Wang Y, Liu K, Zhang WP, Tang C. Structural basis for the recognition of K48-linked ub chain by proteasomal receptor Rpn13. Cell Discovery. 2019;5:19.

     Not in our library10.1038/s41421-019-0089-7

306. 306.

     Liu Y, Lilley DMJ. Crystal structures of cyanine fluorophores stacked onto the end of double-stranded RNA. Biophysical Journal. 2017;113:2336-2343.

     Not in our library10.1016/j.bpj.2017.10.002

307. 307.

     Long X, Parks JW, Stone MD. Integrated magnetic tweezers and single-molecule FRET for investigating the mechanical properties of nucleic acid. Methods. 2016;105:16-25.

     Not in our library10.1016/j.ymeth.2016.06.009

308. 308.

     Lu M, Ma X, Mothes W. Illuminating the virus life cycle with single-molecule FRET imaging. Advances in Virus Research. 2019;105:239-273.

     Not in our library10.1016/bs.aivir.2019.07.004

309. 309.

     Magde D, Elson E, Webb WW. Thermodynamic fluctuations in a reacting system—measurement by Fluorescence Correlation Spectroscopy. Physical Review Letters. 1972;29:705-708.

     Not in our library10.1103/physrevlett.29.705

310. 310.

     Maity H, Reddy G. Folding of protein L with implications for collapse in the denatured state ensemble. Journal of the American Chemical Society. 2016;138:2609-2616.

     Not in our library10.1021/jacs.5b11300

311. 311.

     Mapa K, Sikor M, Kudryavtsev V, Waegemann K, Kalinin S, Seidel CA, Neupert W, Lamb DC, Mokranjac D. The conformational dynamics of the mitochondrial Hsp70 chaperone. Molecular Cell. 2010;38:89-100.

     Not in our library10.1016/j.molcel.2010.03.010

312. 312.

     Margeat E, Kapanidis AN, Tinnefeld P, Wang Y, Mukhopadhyay J, Ebright RH, Weiss S. Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophysical Journal. 2006;90:1419-1431.

     Not in our library10.1529/biophysj.105.069252

313. 313.

     Margittai M, Widengren J, Schweinberger E, Schröder GF, Felekyan S, Haustein E, König M, Fasshauer D, Grubmüller H, Jahn R, Seidel CA. Single-molecule fluorescence resonance energy transfer reveals a dynamic equilibrium between closed and open conformations of syntaxin 1. PNAS. 2003;100:15516-15521.

     Not in our library10.1073/pnas.2331232100

314. 314.

     Martens KJA, van Beljouw SPB, van der Els S, Vink JNA, Baas S, Vogelaar GA, Brouns SJJ, van Baarlen P, Kleerebezem M, Hohlbein J. Visualisation of dCas9 target search in vivo using an open-microscopy framework. Nature Communications. 2019;10:3552.

     Not in our library10.1038/s41467-019-11514-0

315. 315.

     Martinac B. Single-molecule FRET studies of ion channels. Progress in Biophysics and Molecular Biology. 2017;130:192-197.

     Not in our library10.1016/j.pbiomolbio.2017.06.014

316. 316.

     Masliah G, Maris C, König SL, Yulikov M, Aeschimann F, Malinowska AL, Mabille J, Weiler J, Holla A, Hunziker J, Meisner-Kober N, Schuler B, Jeschke G, Allain FH. Structural basis of siRNA recognition by TRBP double-stranded RNA binding domains. The EMBO Journal. 2018;37:e97089.

     Not in our library10.15252/embj.201797089

317. 317.

     Matikonda SS, Hammersley G, Kumari N, Grabenhorst L, Glembockyte V, Tinnefeld P, Ivanic J, Levitus M, Schnermann MJ. Impact of cyanine conformational restraint in the near-infrared range. The Journal of Organic Chemistry. 2020a;85:5907-5915.

     Not in our library10.1021/acs.joc.0c00236

318. 318.

     Matikonda SS, Ivanic J, Gomez M, Hammersley G, Schnermann MJ. Core remodeling leads to long wavelength fluoro-coumarins. Chemical Science. 2020b;11:7302-7307.

     Not in our library10.1039/d0sc02566f

319. 319.

     Matsunaga Y, Sugita Y. Linking time-series of single-molecule experiments with molecular dynamics simulations by machine learning. eLife. 2018;7:e32668.

     Not in our library10.7554/elife.32668

320. 320.

     May PFJ, Pinkney JNM, Zawadzki P, Evans GW, Sherratt DJ, Kapanidis AN. Tethered fluorophore motion: studying large DNA conformational changes by single-fluorophore imaging. Biophysical Journal. 2014;107:1205-1216.

     Not in our library10.1016/j.bpj.2014.07.024

321. 321.

     Mazal H, Aviram H, Riven I, Haran G. Effect of ligand binding on a protein with a complex folding landscape. Physical Chemistry Chemical Physics. 2018;20:3054-3062.

     Not in our library10.1039/c7cp03327c

322. 322.
     Tunable microsecond dynamics of an allosteric switch regulate the activity of a AAA+ disaggregation machine · 2019

     Not checked
323. 323.

     Mazal H, Haran G. Single-molecule FRET methods to study the dynamics of proteins at work. Current Opinion in Biomedical Engineering. 2019;12:8-17.

     Not in our library10.1016/j.cobme.2019.08.007

324. 324.

     McCann JJ, Choi UB, Zheng L, Weninger K, Bowen ME. Optimizing methods to recover absolute FRET efficiency from immobilized single molecules. Biophysical Journal. 2010;99:961-970.

     Not in our library10.1016/j.bpj.2010.04.063

325. 325.

     McCann JJ, Zheng L, Rohrbeck D, Felekyan S, Kühnemuth R, Sutton RB, Seidel CA, Bowen ME. Supertertiary structure of the synaptic MAGuK scaffold proteins is conserved. PNAS. 2012;109:15775-15780.

     Not in our library10.1073/pnas.1200254109

326. 326.

     McKinney SA, Joo C, Ha T. Analysis of single-molecule FRET trajectories using hidden Markov modeling. Biophysical Journal. 2006;91:1941-1951.

     Not in our library10.1529/biophysj.106.082487

327. 327.

     Medintz IL, Clapp AR, Mattoussi H, Goldman ER, Fisher B, Mauro JM. Self-assembled nanoscale biosensors based on quantum dot FRET donors. Nature Materials. 2003;2:630-638.

     Not in our library10.1038/nmat961

328. 328.

     Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 2002;108:599-614.

     Not in our library10.1016/s0092-8674(02)00667-0

329. 329.

     Metskas LA, Rhoades E. Single-Molecule FRET of intrinsically disordered proteins. Annual Review of Physical Chemistry. 2020;71:391-414.

     Not in our library10.1146/annurev-physchem-012420-104917

330. 330.

     Meyer BH, Martinez KL, Segura JM, Pascoal P, Hovius R, George N, Johnsson K, Vogel H. Covalent labeling of cell-surface proteins for in-vivo FRET studies. FEBS Letters. 2006a;580:1654-1658.

     Not in our library10.1016/j.febslet.2006.02.007

331. 331.

     Meyer BH, Segura JM, Martinez KL, Hovius R, George N, Johnsson K, Vogel H. FRET imaging reveals that functional neurokinin-1 receptors are monomeric and reside in membrane microdomains of live cells. PNAS. 2006b;103:2138-2143.

     Not in our library10.1073/pnas.0507686103

332. 332.

     Michalet X, Weiss S, Jäger M. Single-molecule fluorescence studies of protein folding and conformational dynamics. Chemical Reviews. 2006;106:1785-1813.

     Not in our library10.1021/cr0404343

333. 333.

     Michie MS, Götz R, Franke C, Bowler M, Kumari N, Magidson V, Levitus M, Loncarek J, Sauer M, Schnermann MJ. Cyanine conformational restraint in the far-red range. Journal of the American Chemical Society. 2017;139:12406-12409.

     Not in our library10.1021/jacs.7b07272

334. 334.

