SERS-based approaches toward genetic profiling

Bioanalysis

Volumn 7, Issue 2, 2015, Pages 263-278

  De Silva Indrasekara, Agampodi Swarnapali ^a   Fabris, Laura ^a,b  

^a Piscataway   (United States)

^b RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; GOLD; METAL NANOPARTICLE; MICROSATELLITE DNA;

ANALYTIC METHOD; BINDING AFFINITY; DNA FINGERPRINTING; GENETIC PROFILING; HUMAN; MOLECULAR RECOGNITION; NUCLEOTIDE SEQUENCE; RAMAN SPECTROMETRY; REVIEW; BACTERIUM; BASE MISPAIRING; CHEMISTRY; GENETICS; POLYMERASE CHAIN REACTION; SINGLE NUCLEOTIDE POLYMORPHISM;

BACTERIA; BASE PAIR MISMATCH; DNA; GOLD; HUMANS; METAL NANOPARTICLES; MICROSATELLITE REPEATS; POLYMERASE CHAIN REACTION; POLYMORPHISM, SINGLE NUCLEOTIDE; SPECTRUM ANALYSIS, RAMAN;

EID: 84921350752     PISSN: 17576180     EISSN: 17576199     Source Type: Journal    
DOI: 10.4155/bio.14.295     Document Type: Review

References (89)

