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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

8. 8.

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

   Not in our library10.1038/s41566-018-0134-3 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

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 (opens in a new tab)

41. 41.

    Klingsporn JM, et al. Intramolecular insight into adsorbate-substrate interactions via low-temperature, ultrahigh-vacuum tip-enhanced Raman spectroscopy. J. Am. Chem. Soc. 2014;136:3881-3887.

    Not in our library10.1021/ja411899k (opens in a new tab)

42. 42.

    Sriram S, et al. Influence of electric field on SERS: frequency effects, intensity changes, and susceptible bonds. J. Am. Chem. Soc. 2012;134:4646-4653.

    Not in our library10.1021/ja208893q (opens in a new tab)

43. 43.

    Matsuhita R, Horikawa M, Naitoh Y, Nakamura H, Kiguchi M. Conductance and SERS measurement of benzenedithiol molecules bridging between Au electrodes. J. Phys. Chem. C. 2013;117:1791-1795.

    Not in our library10.1021/jp3112638 (opens in a new tab)

44. 44.

    Zhao XM, Chen MD. DFT study on the influence of electric field on surface-enhanced Raman scattering from pyridine-metal complex. J. Raman Spectrosc. 2014;45:62-67.

    Not in our library10.1002/jrs.4422 (opens in a new tab)

45. 45.

    Zhang YX, Shao YF, Zhang WW, Feng YM, Lin W. DFT studies of surface-enhanced Raman spectroscopy of 1,4-benzenedithiol-Au-2 complex under the effect of static electric fields. J. Raman Spectrosc. 2016;47:310-315.

    Not in our library10.1002/jrs.4822 (opens in a new tab)

46. 46.

    Iakhnenko M, et al. Adsorption of cytosine and AZA derivatives of cytidine on Au single crystal surfaces. J. Phys. Chem. C. 2013;117:18423-18433.

    Not in our library10.1021/jp404821t (opens in a new tab)

47. 47.

    Blackie EJ, Le Ru EC, Etchegoin PG. Single-molecule surface-enhanced Raman spectroscopy of nonresonant molecules. J. Am. Chem. Soc. 2009;131:14466-14472.

    Not in our library10.1021/ja905319w (opens in a new tab)

48. 48.

    Sandstrom P, Boncheva M, Akerman B. Nonspecific and thiol-specific binding of DNA to gold nanoparticles. Langmuir. 2003;19:7537-7543.

    Not in our library10.1021/la034348u (opens in a new tab)

49. 49.

    Gearheart LA, Ploehn HJ, Murphy CJ. Oligonucleotide adsorption to gold nanoparticles: a surface-enhanced raman spectroscopy study of intrinsically bent DNA. J. Phys. Chem. B. 2001;105:12609-12615.

    Not in our library10.1021/jp0106606 (opens in a new tab)

50. 50.

    Papadopoulou E, Bell SEJ. Label-free detection of nanomolar unmodified single- and double-stranded DNA by using surface-enhanced Raman spectroscopy on Ag and Au colloids. Chemistry. 2012;18:5394-5400.

    Not in our library10.1002/chem.201103520 (opens in a new tab)

51. 51.

    Papadopoulou E, Bell SEJ. Structure of adenine on metal nanoparticles: pH equilibria and formation of Ag+ complexes detected by surface-enhanced Raman spectroscopy. J. Phys. Chem. C. 2010;114:22644-22651.

    Not in our library10.1021/jp1092256 (opens in a new tab)

52. 52.

    Papadopoulou E, Bell SEJ. Surface enhanced Raman evidence for Ag+ complexes of adenine, deoxyadenosine and 5 ‘-dAMP formed in silver colloids. Analyst. 2010;135:3034-3037.

    Not in our library10.1039/c0an00612b (opens in a new tab)

53. 53.

    Papadopoulou E, Bell SEJ. DNA reorientation on Au nanoparticles: label-free detection of hybridization by surface enhanced Raman spectroscopy. Chem. Commun. 2011;47:10966-10968.

    Not in our library10.1039/c1cc13705k (opens in a new tab)

54. 54.

    Benz F, et al. Single-molecule optomechanics in “picocavities”. Science. 2016;354:726-729.

    Not in our library10.1126/science.aah5243 (opens in a new tab)

55. 55.

    Neacsu CC, Dreyer J, Behr N, Raschke MB. Scanning-probe Raman spectroscopy with single-molecule sensitivity. Phys. Rev. B. 2006;73:193406.

    Not in our library10.1103/physrevb.73.193406 (opens in a new tab)

56. 56.

    Kundu J, et al. Adenine- and adenosine monophosphate (AMP)-gold binding interactions studied by surface-enhanced raman and infrared spectroscopies. J. Phys. Chem. C. 2009;113:14390-14397.

    Not in our library10.1021/jp903126f (opens in a new tab)

57. 57.

    Papadopoulou E, Bell SEJ. Surface-enhanced raman evidence of protonation, reorientation, and Ag+ complexation of deoxyadenosine and deoxyadenosine-5 ‘-monophosphate (dAMP) on Ag and Au surfaces. J. Phys. Chem. C. 2011;115:14228-14235.

    Not in our library10.1021/jp204369f (opens in a new tab)

58. 58.

    Maleki A, Alavi S, Najafi B. Molecular dynamics simulation study of adsorption and patterning of DNA bases on the Au(111) surface. J. Phys. Chem. C. 2011;115:22484-22494.

    Not in our library10.1021/jp207533p (opens in a new tab)

59. 59.

    Zhang R, et al. Distinguishing individual DNA bases in a network by non-resonant tip-enhanced Raman scattering. Angew. Chem. Int. Ed. 2017;56:5561-5564.

    Not in our library10.1002/anie.201702263 (opens in a new tab)

60. 60.

    Johnson CR, Asher SA. UV resonance raman excitation profiles of L-cystine. J. Raman Spectrosc. 1987;18:345-349.

    Not in our library10.1002/jrs.1250180509 (opens in a new tab)

61. 61.

    Clement J-E, Leray A, Bouhelier A, Finot E. Spectral pointillism of enhanced Raman scattering for accessing structural and conformational information on single protein. Phys. Chem. Chem. Phys. 2017;19:458-466.

    Not in our library10.1039/c6cp06667d (opens in a new tab)

62. 62.

    Matteini P, et al. Site-selective surface-enhanced Raman detection of proteins. ACS Nano. 2017;11:918-926.

    Not in our library10.1021/acsnano.6b07523 (opens in a new tab)

63. 63.

    Xu LJ, et al. Label-free detection of native proteins by surface-enhanced Raman spectroscopy using iodide-modified nanoparticles. Anal. Chem. 2014;86:2238-2245.

    Not in our library10.1021/ac403974n (opens in a new tab)

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

Questions about this paper

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.