     Milles S, Tyagi S, Banterle N, Koehler C, VanDelinder V, Plass T, Neal AP, Lemke EA. Click strategies for single-molecule protein fluorescence. Journal of the American Chemical Society. 2012;134:5187-5195.

     Not in our library10.1021/ja210587q

335. 335.
     Plasticity of an Ultrafast Interaction between Nucleoporins and Nuclear Transport Receptors · 2015

     No notice
336. 336.

     Möckel C, Kubiak J, Schillinger O, Kühnemuth R, Della Corte D, Schröder GF, Willbold D, Strodel B, Seidel CAM, Neudecker P. Integrated NMR, fluorescence, and molecular dynamics benchmark study of protein mechanics and hydrodynamics. The Journal of Physical Chemistry B. 2019;123:1453-1480.

     Not in our library10.1021/acs.jpcb.8b08903

337. 337.

     Moffat K. Time-resolved biochemical crystallography: a mechanistic perspective. Chemical Reviews. 2001;101:1569-1582.

     Not in our library10.1021/cr990039q

338. 338.

     Moosa MM, Goodman AZ, Ferreon JC, Lee CW, Ferreon ACM, Deniz AA. Denaturant-specific effects on the structural energetics of a protein-denatured ensemble. European Biophysics Journal. 2018;47:89-94.

     Not in our library10.1007/s00249-017-1260-4

339. 339.

     Morse JC, Girodat D, Burnett BJ, Holm M, Altman RB, Sanbonmatsu KY, Wieden HJ, Blanchard SC. Elongation factor-Tu can repetitively engage aminoacyl-tRNA within the ribosome during the proofreading stage of tRNA selection. PNAS. 2020;117:3610-3620.

     Not in our library10.1073/pnas.1904469117

340. 340.

     Morten MJ, Steinmark IE, Magennis SW. Probing DNA dynamics: stacking-induced fluorescence increase (SIFI) versus FRET. ChemPhotoChem. 2020;4:664-667.

     Not in our library10.1002/cptc.202000069

341. 341.

     Mujumdar RB, Ernst LA, Mujumdar SR, Lewis CJ, Waggoner AS. Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters. Bioconjugate Chemistry. 1993;4:105-111.

     Not in our library10.1021/bc00020a001

342. 342.

     Müller JD, Chen Y, Gratton E. Resolving heterogeneity on the single molecular level with the photon-counting histogram. Biophysical Journal. 2000;78:474-486.

     Not in our library10.1016/s0006-3495(00)76610-0

343. 343.

     Müller BK, Zaychikov E, Bräuchle C, Lamb DC. Pulsed interleaved excitation. Biophysical Journal. 2005;89:3508-3522.

     Not in our library10.1529/biophysj.105.064766

344. 344.

     Munro JB, Altman RB, O'Connor N, Blanchard SC. Identification of two distinct hybrid state intermediates on the ribosome. Molecular Cell. 2007;25:505-517.

     Not in our library10.1016/j.molcel.2007.01.022

345. 345.

     Munro JB, Altman RB, Tung CS, Cate JH, Sanbonmatsu KY, Blanchard SC. Spontaneous formation of the unlocked state of the ribosome is a multistep process. PNAS. 2010;107:709-714.

     Not in our library10.1073/pnas.0908597107

346. 346.

     Munro JB, Gorman J, Ma X, Zhou Z, Arthos J, Burton DR, Koff WC, Courter JR, Smith AB, Kwong PD, Blanchard SC, Mothes W. Conformational dynamics of single HIV-1 envelope trimers on the surface of native virions. Science. 2014;346:759-763.

     Not in our library10.1126/science.1254426

347. 347.

     Munro JB, Lee KK. Probing structural variation and dynamics in the HIV-1 env fusion glycoprotein. Current HIV Research. 2018;16:5-12.

     Not in our library10.2174/1570162x16666171222110025

348. 348.

     Murakami K, Elmlund H, Kalisman N, Bushnell DA, Adams CM, Azubel M, Elmlund D, Levi-Kalisman Y, Liu X, Gibbons BJ, Levitt M, Kornberg RD. Architecture of an RNA polymerase II transcription pre-initiation complex. Science. 2013;342:1238724.

     Not in our library10.1126/science.1238724

349. 349.

     Muschielok A, Andrecka J, Jawhari A, Brückner F, Cramer P, Michaelis J. A nano-positioning system for macromolecular structural analysis. Nature Methods. 2008;5:965-971.

     Not in our library10.1038/nmeth.1259

350. 350.

     Muschielok A, Michaelis J. Application of the nano-positioning system to the analysis of fluorescence resonance energy transfer networks. The Journal of Physical Chemistry B. 2011;115:11927-11937.

     Not in our library10.1021/jp2060377

351. 351.

     Na S, Paek E. Computational methods in mass spectrometry-based structural proteomics for studying protein structure, dynamics, and interactions. Computational and Structural Biotechnology Journal. 2020;18:1391-1402.

     Not in our library10.1016/j.csbj.2020.06.002

352. 352.

     Nagy J, Grohmann D, Cheung AC, Schulz S, Smollett K, Werner F, Michaelis J. Complete architecture of the archaeal RNA polymerase open complex from single-molecule FRET and NPS. Nature Communications. 2015;6:6161.

     Not in our library10.1038/ncomms7161

353. 353.

     Nagy P, Szabó Á, Váradi T, Kovács T, Batta G, Szöllősi J. rFRET: a comprehensive, Matlab-based program for analyzing intensity-based ratiometric microscopic FRET experiments. Cytometry Part A. 2016;89:376-384.

     Not in our library10.1002/cyto.a.22828

354. 354.

     Nagy J, Eilert T, Michaelis J. Precision and accuracy in smFRET based structural studies—A benchmark study of the Fast-Nano-Positioning system. The Journal of Chemical Physics. 2018;148:123308.

     Not in our library10.1063/1.5006477

355. 355.

     Nasir I, Onuchic PL, Labra SR, Deniz AA. Single-molecule fluorescence studies of intrinsically disordered proteins and liquid phase separation. Biochimica Et Biophysica Acta (BBA) - Proteins and Proteomics. 2019;1867:980-987.

     Not in our library10.1016/j.bbapap.2019.04.007

356. 356.

     Nasir I, Bentley EP, Deniz AA. Ratiometric Single-Molecule FRET measurements to probe conformational subpopulations of intrinsically disordered proteins. Current Protocols in Chemical Biology. 2020;12:e80.

     Not in our library10.1002/cpch.80

357. 357.

     Nawrocki G, Karaboga A, Sugita Y, Feig M. Effect of protein-protein interactions and solvent viscosity on the rotational diffusion of proteins in crowded environments. Physical Chemistry Chemical Physics. 2019;21:876-883.

     Not in our library10.1039/c8cp06142d

358. 358.

     Nettels D, Gopich IV, Hoffmann A, Schuler B. Ultrafast dynamics of protein collapse from single-molecule photon statistics. PNAS. 2007;104:2655-2660.

     Not in our library10.1073/pnas.0611093104

359. 359.

     Nettels D, Hoffmann A, Schuler B. Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds. The Journal of Physical Chemistry B. 2008;112:6137-6146.

     Not in our library10.1021/jp076971j

360. 360.

     Nettels D, Müller-Späth S, Küster F, Hofmann H, Haenni D, Rüegger S, Reymond L, Hoffmann A, Kubelka J, Heinz B, Gast K, Best RB, Schuler B. Single-molecule spectroscopy of the temperature-induced collapse of unfolded proteins. PNAS. 2009;106:20740-20745.

     Not in our library10.1073/pnas.0900622106

361. 361.

     Nettels D, Haenni D, Maillot S, Gueye M, Barth A, Hirschfeld V, Hübner CG, Léonard J, Schuler B. Excited-state annihilation reduces power dependence of single-molecule FRET experiments. Physical Chemistry Chemical Physics. 2015;17:32304-32315.

     Not in our library10.1039/c5cp05321h

362. 362.

     Nettels D, Schuler B. University of Zurich. 2020.

     Not in our library

363. 363.