1. Decorte R. Genetic identification in the 21st century - current status and future developments. Forensic Sci. Int. 201(1-3), 160-164 (2010
2. Butler J. Genetics and genomics of core short tandem repeat loci used in human identity testing. J. Forensic Sci. 51(2), 253-265 (2006
3. Chakraborty R, Stivers D, Su B, Zhong Y, Budowle B. The utility of short tandem repeat loci beyond human identification: implications for development of new DNA typing systems. Electrophoresis 20(8), 1682-1696 (1999
4. Larguinho M, Baptista PV. Gold and silver nanoparticles for clinical diagnostics - from genomics to proteomics. J. Proteomics 75(10), 2811-2823 (2012
5. Moskovits M. Surface-enhanced Raman spectroscopy: a brief retrospective. J. Raman Spectrosc. 36(6-7), 485-496 (2005
6. Kang T, Yoo SM, Yoon I, Lee SY, Kim B Patterned multiplex pathogen DNA detection by Au particle-on-wire SERS sensor. Nano Lett. 10(4), 1189-1193 (2010
7. Yoo SM, Kang T, Kang H. et al. Combining a nanowire SERRS sensor and a target recycling reaction for ultrasensitive and multiplex identification of pathogenic fungi. Small 7(23), 3371-3376 (2011
8. Rodriguez-Lorenzo L, Fabris L, Alvarez-Puebla RA. Multiplex optical sensing with surface-enhanced Raman scattering: a critical review. Anal. Chim. Acta 745(0), 10-23 (2012
9. Wang Y, Yan B, Chen L. SERS tags: novel optical nanoprobes for bioanalysis. Chem. Rev. 113(3), 1391-1428 (2013
10. Jun B, Kim G, Noh MS. et al. Surface-enhanced Raman scattering-active nanostructures and strategies for bioassays. Nanomedicine 6(8), 1463-1480 (2011
11. Nolan JP, Duggan E, Liu E, Condello D, Dave I, Stoner SA. Single cell analysis using surface enhanced Raman scattering (SERS) tags. Methods 57(3), 272-279 (2012
12. Xia X, Li W, Zhang Y, Xia Y. Silica-coated dimers of silver nanospheres as surface-enhanced Raman scattering tags for imaging cancer cells. Interface Focus 3(3), 20120092 (2013
13. Qian X, Peng X, Ansari DO. In vivo tumor targeting and spectroscopic detection with surface-enhanced Raman nanoparticle tags. Nat. Biotech. 26(1), 83-90 (2008
14. Zavaleta CL, Smith BR, Walton I. et al. Multiplexed imaging of surface enhanced Raman scattering nanotags in living mice using noninvasive Raman spectroscopy. Proc. Natl Acad. Sci. USA 106(32), 13511-13516 (2009
15. Hobro AJ, Abdali S, Blanch EW. SERS study of methylated and nonmethylated ribonucleosides and the effect of aggregating agents. J. Raman Spectrosc. 43(2), 187-195 (2012
16. Shen HB, Xia JF, Zhang F, Yang HF, Zhang ZR. Surface enhanced Raman scattering (SERS) spectra of AMP and DNA in silver sol. Spectrosc Spect Anal. 21(6), 798-800 (2001
17. Kneipp K, Dasari RR, Wang Y. Near-infrared surfaceenhanced Raman-scattering (Nir Sers) on colloidal silver and gold. Appl. Spectrosc. 48(8), 951-957 (1994
18. Kelly K, Coronado E, Zhao L, Schatz G. The optical properties of metal nanoparticles: the influence of size, shape, and dielectric environment. J. Phys. Chem. B. 107(3), 668-677 (2003
19. Xue C, Millstone JE, Li S, Mirkin CA. Plasmon-driven synthesis of triangular core-shell nanoprisms from gold seeds. Angew. Chem. Int. Ed. 46(44), 8436-8439 (2007
20. Indrasekara ASDS, Meyers S, Shubeita S, Feldman LC, Gustafsson T, Fabris L. Gold nanostar substrates for SERSbased chemical sensing in the femtomolar regime. Nanoscale 6(15), 8891-8899 (2014
21. Rycenga M, Camargo PHC, Li W, Moran CH, Xia Y. Understanding the SERS effects of single silver nanoparticles and their dimers, one at a time. J. Phys. Chem. Lett. 1(4), 696-703 (2010
22. Indrasekara ASDS, Paladini BJ, Naczynski DJ, Starovoytov V, Moghe PV, Fabris L. Dimeric gold nanoparticle assemblies as tags for SERS-based cancer detection. Adv. Healthcare Mater. 2(10), 1370-1376 (2013
23. Camafeita LE, SanchezCortes S, GarciaRamos JV. SERS of guanine and its alkyl derivatives on gold sols. J. Raman Spectrosc. 27(7), 533-537 (1996
