SERS discrimination of single DNA bases in single oligonucleotides by electro-plasmonic trapping

Abstract

Surface-enhanced Raman spectroscopy (SERS) sensing of DNA bases by plasmonic nanopores could pave a way to novel methods for DNA analyses and new generation single-molecule sequencing platforms. The SERS discrimination of single DNA bases depends critically on the time that a DNA strand resides within the plasmonic hot spot. In fact, DNA molecules flow through the nanopores so rapidly that the SERS signals collected are not sufficient for single-molecule analysis. Here, we report an approach to control the residence time of molecules in the hot spot by an electro-plasmonic trapping effect. By directly adsorbing molecules onto a gold nanoparticle and then trapping the single nanoparticle in a plasmonic nanohole up to several minutes, we demonstrate single-molecule SERS detection of all four DNA bases as well as discrimination of single nucleobases in a single oligonucleotide. Our method can be extended easily to label-free sensing of single-molecule amino acids and proteins.

Full text

Its licence does not allow us to show the full text. Read it at PubMed Central:

References 63

1. 1.

   Pieczonka NPW, Aroca RF. Single molecule analysis by surfaced-enhanced Raman scattering. Chem. Soc. Rev. 2008;37:946-954.

   Not in our library10.1039/b709739p

2. 2.
   High spatial resolution nanoslit SERS for single-molecule nucleobase sensing · 2018

   Not checked
3. 3.

   Belkin M, Chao S-H, Jonsson MP, Dekker C, Aksimentiev A. Plasmonic nanopores for trapping, controlling displacement, and sequencing of DNA. ACS Nano. 2015;9:10598-10611.

   Not in our library10.1021/acsnano.5b04173

4. 4.

   Le Ru EC, Meyer M, Etchegoin PG. Proof of single-mokeule sensitivity in surface enhanced Raman scattering (SERS) by means of a two-analyte technique. J. Phys. Chem. B. 2006;110:1944-1948.

   Not in our library10.1021/jp054732v

5. 5.

   Huang J-A, Zhang Y-L, Ding H, Sun H-B. SERS-enabled lab-on-a-chip systems. Adv. Optical Mater. 2015;3:618-633.

   Not in our library10.1002/adom.201400534

6. 6.

   Ndukaife JC, et al. High-resolution large-ensemble nanoparticle trapping with multifunctional thermoplasmonic nanohole metasurface. ACS Nano. 2018;12:5376-5384.

   Not in our library10.1021/acsnano.8b00318

7. 7.

   Juan ML, Righini M, Quidant R. Plasmon nano-optical tweezers. Nat. Photonics. 2011;5:349-356.

   Not in our library10.1038/nphoton.2011.56

8. 8.

   Lin L, et al. Opto-thermoelectric nanotweezers. Nat. Photonics. 2018;12:195-201.

   Not in our library10.1038/s41566-018-0134-3

9. 9.

   Paik K-H, et al. Control of DNA capture by nanofluidic transistors. ACS Nano. 2012;6:6767-6775.

   Not in our library10.1021/nn3014917

10. 10.

    Zhang M, et al. Thermophoresis-controlled size-dependent DNA translocation through an array of nanopores. ACS Nano. 2018;12:4574-4582.

    Not in our library10.1021/acsnano.8b00961

11. 11.

    Al Sulaiman D, Cadinu P, Ivanov AP, Edel JB, Ladame S. Chemically modified hydrogel-filled nanopores: a tunable platform for single-molecule sensing. Nano Lett. 2018;18:6084-6093.

    Not in our library10.1021/acs.nanolett.8b03111

12. 12.

    Deamer D, Akeson M, Branton D. Three decades of nanopore sequencing. Nat. Biotechnol. 2016;34:518-524.

    Not in our library10.1038/nbt.3423

13. 13.

    Tian S, et al. Aluminum nanocrystals: a sustainable substrate for quantitative SERS-based DNA detection. Nano Lett. 2017;17:5071-5077.

    Not in our library10.1021/acs.nanolett.7b02338

14. 14.

    Xu L-J, et al. Label-free surface-enhanced Raman spectroscopy detection of DNA with single-base sensitivity. J. Am. Chem. Soc. 2015;137:5149-5154.

    Not in our library10.1021/jacs.5b01426

15. 15.

    Restrepo-Perez L, Joo C, Dekker C. Paving the way to single-molecule protein sequencing. Nat. Nanotechnol. 2018;13:786-796.

    Not in our library10.1038/s41565-018-0236-6

16. 16.

    Hrelescu C, Sau TK, Rogach AL, Jackel F, Feldmann J. Single gold nanostars enhance Raman scattering. Appl. Phys. Lett. 2009;94:153113.

    Not in our library10.1063/1.3119642

17. 17.

    Khoury CG, Vo-Dinh T. Gold nanostars for surface-enhanced raman scattering: synthesis, characterization and optimization. J. Phys. Chem. C. 2008;112:18849-18859.

    Not in our library10.1021/jp8054747

18. 18.

    Niu WX, Chua YAA, Zhang WQ, Huang HJ, Lu XM. Highly symmetric gold nanostars: crystallographic control and surface-enhanced raman scattering property. J. Am. Chem. Soc. 2015;137:10460-10463.

    Not in our library10.1021/jacs.5b05321

19. 19.

    Benz F, et al. SERS of individual nanoparticles on a mirror: size does matter, but so does shape. J. Phys. Chem. Lett. 2016;7:2264-2269.

    Not in our library10.1021/acs.jpclett.6b00986

20. 20.