     Neubauer H, Gaiko N, Berger S, Schaffer J, Eggeling C, Tuma J, Verdier L, Seidel CA, Griesinger C, Volkmer A. Orientational and dynamical heterogeneity of rhodamine 6G terminally attached to a DNA helix revealed by NMR and single-molecule fluorescence spectroscopy. Journal of the American Chemical Society. 2007;129:12746-12755.

     Not in our library10.1021/ja0722574

364. 364.

     Nickels PC, Wünsch B, Holzmeister P, Bae W, Kneer LM, Grohmann D, Tinnefeld P, Liedl T. Molecular force spectroscopy with a DNA origami-based nanoscopic force clamp. Science. 2016;354:305-307.

     Not in our library10.1126/science.aah5974

365. 365.

     Nienhaus GU. Exploring protein structure and dynamics under denaturing conditions by single-molecule FRET analysis. Macromolecular Bioscience. 2006;6:907-922.

     Not in our library10.1002/mabi.200600158

366. 366.

     Nir E, Michalet X, Hamadani KM, Laurence TA, Neuhauser D, Kovchegov Y, Weiss S. Shot-noise limited single-molecule FRET histograms: comparison between theory and experiments. The Journal of Physical Chemistry B. 2006;110:22103-22124.

     Not in our library10.1021/jp063483n

367. 367.

     Oh E, Hong MY, Lee D, Nam SH, Yoon HC, Kim HS. Inhibition assay of biomolecules based on fluorescence resonance energy transfer (FRET) between quantum dots and gold nanoparticles. Journal of the American Chemical Society. 2005;127:3270-3271.

     Not in our library10.1021/ja0433323

368. 368.

     Okamoto K, Hibino K, Sako Y. In-cell single-molecule FRET measurements reveal three conformational state changes in RAF protein. Biochimica Et Biophysica Acta (BBA) - General Subjects. 2020;1864:129358.

     Not in our library10.1016/j.bbagen.2019.04.022

369. 369.

     Okumus B, Wilson TJ, Lilley DM, Ha T. Vesicle encapsulation studies reveal that single molecule ribozyme heterogeneities are intrinsic. Biophysical Journal. 2004;87:2798-2806.

     Not in our library10.1529/biophysj.104.045971

370. 370.

     Olofsson L, Felekyan S, Doumazane E, Scholler P, Fabre L, Zwier JM, Rondard P, Seidel CA, Pin JP, Margeat E. Fine tuning of sub-millisecond conformational dynamics controls metabotropic glutamate receptors agonist efficacy. Nature Communications. 2014;5:5206.

     Not in our library10.1038/ncomms6206

371. 371.

     Orevi T, Lerner E, Rahamim G, Amir D, Haas E. Ensemble and single-molecule detected time-resolved FRET methods in studies of protein conformations and dynamics. Methods in Molecular Biology. 2014;1076:113-169.

     Not in our library10.1007/978-1-62703-649-8_7

372. 372.

     Ouellet J, Schorr S, Iqbal A, Wilson TJ, Lilley DM. Orientation of cyanine fluorophores terminally attached to DNA via long, flexible tethers. Biophysical Journal. 2011;101:1148-1154.

     Not in our library10.1016/j.bpj.2011.07.007

373. 373.

     Palmer AG. NMR characterization of the dynamics of biomacromolecules. Chemical Reviews. 2004;104:3623-3640.

     Not in our library10.1021/cr030413t

374. 374.

     Park SR, Hauver J, Zhang Y, Revyakin A, Coleman RA, Tjian R, Chu S, Pertsinidis A. A single-molecule surface-based platform to detect the assembly and function of the human RNA polymerase II transcription machinery. Structure. 2020;28:1337-1343.

     Not in our library10.1016/j.str.2020.07.009

375. 375.

     Pati AK, El Bakouri O, Jockusch S, Zhou Z, Altman RB, Fitzgerald GA, Asher WB, Terry DS, Borgia A, Holsey MD, Batchelder JE, Abeywickrama C, Huddle B, Rufa D, Javitch JA, Ottosson H, Blanchard SC. Tuning the Baird aromatic triplet-state energy of cyclooctatetraene to maximize the self-healing mechanism in organic fluorophores. PNAS. 2020;117:24305-24315.

     Not in our library10.1073/pnas.2006517117

376. 376.

     Periasamy A, Wallrabe H, Chen Y, Barroso M. Chapter 22: quantitation of protein-protein interactions: confocal FRET microscopy. Methods in Cell Biology. 2008;89:569-598.

     Not in our library10.1016/s0091-679x(08)00622-5

377. 377.

     Peter MF, Gebhardt C, Mächtel R, Glaenzer J, Thomas GH, Cordes T, Hagelueken G. Cross-validation of distance measurements in proteins by PELDOR/DEER and single-molecule FRET. bioRxiv. 2020.

     Not in our library10.1101/2020.11.23.394080

378. 378.

     Peulen TO, Opanasyuk O, Seidel CAM. Combining graphical and analytical methods with molecular simulations to analyze time-resolved FRET measurements of labeled macromolecules accurately. The Journal of Physical Chemistry B. 2017;121:8211-8241.

     Not in our library10.1021/acs.jpcb.7b03441

379. 379.

     Peulen TO, Hengstenberg CS, Biehl R, Dimura M, Lorenz C, Valeri A, Ince S, Vöpel T, Faragó B, Gohlke H, Klare JP, Stadler AM, Seidel CAM, Herrmann C. Integrative dynamic structural biology unveils conformers essential for the oligomerization of a large GTPase. arXiv. 2020.

     Not in our library10.7554/elife.79565

380. 380.

     Pfiffi D, Bier BA, Marian CM, Schaper K, Seidel CA. Diphenylhexatrienes as photoprotective agents for ultrasensitive fluorescence detection. The Journal of Physical Chemistry A. 2010;114:4099-4108.

     Not in our library10.1021/jp909033x

381. 381.

     Pieper CM, Enderlein J. Fluorescence correlation spectroscopy as a tool for measuring the rotational diffusion of macromolecules. Chemical Physics Letters. 2011;516:1-11.

     Not in our library10.1016/j.cplett.2011.06.091

382. 382.

     Pirchi M, Ziv G, Riven I, Cohen SS, Zohar N, Barak Y, Haran G. Single-molecule fluorescence spectroscopy maps the folding landscape of a large protein. Nature Communications. 2011;2:493.

     Not in our library10.1038/ncomms1504

383. 383.

     Pirchi M, Tsukanov R, Khamis R, Tomov TE, Berger Y, Khara DC, Volkov H, Haran G, Nir E. Photon-by-photon hidden Markov model analysis for microsecond single-molecule FRET kinetics. The Journal of Physical Chemistry B. 2016;120:13065-13075.

     Not in our library10.1021/acs.jpcb.6b10726

384. 384.

     Plochowietz A, Crawford R, Kapanidis AN. Characterization of organic fluorophores for in vivo FRET studies based on electroporated molecules. Phys. Chem. Chem. Phys. 2014;16:12688-12694.

     Not in our library10.1039/c4cp00995a

385. 385.

     Plochowietz A, El-Sagheer AH, Brown T, Kapanidis AN. Stable end-sealed DNA as robust nano-rulers for in vivo single-molecule fluorescence. Chemical Science. 2016;7:4418-4422.

     Not in our library10.1039/c6sc00639f

386. 386.

     Plochowietz A, Farrell I, Smilansky Z, Cooperman BS, Kapanidis AN. In vivo single-RNA tracking shows that most tRNA diffuses freely in live Bacteria. Nucleic Acids Research. 2017;45:926-937.

     Not in our library10.1093/nar/gkw787

387. 387.

     Ploetz E, Lerner E, Husada F, Roelfs M, Chung S, Hohlbein J, Weiss S, Cordes T. Förster resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers. Scientific Reports. 2016;6:33257.

     Not in our library10.1038/srep33257

388. 388.

     Popov KI, Makepeace KAT, Petrotchenko EV, Dokholyan NV, Borchers CH. Insight into the structure of the "Unstructured" Tau Protein. Structure. 2019;27:1710-1715.

     Not in our library10.1016/j.str.2019.09.003

389. 389.