24. Wei H, Li J, Wang Y, Wang E. Silver nanoparticles coated with adenine: preparation, self-assembly and application in surface-enhanced Raman scattering. Nanotechnology 18(17), 175610 (2007
25. Bell SEJ, Sirimuthu NMS. Surface-enhanced Raman spectroscopy (SERS) for sub-micromolar detection of DNA/RNA mononucleotides. J. Am. Chem. Soc. 128(49), 15580-15581 (2006
26. Kattumuri V, Chandrasekhar M, Guha S. et al. Agarosestabilized gold nanoparticles for surface-enhanced Raman spectroscopic detection of DNA nucleosides. Appl. Phys. Lett. 88(15), 153114 (2006
27. Grajcar L, Baron MH. A SERS probe of adenyl residues available for intermolecular interactions. Part I - adenyl 'fingerprint'. J. Raman Spectrosc. 32(11), 912-918 (2001
28. Kneipp K, Kneipp H, Kartha VB. et al. Detection and identification of a single DNA base molecule using surfaceenhanced Raman scattering (SERS). Phys. Rev. E. 57(6), R6281-R6284 (1998
29. Helmenstine AM, Li YS, Vodinh T. Surface-enhanced Raman-scattering analysis of etheno adducts of adenine. Vibrational Spectroscopy 4(3), 359-364 (1993
30. Sun L, Sun Y, Xu F. et al. Atomic force microscopy and surface-enhanced Raman scattering detection of DNA based on DNA-nanoparticle complexes. Nanotechnology 20(12), 125502 (2009
31. 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. 105(50), 12609-12615 (2001
32. Kneipp K, Pohle W, Fabian H. Surface enhanced Ramanspectroscopy on nucleic-acids and related-compounds adsorbed on colloidal silver particles. J. Mol. Struct. 244, 183-192 (1991
33. Van Lierop D, Krpetic Z, Guerrini L. et al. Positively charged silver nanoparticles and their effect on surface-enhanced Raman scattering of dye-labelled oligonucleotides. Chem. Commun. 48(66), 8192-8194 (2012
34. Graham D, Mallinder BJ, Smith WE. Detection and identification of labeled DNA by surface enhanced resonance Raman scattering. Biopolymers 57(2), 85-91 (2000
35. Vo-Dinh T, Houck K, Stokes DL. Surface-enhanced raman gene probes. Anal. Chem. 66(20), 3379-3383 (1994
36. 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. Chem. Eur. J. 18(17), 5394-5400 (2012
37. Wrzesien J, Graham D. Synthesis of SERS active nanoparticles for detection of biomolecules. Tetrahedron 68(4), 1230-1240 (2012
38. Graham D, Mallinder BJ, Whitcombe D, Watson ND, Smith WE. Simple multiplex genotyping by surface-enhanced resonance Raman scattering. Anal. Chem. 74(5), 1069-1074 (2002
39. Dou X, Takama T, Yamaguchi Y. et al. Quantitative analysis of double-stranded DNA amplified by a polymerase chain reaction employing surface-enhanced Raman spectroscopy. Appl. Opt. 37(4), 759-763 (1998
40. Li J, Ma W, You L, Guo J, Hu J, Wang C. Highly sensitive detection of target ssDNA based on SERS liquid chip using suspended magnetic nanospheres as capturing substrates. Langmuir 29(20), 6147-6155 (2013
41. Lee J, Nam J, Jeon K. et al. Tuning and maximizing the singlemolecule surface-enhanced Raman scattering from DNAtethered nanodumbbells. ACS Nano 6(11), 9574-9584 (2012
42. Yan M, Xiang Y, Liu L, Chai L, Li X, Feng T. Silver nanocrystals with special shapes: controlled synthesis and their surface-enhanced Raman scattering properties. RSC Adv. 4(1), 98-104 (2014
43. Li JF, Tian XD, Li SB. et al. Surface analysis using shell-isolated nanoparticle-enhanced Raman spectroscopy. Nat. Protoc. 8(1), 52-65 (2013
44. Kim J, Lee J. Multiplexed DNA detection with DNAfunctionalized silver and silver/gold nanoparticle superstructure probes. Bull. Korean Chem. Soc. 33(1), 221-226 (2012
45. Li JF, Huang YF, Ding Y. et al. Shell-isolated nanoparticleenhanced Raman spectroscopy. Nature 464(7287), 392-395 (2010
46. Lim D, Jeon K, Kim HM, Nam J, Suh YD. Nanogapengineerable Raman-active nanodumbbells for single-molecule detection. Nat. Mater. 9(1), 60-67 (2010