    Ndukaife JC, et al. Long-range and rapid transport of individual nano-objects by a hybrid electrothermoplasmonic nanotweezer. Nat. Nanotechnol. 2016;11:53-59.

    Not in our library10.1038/nnano.2015.248

21. 21.

    Urban AS, et al. Optical trapping and manipulation of plasmonic nanoparticles: fundamentals, applications, and perspectives. Nanoscale. 2014;6:4458-4474.

    Not in our library10.1039/c3nr06617g

22. 22.

    Schoch RB, Han J, Renaud P. Transport phenomena in nanofluidics. Rev. Mod. Phys. 2008;80:839-883.

    Not in our library10.1103/revmodphys.80.839

23. 23.

    Zhao YJ, Xing WH, Xu NP, Wong FS. Effects of inorganic electrolytes on Zeta potentials of ceramic microfiltration membranes. Sep. Purif. Technol. 2005;42:117-121.

    Not in our library10.1016/j.seppur.2004.06.011

24. 24.

    Huang JA, et al. Ordered Ag/Si nanowires array: wide-range surface-enhanced raman spectroscopy for reproducible biomolecule detection. Nano Lett. 2013;13:5039-5045.

    Not in our library10.1021/nl401920u

25. 25.

    Kerman S, et al. Raman fingerprinting of single dielectric nanoparticles in plasmonic nanopores. Nanoscale. 2015;7:18612-18618.

    Not in our library10.1039/c5nr05341b

26. 26.

    Kim JY, Han D, Crouch GM, Kwon SR, Bohn PW. Capture of single silver nanoparticles in nanopore arrays detected by simultaneous amperometry and surface-enhanced raman scattering. Anal. Chem. 2019;91:4568-4576.

    Not in our library10.1021/acs.analchem.8b05748

27. 27.

    Penders J, et al. Single particle automated raman trapping analysis. Nat. Commun. 2018;9:4256.

    Not in our library10.1038/s41467-018-06397-6

28. 28.

    Kleinman SL, et al. Single-molecule surface-enhanced raman spectroscopy of crystal violet isotopologues: theory and experiment. J. Am. Chem. Soc. 2011;133:4115-4122.

    Not in our library10.1021/ja110964d

29. 29.

    Dieringer JA, Lettan RB, Scheidt KA, Van Duyne RP. A frequency domain existence proof of single-molecule surface-enhanced Raman Spectroscopy. J. Am. Chem. Soc. 2007;129:16249-16256.

    Not in our library10.1021/ja077243c

30. 30.

    Koo KM, Sina AAI, Carrascosa LG, Shiddiky MJA, Trau M. DNA-bare gold affinity interactions: mechanism and applications in biosensing. Anal. Methods. 2015;7:7042-7054.

    Not in our library10.1039/c5ay01479d

31. 31.

    Madzharova F, Heiner Z, Guehlke M, Kneipp J. Surface-enhanced hyper-Raman spectra of adenine, guanine, cytosine, thymine, and uracil. J. Phys. Chem. C. 2016;120:15415-15423.

    Not in our library10.1021/acs.jpcc.6b02753

32. 32.

    Otto C, Vandentweel TJJ, Demul FFM, Greve J. Surface-enhanced raman-spectroscopy of DNA bases. J. Raman Spectrosc. 1986;17:289-298.

    Not in our library10.1002/jrs.1250170311

33. 33.

    Ichimura T, et al. Subnanometric near-field raman investigation in the vicinity of a metallic nanostructure. Phys. Rev. Lett. 2009;102:186101.

    Not in our library10.1103/physrevlett.102.186101

34. 34.

    Ichimura T, et al. Temporal fluctuation of tip-enhanced Raman spectra of adenine molecules. J. Phys. Chem. C. 2007;111:9460-9464.

    Not in our library10.1021/jp070420b

35. 35.

    Watanabe H, Ishida Y, Hayazawa N, Inouye Y, Kawata S. Tip-enhanced near-field Raman analysis of tip-pressurized adenine molecule. Phys. Rev. B. 2004;69:155418.

    Not in our library10.1103/physrevb.69.155418

36. 36.

    Sass JK, Neff H, Moskovits M, Holloway S. Electric field gradient effects on the spectroscopy of adsorbed molecules. J. Phys. Chem. 1981;85:621-623.

    Not in our library10.1021/j150606a002

37. 37.

    Chulhai DV, Jensen L. Determining molecular orientation with surface-enhanced Raman scattering using inhomogenous electric fields. J. Phys. Chem. C. 2013;117:19622-19631.

    Not in our library10.1021/jp4062626

38. 38.

    Moskovits M, Dilella DP, Maynard KJ. Surface Raman-spectroscopy of a number of cyclic aromatic-molecules adsorbed on silver—selection-rules and molecular-reorientation. Langmuir. 1988;4:67-76.

    Not in our library10.1021/la00079a012

39. 39.

    Yang J-M, et al. An in situ SERS study of ionic transport and the Joule heating effect in plasmonic nanopores. Chem. Commun. 2018;54:13236-13239.

    Not in our library10.1039/c8cc07153e

40. 40.

    Park K-D, et al. Variable-temperature tip-enhanced Raman spectroscopy of single-molecule fluctuations and dynamics. Nano Lett. 2016;16:479-487.

    Not in our library10.1021/acs.nanolett.5b04135

Cited by papers we hold 2

• Plasmonic Nanoarchitectures for Single‐Molecule Explorations: An Overview · 2022
  Not checked
• doi:10.37188/lam.2021.013 · 2021
  Not checked

Reads

A person counts once a day per paper. We keep no cookie and no address: a reader is a hash that changes every day. Any month under five reads shows no number.