     Preus S, Noer SL, Hildebrandt LL, Gudnason D, Birkedal V. iSMS: single-molecule FRET microscopy software. Nature Methods. 2015;12:593-594.

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390. 390.

     Preus S, Hildebrandt LL, Birkedal V. Optimal background estimators in single-molecule FRET microscopy. Biophysical Journal. 2016;111:1278-1286.

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391. 391.

     Preuss S, Gudnason D, Birkedal V. Aarhus University. 2020.

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392. 392.

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393. 393.

     Quast RB, Margeat E. Studying GPCR conformational dynamics by single molecule fluorescence. Molecular and Cellular Endocrinology. 2019;493:110469.

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394. 394.

     Rahamim G, Chemerovski-Glikman M, Rahimipour S, Amir D, Haas E. Resolution of two sub-populations of conformers and their individual dynamics by time resolved ensemble level FRET measurements. PLOS ONE. 2015;10:e0143732.

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395. 395.

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396. 396.

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399. 399.

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400. 400.

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401. 401.

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403. 403.

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406. 406.

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407. 407.

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     Rothwell PJ, Berger S, Kensch O, Felekyan S, Antonik M, Wöhrl BM, Restle T, Goody RS, Seidel CA. Multiparameter single-molecule fluorescence spectroscopy reveals heterogeneity of HIV-1 reverse transcriptase:primer/template complexes. PNAS. 2003;100:1655-1660.

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410. 410.

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411. 411.

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413. 413.

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     Sali A, Berman HM, Schwede T, Trewhella J, Kleywegt G, Burley SK, Markley J, Nakamura H, Adams P, Bonvin AM, Chiu W, Peraro MD, Di Maio F, Ferrin TE, Grünewald K, Gutmanas A, Henderson R, Hummer G, Iwasaki K, Johnson G, Lawson CL, Meiler J, Marti-Renom MA, Montelione GT, Nilges M, Nussinov R, Patwardhan A, Rappsilber J, Read RJ, Saibil H, Schröder GF, Schwieters CD, Seidel CA, Svergun D, Topf M, Ulrich EL, Velankar S, Westbrook JD. Outcome of the first wwPDB hybrid/Integrative methods task force workshop. Structure. 2015;23:1156-1167.

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     Sanabria H, Rodnin D, Hemmen K, Peulen TO, Felekyan S, Fleissner MR, Dimura M, Koberling F, Kühnemuth R, Hubbell W, Gohlke H, Seidel CAM. Resolving dynamics and function of transient states in single enzyme molecules. Nature Communications. 2020;11:1231.

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417. 417.

     Sanborn ME, Connolly BK, Gurunathan K, Levitus M. Fluorescence properties and photophysics of the sulfoindocyanine Cy3 linked covalently to DNA. The Journal of Physical Chemistry B. 2007;111:11064-11074.

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     Sánchez-Rico C, Voith von Voithenberg L, Warner L, Lamb DC, Sattler M. Effects of fluorophore attachment on protein conformation and dynamics studied by spFRET and NMR spectroscopy. Chemistry - a European Journal. 2017;23:14267-14277.

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     Santoso Y, Joyce CM, Potapova O, Le Reste L, Hohlbein J, Torella JP, Grindley ND, Kapanidis AN. Conformational transitions in DNA polymerase I revealed by single-molecule FRET. PNAS. 2010a;107:715-720.

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421. 421.

     Sasmal DK, Pulido LE, Kasal S, Huang J. Single-molecule fluorescence resonance energy transfer in molecular biology. Nanoscale. 2016;8:19928-19944.

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422. 422.

     Schafer FP, Zhang F-G, Jethwa J. Intramolecular TT-energy transfer in bifluorophoric laser dyes. Applied Physics B Photophysics and Laser Chemistry. 1982;28:37-41.

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423. 423.

     Schaffer J, Volkmer A, Eggeling C, Subramaniam V, Striker G, Seidel CAM. Identification of single molecules in aqueous solution by time-resolved fluorescence anisotropy. The Journal of Physical Chemistry A. 1999;103:331-336.

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424. 424.

     Schalch T, Duda S, Sargent DF, Richmond TJ. X-ray structure of a tetranucleosome and its implications for the chromatin fibre. Nature. 2005;436:138-141.

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425. 425.

     Schepers B, Gohlke H. AMBER-DYES in AMBER: implementation of fluorophore and linker parameters into AmberTools. The Journal of Chemical Physics. 2020;152:221103.

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426. 426.

     Schirhagl R, Chang K, Loretz M, Degen CL. Nitrogen-vacancy centers in diamond: nanoscale sensors for physics and biology. Annual Review of Physical Chemistry. 2014;65:83-105.

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427. 427.

     Schirra RT, Zhang P. Correlative fluorescence and electron microscopy. Current Protocols in Cytometry. 2014;10:1-10.

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428. 428.

     Schlichting I, Almo SC, Rapp G, Wilson K, Petratos K, Lentfer A, Wittinghofer A, Kabsch W, Pai EF, Petsko GA. Time-resolved X-ray crystallographic study of the conformational change in Ha-Ras p21 protein on GTP hydrolysis. Nature. 1990;345:309-315.

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429. 429.

     Schlichting I, Chu K. Trapping intermediates in the crystal: ligand binding to myoglobin. Current Opinion in Structural Biology. 2000;10:744-752.

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430. 430.

     Schluesche P, Stelzer G, Piaia E, Lamb DC, Meisterernst M. NC2 mobilizes TBP on core promoter TATA boxes. Nature Structural & Molecular Biology. 2007;14:1196-1201.

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431. 431.

     Schmid S, Götz M, Hugel T. Single-molecule analysis beyond dwell times: demonstration and assessment in and out of equilibrium. Biophysical Journal. 2016;111:1375-1384.

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432. 432.

     Schneider S, Paulsen H, Reiter KC, Hinze E, Schiene-Fischer C, Hübner CG. Single molecule FRET investigation of pressure-driven unfolding of cold shock protein A. The Journal of Chemical Physics. 2018;148:123336.

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433. 433.

     Schotte F, Lim M, Jackson TA, Smirnov AV, Soman J, Olson JS, Phillips GN, Wulff M, Anfinrud PA. Watching a protein as it functions with 150-ps time-resolved x-ray crystallography. Science. 2003;300:1944-1947.

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434. 434.

     Schrimpf W, Barth A, Hendrix J, Lamb DC. PAM: a framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data. Biophysical Journal. 2018;114:1518-1528.

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435. 435.

     Schuler B, Lipman EA, Eaton WA. Probing the free-energy surface for protein folding with single-molecule fluorescence spectroscopy. Nature. 2002;419:743-747.

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436. 436.

     Schuler B, Lipman EA, Steinbach PJ, Kumke M, Eaton WA. Polyproline and the "spectroscopic ruler" revisited with single-molecule fluorescence. PNAS. 2005;102:2754-2759.

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437. 437.

     Schuler B, Soranno A, Hofmann H, Nettels D. Single-molecule FRET spectroscopy and the polymer physics of unfolded and intrinsically disordered proteins. Annual Review of Biophysics. 2016;45:207-231.

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438. 438.

     Schuler B. Perspective: chain dynamics of unfolded and intrinsically disordered proteins from nanosecond fluorescence correlation spectroscopy combined with single-molecule FRET. The Journal of Chemical Physics. 2018;149:10901.

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439. 439.

     Schuler B, Borgia A, Borgia MB, Heidarsson PO, Holmstrom ED, Nettels D, Sottini A. Binding without folding - the biomolecular function of disordered polyelectrolyte complexes. Current Opinion in Structural Biology. 2020;60:66-76.

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440. 440.

     Schuler B, Hofmann H. Single-molecule spectroscopy of protein folding dynamics—expanding scope and timescales. Current Opinion in Structural Biology. 2013;23:36-47.

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     Seefeldt B, Kasper R, Seidel T, Tinnefeld P, Dietz KJ, Heilemann M, Sauer M. Fluorescent proteins for single-molecule fluorescence applications. Journal of Biophotonics. 2008;1:74-82.

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     Segal M, Ingargiola A, Lerner E, Chung S, White JA, Streets A, Weiss S, Michalet X. High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins. Methods. 2019;169:21-45.