47. Liu M, Wang Z, Zong S. et al. SERS-based DNA detection in aqueous solutions using oligonucleotide-modified Ag nanoprisms and gold nanoparticles. Anal. BioAnal. Chem. 405(18), 6131-6136 (2013
48. Qian X, Zhou X, Nie S. Surface-enhanced Raman nanoparticle beacons based on bioconjugated gold nanocrystals and long range plasmonic coupling. J. Am. Chem. Soc. 130(45), 14934-14935 (2008
49. Wang H, Vo-Dinh T. Plasmonic coupling interference (PCI) nanoprobes for nucleic acid detection. Small 7(21), 3067-3074 (2011
50. Hu J, Zhang C. Sensitive detection of nucleic acids with rolling circle amplification and surface-enhanced Raman scattering spectroscopy. Anal. Chem. 82(21), 8991-8997 (2010
51. Li J, Wei C, Ma W. et al. Multiplexed SERS detection of DNA targets in a sandwich-hybridization assay using SERS-encoded core-shell nanospheres. J. Mater. Chem. 22(24), 12100-12106 (2012
52. Zhang Z, Wen Y, Ma Y, Luo J, Jiang L, Song Y. Mixed DNAfunctionalized nanoparticle probes for surface-enhanced Raman scattering-based multiplex DNA detection. Chem. Commun. 47(26), 7407-7409 (2011
53. Sun L, Yu C, Irudayaraj J. Surface-enhanced raman scattering based nonfluorescent probe for multiplex DNA detection. Anal. Chem. 79(11), 3981-3988 (2007
54. Zavaleta CL, Smith BR, Walton I. et al. Multiplexed imaging of surface enhanced Raman scattering nanotags in living mice using noninvasive Raman spectroscopy. Proc. Natl Acad. Sci USA 106(32), 13511-13516 (2009
55. Yazdi SH, Giles KL, White IM. Multiplexed detection of DNA sequences using a competitive displacement assay in a microfluidic SERRS-based device. Anal. Chem. 85(21), 10605-10611 (2013
56. Zhang L, Gross ML. Matrix-assisted laser desorption/ionization mass spectrometry methods for oligodeoxynucleotides: improvements in matrix, detection limits, quantification, and sequencing. J. Am. Soc. Mass Spectrom. 11(10), 854-865 (2000
57. Ganem B, Li Y, Henion JD. Detection of oligonucleotide duplex forms by ion-spray mass spectrometry. Tetrahedron Lett. 34(9), 1445-1448 (1993
58. Dubertret B, Calame M, Libchaber AJ. Single-mismatch detection using gold-quenched fluorescent oligonucleotides. Nat. Biotech. 19(4), 365-370 (2001
59. Pal S, Kim MJ, Song JM. Quantitation of surface coverage of oligonucleotides bound to chip surfaces: a fluorescence-based approach using alkaline phosphatase digestion. Lab. Chip. 8(8), 1332-1341 (2008
60. Jacobs MV, Snijders PJ, van den Brule AJ, Helmerhorst TJ, Meijer CJ, Walboomers JM. A general primer GP5+/GP6(+)- mediated PCR-enzyme immunoassay method for rapid detection of 14 high-risk and 6 low-risk human papillomavirus genotypes in cervical scrapings. J. Clin. Microbiol. 35(3), 791-795 (1997
61. Lowe AJ, Huh YS, Strickland AD, Erickson D, Batt CA. Multiplex single nucleotide polymorphism genotyping utilizing ligase detection reaction coupled surface enhanced Raman spectroscopy. Anal. Chem. 82(13), 5810-5814 (2010
62. Cao YC, Jin R, Mirkin CA. Nanoparticles with Raman spectroscopic fingerprints for DNA and RNA detection. Science 297(5586), 1536-1540 (2002
63. Papadopoulou E, Bell SEJ. Label-Free detection of single-base mismatches in DNA by surface-enhanced raman spectroscopy. Angew. Chem. Int. Ed. Engl. 50(39), 9058-9061 (2011
64. Van Lierop D, Faulds K, Graham D. Separation free DNA detection using surface enhanced Raman scattering. Anal. Chem. 83(15), 5817-5821 (2011
65. Harper MM, Robertson B, Ricketts A, Faulds K. Specific detection of DNA through coupling of a TaqMan assay with surface enhanced Raman scattering (SERS). Chem. Commun. 48(75), 9412-9414 (2012
66. Barhoumi A, Halas NJ. Label-free detection of DNA hybridization using surface enhanced Raman spectroscopy. J. Am. Chem. Soc. 132(37), 12792-12793 (2010
67. Huh YS, Lowe AJ, Strickland AD, Batt CA, Erickson D. Surface-enhanced Raman scattering based ligase detection reaction. J. Am. Chem. Soc. 131(6), 2208-2213 (2009