     Not in our library10.1016/j.ymeth.2019.07.021

443. 443.

     Sekhar A, Kay LE. An NMR view of protein dynamics in health and disease. Annual Review of Biophysics. 2019;48:297-319.

     Not in our library10.1146/annurev-biophys-052118-115647

444. 444.

     Selvin PR, Ha T. Single-Molecule Techniques. 2008.

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445. 445.

     Sgouralis I, Madaan S, Djutanta F, Kha R, Hariadi RF, Pressé S. A Bayesian nonparametric approach to single molecule Förster resonance energy transfer. The Journal of Physical Chemistry B. 2019;123:675-688.

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446. 446.

     Sgouralis I, Pressé S. An introduction to infinite HMMs for single-molecule data analysis. Biophysical Journal. 2017;112:2021-2029.

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447. 447.

     Shaner NC, Patterson GH, Davidson MW. Advances in fluorescent protein technology. Journal of Cell Science. 2007;120:4247-4260.

     Not in our library10.1242/jcs.005801

448. 448.

     Shaw RA, Johnston-Wood T, Ambrose B, Craggs TD, Hill JG. CHARMM-DYES: parameterization of fluorescent dyes for use with the CHARMM force field. Journal of Chemical Theory and Computation. 2020;16:7817-7824.

     Not in our library10.1021/acs.jctc.0c00721

449. 449.

     Sherman E, Haran G. Coil-globule transition in the denatured state of a small protein. PNAS. 2006;103:11539-11543.

     Not in our library10.1073/pnas.0601395103

450. 450.

     Shi L, De Paoli V, Rosenzweig N, Rosenzweig Z. Synthesis and application of quantum dots FRET-based protease sensors. Journal of the American Chemical Society. 2006;128:10378-10379.

     Not in our library10.1021/ja063509o

451. 451.

     Shoura MJ, Ranatunga R, Harris SA, Nielsen SO, Levene SD. Contribution of fluorophore dynamics and solvation to resonant energy transfer in protein-DNA complexes: a molecular-dynamics study. Biophysical Journal. 2014;107:700-710.

     Not in our library10.1016/j.bpj.2014.06.023

452. 452.

     Shuang B, Cooper D, Taylor JN, Kisley L, Chen J, Wang W, Li CB, Komatsuzaki T, Landes CF. Fast step transition and state identification (STaSI) for discrete single-molecule data analysis. The Journal of Physical Chemistry Letters. 2014;5:3157-3161.

     Not in our library10.1021/jz501435p

453. 453.

     Sindbert S, Kalinin S, Nguyen H, Kienzler A, Clima L, Bannwarth W, Appel B, Müller S, Seidel CA. Accurate distance determination of nucleic acids via förster resonance energy transfer: implications of dye linker length and rigidity. Journal of the American Chemical Society. 2011;133:2463-2480.

     Not in our library10.1021/ja105725e

454. 454.

     Sisamakis E, Valeri A, Kalinin S, Rothwell PJ, Seidel CA. Accurate single-molecule FRET studies using multiparameter fluorescence detection. Methods in Enzymology. 2010;475:455-514.

     Not in our library10.1016/s0076-6879(10)75018-7

455. 455.

     Slavin M, Kalisman N, Marsh J. A. Structural analysis of protein complexes by cross-linking and mass spectrometry. Methods in Molecular Biology. 2018;173-183.

     Not in our library10.1007/978-1-4939-7759-8_11

456. 456.

     Soleimaninejad H, Chen MZ, Lou X, Smith TA, Hong Y. Measuring macromolecular crowding in cells through fluorescence anisotropy imaging with an AIE fluorogen. Chemical Communications. 2017;53:2874-2877.

     Not in our library10.1039/c6cc09916e

457. 457.

     Somssich M, Ma Q, Weidtkamp-Peters S, Stahl Y, Felekyan S, Bleckmann A, Seidel CA, Simon R. Real-time dynamics of peptide ligand-dependent receptor complex formation in planta. Science Signaling. 2015;8:ra76.

     Not in our library10.1126/scisignal.aab0598

458. 458.

     Song F, Chen P, Sun D, Wang M, Dong L, Liang D, Xu RM, Zhu P, Li G. Cryo-EM study of the chromatin fiber reveals a double helix twisted by tetranucleosomal units. Science. 2014;344:376-380.

     Not in our library10.1126/science.1251413

459. 459.

     Soranno A, Buchli B, Nettels D, Cheng RR, Müller-Späth S, Pfeil SH, Hoffmann A, Lipman EA, Makarov DE, Schuler B. Quantifying internal friction in unfolded and intrinsically disordered proteins with single-molecule spectroscopy. PNAS. 2012;109:17800-17806.

     Not in our library10.1073/pnas.1117368109

460. 460.

     Soranno A, Koenig I, Borgia MB, Hofmann H, Zosel F, Nettels D, Schuler B. Single-molecule spectroscopy reveals polymer effects of disordered proteins in crowded environments. PNAS. 2014;111:4874-4879.

     Not in our library10.1073/pnas.1322611111

461. 461.

     Sottini A, Borgia A, Borgia MB, Bugge K, Nettels D, Chowdhury A, Heidarsson PO, Zosel F, Best RB, Kragelund BB, Schuler B. Polyelectrolyte interactions enable rapid association and dissociation in high-affinity disordered protein complexes. Nature Communications. 2020;11:5736.

     Not in our library10.1038/s41467-020-18859-x

462. 462.

     Spiegel JD, Fulle S, Kleinschmidt M, Gohlke H, Marian CM. Failure of the IDA in FRET systems at close inter-dye distances is moderated by frequent low κ2 Values. The Journal of Physical Chemistry B. 2016;120:8845-8862.

     Not in our library10.1021/acs.jpcb.6b05754

463. 463.

     Squires AH, Moerner WE. Direct single-molecule measurements of phycocyanobilin photophysics in monomeric C-phycocyanin. PNAS. 2017;114:9779-9784.

     Not in our library10.1073/pnas.1705435114

464. 464.

     Steffen FD, Sigel RK, Börner R. An atomistic view on carbocyanine photophysics in the realm of RNA. Physical Chemistry Chemical Physics. 2016;18:29045-29055.

     Not in our library10.1039/c6cp04277e

465. 465.

     Steffen FD, Börner R, Freisinger E, Sigel RKO. Stick, flick, click: DNA-guided fluorescent labeling of long RNA for single-molecule FRET. CHIMIA International Journal for Chemistry. 2019;73:257-261.

     Not in our library10.2533/chimia.2019.257

466. 466.

     Steffen FD, Khier M, Kowerko D, Cunha RA, Börner R, Sigel RKO. Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts. Nature Communications. 2020;11:104.

     Not in our library10.1038/s41467-019-13683-4

467. 467.

     Stein IH, Steinhauer C, Tinnefeld P. Single-molecule four-color FRET visualizes energy-transfer paths on DNA origami. Journal of the American Chemical Society. 2011;133:4193-4195.

     Not in our library10.1021/ja1105464

468. 468.

     Steiner M, Karunatilaka KS, Sigel RK, Rueda D. Single-molecule studies of group II intron ribozymes. PNAS. 2008;105:13853-13858.

     Not in our library10.1073/pnas.0804034105

469. 469.

     Steinmetzger C, Bäuerlein C, Höbartner C. Supramolecular fluorescence resonance energy transfer in nucleobase‐modified fluorogenic RNA aptamers. Angewandte Chemie International Edition. 2020;59:6760-6764.

     Not in our library10.1002/anie.201916707

470. 470.

     Stella S, Mesa P, Thomsen J, Paul B, Alcón P, Jensen SB, Saligram B, Moses ME, Hatzakis NS, Montoya G. Conformational activation promotes CRISPR-Cas12a catalysis and resetting of the endonuclease activity. Cell. 2018;175:1856-1871.

     Not in our library10.1016/j.cell.2018.10.045

471. 471.

     Strickler SJ, Berg RA. Relationship between absorption intensity and fluorescence lifetime of molecules. The Journal of Chemical Physics. 1962;37:814-822.

     Not in our library10.1063/1.1733166

472. 472.

     Stryer L, Haugland RP. Energy transfer: a spectroscopic ruler. PNAS. 1967;58:719-726.

     Not in our library10.1073/pnas.58.2.719

473. 473.

     Sturzenegger F, Zosel F, Holmstrom ED, Buholzer KJ, Makarov DE, Nettels D, Schuler B. Transition path times of coupled folding and binding reveal the formation of an encounter complex. Nature Communications. 2018;9:4708.

     Not in our library10.1038/s41467-018-07043-x

474. 474.

     Sugita Y, Feig M. All-atom molecular dynamics simulation of proteins in crowded environments. In-Cell NMR Spectroscopy. 2020;10:228-248.

     Not in our library10.1039/9781788013079-00228

475. 475.

     Sung HL, Nesbitt DJ. Correction: high pressure single-molecule FRET studies of the lysine riboswitch: cationic and osmolytic effects on pressure induced denaturation. Physical Chemistry Chemical Physics. 2020;22:17008-17009.

     Not in our library10.1039/d0cp90155e

476. 476.

     Sustarsic M, Plochowietz A, Aigrain L, Yuzenkova Y, Zenkin N, Kapanidis A. Optimized delivery of fluorescently labeled proteins in live bacteria using electroporation. Histochemistry and Cell Biology. 2014;142:113-124.

     Not in our library10.1007/s00418-014-1213-2

477. 477.

     Sustarsic M, Kapanidis AN. Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells. Current Opinion in Structural Biology. 2015;34:52-59.

     Not in our library10.1016/j.sbi.2015.07.001

478. 478.

     Swoboda M, Grieb MS, Hahn S, Schlierf M, Toseland C. P, Fili N. Measuring two at the same time: combining magnetic tweezers with single-molecule FRET. Exs. Basel. 2014;253-276.

     Not in our library10.1007/978-3-0348-0856-9_12

479. 479.

     Szalai AM, Siarry B, Lukin J, Giusti S, Unsain N, Cáceres A, Steiner F, Tinnefeld P, Refojo D, Jovin TM, Stefani FD. Super-resolution imaging of energy transfer by Intensity-Based STED-FRET. Nano Letters. 2021;21:2296-2303.

     Not in our library10.1021/acs.nanolett.1c00158

480. 480.

     Tagari M, Newman R, Chagoyen M, Carazo JM, Henrick K. New electron microscopy database and deposition system. Trends in Biochemical Sciences. 2002;27:589.

     Not in our library10.1016/s0968-0004(02)02176-x

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     Tang C, Gong Z. Integrating non-NMR distance restraints to augment NMR depiction of protein structure and dynamics. Journal of Molecular Biology. 2020;432:2913-2929.

     Not in our library10.1016/j.jmb.2020.01.023

482. 482.

     Tardif C, Nadeau G, Labrecque S, Côté D, Lavoie-Cardinal F. Fluorescence lifetime imaging nanoscopy for measuring Förster resonance energy transfer in cellular nanodomains. Neurophotonics. 2019;6:1.

     Not in our library10.1117/1.nph.6.1.015002

483. 483.

     Targowski P, Ziętek B, Bączyński A. Luminescence quenching of rhodamines by cyclooctatetraene. Zeitschrift Für Naturforschung A. 1987;42:1009-1013.

     Not in our library10.1515/zna-1987-0914

484. 484.

     Tassis K, Vietrov R, de Koning M, de Boer M, Gouridis G, Cordes T. Single‐molecule studies of conformational states and dynamics in the ABC importer OpuA. FEBS Letters. 2020;12:14026.

     Not in our library10.1002/1873-3468.14026

485. 485.

     Tellinghuisen J, Goodwin PM, Ambrose WP, Martin JC, Keller RA. Analysis of fluorescence lifetime data for single rhodamine molecules in flowing sample streams. Analytical Chemistry. 1994;66:64-72.

     Not in our library10.1021/ac00073a013

486. 486.

     Terry DS, Kolster RA, Quick M, LeVine MV, Khelashvili G, Zhou Z, Weinstein H, Javitch JA, Blanchard SC. A partially-open inward-facing intermediate conformation of LeuT is associated with Na+ release and substrate transport. Nature Communications. 2018;9:230.

     Not in our library10.1038/s41467-017-02202-y

487. 487.
     DeepFRET, a software for rapid and automated single-molecule FRET data classification using deep learning · 2020

     Not checked
488. 488.

     Tisler J, Reuter R, Lämmle A, Jelezko F, Balasubramanian G, Hemmer PR, Reinhard F, Wrachtrup J. Highly efficient FRET from a single nitrogen-vacancy center in nanodiamonds to a single organic molecule. ACS Nano. 2011;5:7893-7898.

     Not in our library10.1021/nn2021259

489. 489.

     Tomov TE, Tsukanov R, Masoud R, Liber M, Plavner N, Nir E. Disentangling subpopulations in single-molecule FRET and ALEX experiments with photon distribution analysis. Biophysical Journal. 2012;102:1163-1173.

     Not in our library10.1016/j.bpj.2011.11.4025

490. 490.

     Torella JP, Holden SJ, Santoso Y, Hohlbein J, Kapanidis AN. Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis. Biophysical Journal. 2011;100:1568-1577.

     Not in our library10.1016/j.bpj.2011.01.066

491. 491.

     Torres T, Levitus M. Measuring conformational dynamics: a new FCS-FRET approach. The Journal of Physical Chemistry B. 2007;111:7392-7400.

     Not in our library10.1021/jp070659s

492. 492.

     Tosatto L, Horrocks MH, Dear AJ, Knowles TP, Dalla Serra M, Cremades N, Dobson CM, Klenerman D. Single-molecule FRET studies on alpha-synuclein oligomerization of Parkinson's disease genetically related mutants. Scientific Reports. 2015;5:16696.

     Not in our library10.1038/srep16696

493. 493.

     Traeger JC, Schwartz DK. Surface-mediated DNA hybridization: effects of DNA conformation, surface chemistry, and electrostatics. Langmuir. 2017;33:12651-12659.

     Not in our library10.1021/acs.langmuir.7b02675

494. 494.

     Treutlein B, Muschielok A, Andrecka J, Jawhari A, Buchen C, Kostrewa D, Hög F, Cramer P, Michaelis J. Dynamic architecture of a minimal RNA polymerase II open promoter complex. Molecular Cell. 2012;46:136-146.

     Not in our library10.1016/j.molcel.2012.02.008

495. 495.

     Tsytlonok M, Sanabria H, Wang Y, Felekyan S, Hemmen K, Phillips AH, Yun MK, Waddell MB, Park CG, Vaithiyalingam S, Iconaru L, White SW, Tompa P, Seidel CAM, Kriwacki R. Dynamic anticipation by Cdk2/Cyclin A-bound p27 mediates signal integration in cell cycle regulation. Nature Communications. 2019;10:1676.

     Not in our library10.1038/s41467-019-09446-w

496. 496.

     Tsytlonok M, Hemmen K, Hamilton G, Kolimi N, Felekyan S, Seidel CAM, Tompa P, Sanabria H. Specific conformational dynamics and expansion underpin a multi-step mechanism for specific binding of p27 with Cdk2/Cyclin A. Journal of Molecular Biology. 2020;432:2998-3017.

     Not in our library10.1016/j.jmb.2020.02.010

497. 497.

     Tyagi S, VanDelinder V, Banterle N, Fuertes G, Milles S, Agez M, Lemke EA. Continuous throughput and long-term observation of single-molecule FRET without immobilization. Nature Methods. 2014;11:297-300.

     Not in our library10.1038/nmeth.2809

498. 498.

     Tyagi S, Lemke EA. Single-molecule FRET and crosslinking studies in structural biology enabled by noncanonical amino acids. Current Opinion in Structural Biology. 2015;32:66-73.

     Not in our library10.1016/j.sbi.2015.02.009

499. 499.