68. Sun L, Irudayaraj J. PCR-free quantification of multiple splice variants in a cancer gene by surface-enhanced Raman spectroscopy. J. Phys. Chem. B. 113(42), 14021-14025 (2009
69. Shamsaie A, Heim J, Yanik AA, Irudayaraj J. Intracellular quantification by surface enhanced Raman spectroscopy. Chem. Phys. Lett. 461(1-3), 131-135 (2008
70. Sun L, Irudayaraj J. Quantitative surface-enhanced Raman for gene expression estimation. Biophys. J. 96(11), 4709-4716 (2009
71. Prado E, Daugey N, Plumet S, Servant L, Lecomte S. Quantitative label-free RNA detection using surfaceenhanced Raman spectroscopy. Chem. Commun. 47(26), 7425-7427 (2011
72. Van Lierop D, Larmour IA, Faulds K, Graham D. SERS primers and their mode of action for pathogen DNA detection. Anal. Chem. 85(3), 1408-1414 (2013
73. Hu J, Zhang C. Surface-enhanced Raman scattering technology and its application to gene analysis. Prog. Chem. 22(8), 1641-1647 (2010
74. Li Y, Lei C, Zeng Y, Ji X, Zhang S. Sensitive SERS detection of DNA and lysozyme based on polymerase assisted cross strand-displacement amplification. Chem. Commun. 48(88), 10892-10894 (2012
75. Ye S, Yang Y, Xiao J, Zhang S. Surface-enhanced Raman scattering assay combined with autonomous DNA machine for detection of specific DNA and cancer cells. Chem. Commun. 48(68), 8535-8537 (2012
76. Papadopoulou E, Bell SEJ. DNA reorientation on Au nanoparticles: label-free detection of hybridization by surface enhanced Raman spectroscopy. Chem. Commun. 47(39), 10966-10968 (2011
77. Vo-Dinh T, Allain LR, Stokes DL. Cancer gene detection using surface-enhanced Raman scattering (SERS). J. Raman Spectrosc. 33(7), 511-516 (2002
78. Culha M, Stokes D, Vo-Dinh T. Surface-enhanced Raman scattering for cancer diagnostics: detection of the BClL2 gene. Expert Rev. Mol. Diagn. 3(5), 669-675 (2003
79. Foster JT, Okinaka RT, Svensson R. et al. Real-time PCR assays of single-nucleotide polymorphisms defining the major Brucella clades. J. Clin. Microbiol. 46(1), 296-301 (2008
80. Shen W, Deng H, Teo AKL, Gao Z. Colorimetric detection of single-nucleotide polymorphisms with a real-time PCR-like sensitivity. Chem. Commun. 48(82), 10225-10227 (2012
81. Yoo SM, Kang T, Kim B, Lee SY. Detection of single nucleotide polymorphisms by a gold nanowire-on-film SERS sensor coupled with S1 nuclease treat. Chem. Eur. J. 17(31), 8657-8662 (2011
82. Henkel JH, Aberle SW, Kundi M, Popow-Kraupp T. Improved detection of respiratory syncytial virus in nasal aspirates by seminested RT-PCR. J. Med. Virol. 53(4), 366-371 (1997
83. Haque R, Kress K, Wood S. et al. Diagnosis of pathogenic Entamoeba histolytica infection using a stool ELISA based on monoclonal antibodies to the galactose-specific adhesin. J. Inf. Dis. 167(1), 247-249 (1993
84. Yanagihara K, Kitagawa Y, Tomonaga M. et al. Evaluation of pathogen detection from clinical samples by real-time polymerase chain reaction using a sepsis pathogen DNA detection kit. Crit. Care 14(4), R159 (2010
85. Foudeh AM, Daoud JT, Faucher SP, Veres T, Tabrizian M. Sub-femtomole detection of 16s rRNA from Legionella pneumophila using surface plasmon resonance imaging. Biosens. Bioelectron. 52(0), 129-135 (2014
86. Premasiri WR, Moir DT, Klempner MS, Krieger N, Jones G, Ziegler LD. Characterization of the surface enhanced Raman scattering (SERS) of bacteria. J. Phys. Chem. B. 109(1), 312-320 (2005
87. Jarvis RM, Goodacre R. Characterisation and identification of bacteria using SERS. Chem. Soc. Rev. 37(5), 931-936 (2008
88. Patel IS, Premasiri WR, Moir DT, Ziegler LD. Barcoding bacterial cells: a SERS-based methodology for pathogen identification. J. Raman Spectrosc. 39(11), 1660-1672 (2008
89. Marotta NE, Beavers KR, Bottomley LA. Limitations of surface enhanced Raman scattering in sensing DNA hybridization demonstrated by label-free DNA oligos as molecular rulers of distance-dependent enhancement. Anal. Chem. 85(3), 1440-1446 (2013