     Ulrich EL, Akutsu H, Doreleijers JF, Harano Y, Ioannidis YE, Lin J, Livny M, Mading S, Maziuk D, Miller Z, Nakatani E, Schulte CF, Tolmie DE, Kent Wenger R, Yao H, Markley JL. BioMagResBank. Nucleic Acids Research. 2008;36:D402-D408.

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500. 500.

     Ulrich EL, Baskaran K, Dashti H, Ioannidis YE, Livny M, Romero PR, Maziuk D, Wedell JR, Yao H, Eghbalnia HR, Hoch JC, Markley JL. NMR-STAR: comprehensive ontology for representing, archiving and exchanging data from nuclear magnetic resonance spectroscopic experiments. Journal of Biomolecular NMR. 2019;73:5-9.

     Not in our library10.1007/s10858-018-0220-3

501. 501.

     Uphoff S, Holden SJ, Le Reste L, Periz J, van de Linde S, Heilemann M, Kapanidis AN. Monitoring multiple distances within a single molecule using switchable FRET. Nature Methods. 2010;7:831-836.

     Not in our library10.1038/nmeth.1502

502. 502.

     Uphoff S, Gryte K, Evans G, Kapanidis AN. Improved temporal resolution and linked hidden markov modeling for switchable single-molecule FRET. ChemPhysChem. 2011;12:571-579.

     Not in our library10.1002/cphc.201000834

503. 503.

     Vallat B, Webb B, Westbrook JD, Sali A, Berman HM. Development of a prototype system for archiving integrative/hybrid structure models of biological macromolecules. Structure. 2018;26:894-904.

     Not in our library10.1016/j.str.2018.03.011

504. 504.

     Vallat B, Hanke CA, Lawson CL, Westbrook JD, Berman HM, Seidel CAM. GitHub. 2020.

     Not in our library

505. 505.

     van de Meent JW, Bronson JE, Wiggins CH, Gonzalez RL. Empirical bayes methods enable advanced population-level analyses of single-molecule FRET experiments. Biophysical Journal. 2014;106:1327-1337.

     Not in our library10.1016/j.bpj.2013.12.055

506. 506.

     van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, Uversky VN, Wright PE, Babu MM. Classification of intrinsically disordered regions and proteins. Chemical Reviews. 2014;114:6589-6631.

     Not in our library10.1021/cr400525m

507. 507.

     van der Meer BW. Kappa-squared: from nuisance to new sense. Reviews in Molecular Biotechnology. 2002;82:181-196.

     Not in our library10.1016/s1389-0352(01)00037-x

508. 508.

     van der Velde JH, Ploetz E, Hiermaier M, Oelerich J, de Vries JW, Roelfes G, Cordes T. Mechanism of intramolecular photostabilization in self-healing cyanine fluorophores. ChemPhysChem. 2013;14:4084-4093.

     Not in our library10.1002/cphc.201300785

509. 509.

     van der Velde JHM, Oelerich J, Huang J, Smit JH, Aminian Jazi A, Galiani S, Kolmakov K, Gouridis G, Eggeling C, Herrmann A, Roelfes G, Cordes T. A simple and versatile design concept for fluorophore derivatives with intramolecular photostabilization. Nature Communications. 2016;7:10144.

     Not in our library10.1038/ncomms10144

510. 510.

     Vandenberk N, Barth A, Borrenberghs D, Hofkens J, Hendrix J. Evaluation of Blue and Far-Red Dye Pairs in Single-Molecule Förster Resonance Energy Transfer Experiments. The Journal of Physical Chemistry B. 2018;122:4249-4266.

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511. 511.

     Verkade P, Collinson L. Correlative Imaging. 2019.

     Not in our library10.1002/9781119086420

512. 512.

     Viegas A, Dollinger P, Verma N, Kubiak J, Viennet T, Seidel CAM, Gohlke H, Etzkorn M, Kovacic F, Jaeger K-E. Structural and dynamic insights revealing how lipase binding domain MD1 of Pseudomonas aeruginosa foldase affects lipase activation. Scientific Reports. 2020;10:3578.

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513. 513.

     Voelz VA, Jäger M, Yao S, Chen Y, Zhu L, Waldauer SA, Bowman GR, Friedrichs M, Bakajin O, Lapidus LJ, Weiss S, Pande VS. Slow unfolded-state structuring in Acyl-CoA binding protein folding revealed by simulation and experiment. Journal of the American Chemical Society. 2012;134:12565-12577.

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514. 514.

     Vogelsang J, Kasper R, Steinhauer C, Person B, Heilemann M, Sauer M, Tinnefeld P. A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes. Angewandte Chemie International Edition. 2008;47:5465-5469.

     Not in our library10.1002/anie.200801518

515. 515.

     Voith von Voithenberg L, Sánchez-Rico C, Kang HS, Madl T, Zanier K, Barth A, Warner LR, Sattler M, Lamb DC. Recognition of the 3' splice site RNA by the U2AF heterodimer involves a dynamic population shift. PNAS. 2016;113:E7169-E7175.

     Not in our library10.1073/pnas.1605873113

516. 516.

     Volkov IL, Lindén M, Aguirre Rivera J, Ieong KW, Metelev M, Elf J, Johansson M. tRNA tracking for direct measurements of protein synthesis kinetics in live cells. Nature Chemical Biology. 2018;14:618-626.

     Not in our library10.1038/s41589-018-0063-y

517. 517.

     Vöpel T, Hengstenberg CS, Peulen TO, Ajaj Y, Seidel CA, Herrmann C, Klare JP. Triphosphate induced dimerization of human guanylate binding protein 1 involves association of the C-terminal helices: a joint double electron-electron resonance and FRET study. Biochemistry. 2014;53:4590-4600.

     Not in our library10.1021/bi500524u

518. 518.

     Vušurović N, Altman RB, Terry DS, Micura R, Blanchard SC. Pseudoknot formation seeds the twister ribozyme cleavage reaction coordinate. Journal of the American Chemical Society. 2017;139:8186-8193.

     Not in our library10.1021/jacs.7b01549

519. 519.

     Wahl M, Rahn H-J, Röhlicke T, Kell G, Nettels D, Hillger F, Schuler B, Erdmann R. Scalable time-correlated photon counting system with multiple independent input channels. Review of Scientific Instruments. 2008;79:123113.

     Not in our library10.1063/1.3055912

520. 520.

     Wang L, Pulk A, Wasserman MR, Feldman MB, Altman RB, Cate JHD, Blanchard SC. Allosteric control of the ribosome by small-molecule antibiotics. Nature Structural & Molecular Biology. 2012;19:957-963.

     Not in our library10.1038/nsmb.2360

521. 521.
     Single molecule FRET reveals pore size and opening mechanism of a mechano-sensitive ion channel · 2014

     No notice
522. 522.

     Wang S, Vafabakhsh R, Borschel WF, Ha T, Nichols CG. Structural dynamics of potassium-channel gating revealed by single-molecule FRET. Nature Structural & Molecular Biology. 2016;23:31-36.

     Not in our library10.1038/nsmb.3138

523. 523.

     Wang Y, Lu HP. Bunching effect in single-molecule T4 lysozyme nonequilibrium conformational dynamics under enzymatic reactions. The Journal of Physical Chemistry B. 2010;114:6669-6674.

     Not in our library10.1021/jp1004506

524. 524.

     Wang W, Wang D. Extreme fuzziness: direct interactions between two IDPs. Biomolecules. 2019;9:81.

     Not in our library10.3390/biom9030081

525. 525.

     Wasserman MR, Alejo JL, Altman RB, Blanchard SC. Multiperspective smFRET reveals rate-determining late intermediates of ribosomal translocation. Nature Structural & Molecular Biology. 2016;23:333-341.

     Not in our library10.1038/nsmb.3177

526. 526.

     Watrob HM, Pan C-P, Barkley MD. Two-Step FRET as a Structural Tool. Journal of the American Chemical Society. 2003;125:7336-7343.

     Not in our library10.1021/ja034564p

527. 527.

     Webb B, Viswanath S, Bonomi M, Pellarin R, Greenberg CH, Saltzberg D, Sali A. Integrative structure modeling with the integrative modeling platform. Protein Science. 2018;27:245-258.

     Not in our library10.1002/pro.3311

528. 528.

     Weidtkamp-Peters S, Felekyan S, Bleckmann A, Simon R, Becker W, Kühnemuth R, Seidel CA. Multiparameter fluorescence image spectroscopy to study molecular interactions. Photochemical & Photobiological Sciences. 2009;8:470-480.

     Not in our library10.1039/b903245m

529. 529.

     Weiss S. Fluorescence spectroscopy of single biomolecules. Science. 1999;283:1676-1683.

     Not in our library10.1126/science.283.5408.1676

530. 530.

     White SS, Li H, Marsh RJ, Piper JD, Leonczek ND, Nicolaou N, Bain AJ, Ying L, Klenerman D. Characterization of a single molecule DNA switch in free solution. Journal of the American Chemical Society. 2006;128:11423-11432.

     Not in our library10.1021/ja0614870

531. 531.

     Whitford PC, Geggier P, Altman RB, Blanchard SC, Onuchic JN, Sanbonmatsu KY. Accommodation of aminoacyl-tRNA into the ribosome involves reversible excursions along multiple pathways. RNA. 2010;16:1196-1204.

     Not in our library10.1261/rna.2035410

532. 532.

     Widengren J, Schweinberger E, Berger S, Seidel CAM. Two new concepts to measure fluorescence resonance energy transfer via fluorescence correlation spectroscopy: Theory and Experimental Realizations. The Journal of Physical Chemistry A. 2001;105:6851-6866.

     Not in our library10.1021/jp010301a

533. 533.

     Widengren J, Kudryavtsev V, Antonik M, Berger S, Gerken M, Seidel CAM. Single-molecule detection and identification of multiple species by multiparameter fluorescence detection. Analytical Chemistry. 2006;78:2039-2050.

     Not in our library10.1021/ac0522759

534. 534.

     Widengren J, Chmyrov A, Eggeling C, Löfdahl PA, Seidel CA. Strategies to improve photostabilities in ultrasensitive fluorescence spectroscopy. The Journal of Physical Chemistry A. 2007;111:429-440.

     Not in our library10.1021/jp0646325

535. 535.
     The FAIR Guiding Principles for scientific data management and stewardship · 2016

     No notice
536. 536.

     Wilson H, Wang Q. ABEL-FRET: tether-free single-molecule FRET with hydrodynamic profiling. bioRxiv. 2019.

     Not in our library10.1101/786897

537. 537.

     Wozniak AK, Schröder GF, Grubmüller H, Seidel CAM, Oesterhelt F. Single-molecule FRET measures bends and kinks in DNA. PNAS. 2008;105:18337-18342.

     Not in our library10.1073/pnas.0800977105

538. 538.

     Wranne MS, Füchtbauer AF, Dumat B, Bood M, El-Sagheer AH, Brown T, Gradén H, Grøtli M, Wilhelmsson LM. Toward complete sequence flexibility of nucleic acid base analogue FRET. Journal of the American Chemical Society. 2017;139:9271-9280.

     Not in our library10.1021/jacs.7b04517

539. 539.

     Wright PE, Dyson HJ. Intrinsically disordered proteins in cellular signalling and regulation. Nature Reviews Molecular Cell Biology. 2015;16:18-29.

     Not in our library10.1038/nrm3920

540. 540.

     Wu S, Wang D, Liu J, Feng Y, Weng J, Li Y, Gao X, Liu J, Wang W. The dynamic multisite interactions between two intrinsically disordered proteins. Angewandte Chemie International Edition. 2017;56:7515-7519.

     Not in our library10.1002/anie.201701883

541. 541.

     Wunderlich B, Nettels D, Benke S, Clark J, Weidner S, Hofmann H, Pfeil SH, Schuler B. Microfluidic mixer designed for performing single-molecule kinetics with confocal detection on timescales from milliseconds to minutes. Nature Protocols. 2013;8:1459-1474.

     Not in our library10.1038/nprot.2013.082

542. 542.
     Identifying weak interdomain interactions that stabilize the supertertiary structure of the N-terminal tandem PDZ domains of PSD-95 · 2018

     Not checked
543. 543.

     Yim SW, Kim T, Laurence TA, Partono S, Kim D, Kim Y, Weiss S, Reitmair A. Four-Color Alternating-Laser excitation Single-Molecule fluorescence spectroscopy for Next-Generation biodetection assays. Clinical Chemistry. 2012;58:707-716.

     Not in our library10.1373/clinchem.2011.176958

544. 544.

     Yoo J, Louis JM, Gopich IV, Chung HS. Three-color single-molecule FRET and fluorescence lifetime analysis of fast protein folding. The Journal of Physical Chemistry B. 2018;122:11702-11720.

     Not in our library10.1021/acs.jpcb.8b07768

545. 545.
     Fast three-color single-molecule FRET using statistical inference · 2020

     Not checked
546. 546.

     Young J, Westbrook J. Creating and maintaining a data archive for 3D structures of biological macromolecules. F1000Research. 2019;8:1111762.

     Not in our library10.7490/f1000research.1111762.1

547. 547.

     Zarrabi N, Schluesche P, Meisterernst M, Börsch M, Lamb DC. Analyzing the dynamics of single TBP-DNA-NC2 complexes using hidden Markov models. Biophysical Journal. 2018;115:2310-2326.

     Not in our library10.1016/j.bpj.2018.11.015

548. 548.

     Zelger-Paulus S, Hadzic M, Sigel RKO, Börner R, Arluison V, Wien F. Encapsulation of fluorescently labeled RNAs into surface-tethered vesicles for single-molecule FRET studies in TIRF microscopy. Methods in Molecular Biology. 2020;1-16.

     Not in our library10.1007/978-1-0716-0278-2_1

549. 549.

     Zhao R, Marshall M, Alemán EA, Lamichhane R, Feig A, Rueda D. Laser-assisted single-molecule refolding (LASR). Biophysical Journal. 2010a;99:1925-1931.

     Not in our library10.1016/j.bpj.2010.07.019

550. 550.

     Zhao Y, Terry D, Shi L, Weinstein H, Blanchard SC, Javitch JA. Single-molecule dynamics of gating in a neurotransmitter transporter homologue. Nature. 2010b;465:188-193.

     Not in our library10.1038/nature09057

551. 551.

     Zhao M, Steffen FD, Börner R, Schaffer MF, Sigel RKO, Freisinger E. Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy. Nucleic Acids Research. 2018;46:e13.

     Not in our library10.1093/nar/gkx1100

552. 552.

     Zheng Q, Juette MF, Jockusch S, Wasserman MR, Zhou Z, Altman RB, Blanchard SC. Ultra-stable organic fluorophores for single-molecule research. Chem. Soc. Rev. 2014;43:1044-1056.

     Not in our library10.1039/c3cs60237k

553. 553.

     Zhuang X, Bartley LE, Babcock HP, Russell R, Ha T, Herschlag D, Chu S. A single-molecule study of RNA catalysis and folding. Science. 2000;288:2048-2051.

     Not in our library10.1126/science.288.5473.2048

554. 554.

     Zijlstra N, Dingfelder F, Wunderlich B, Zosel F, Benke S, Nettels D, Schuler B. Rapid microfluidic dilution for Single-Molecule spectroscopy of Low-Affinity biomolecular complexes. Angewandte Chemie International Edition. 2017;56:7126-7129.

     Not in our library10.1002/anie.201702439

555. 555.
     A proline switch explains kinetic heterogeneity in a coupled folding and binding reaction · 2018

     Not checked
556. 556.

     Zosel F, Holla A, Schuler B. Labeling of proteins for single-molecule fluorescence spectroscopy. ChemRxiv. 2020a.

     Not in our library10.26434/chemrxiv.11537913

557. 557.

     Zosel F, Soranno A, Buholzer KJ, Nettels D, Schuler B. Depletion interactions modulate the binding between disordered proteins in crowded environments. PNAS. 2020b;117:13480-13489.

     Not in our library10.1073/pnas.1921617117

Cited by papers we hold 2

• Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins · 2023
  No notice
• Visualizing the disordered nuclear transport machinery in situ · 2023
  No notice

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