A reusable laser wrapped graphene-Ag array based SERS sensor for trace detection of genomic DNA methylation

Biosensors and Bioelectronics

Volumn 92, Issue , 2017, Pages 755-762

  Ouyang, Lei ^a,b   Hu, Yaowu ^c   Zhu, Lihua ^a   Cheng, Gary J ^c   Irudayaraj, Joseph ^b  

^a HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY   (China)

^b Purdue University   (United States)

^c SCHOOL OF INDUSTRIAL ENGINEERING   (United States)

Author keywords

DNA methylation; Graphene Ag array; Laser wrapping; SERS

Indexed keywords

ALKYLATION; DNA; ELECTROMAGNETIC FIELDS; GENE EXPRESSION; GENES; GRAPHENE; METHYLATION; RAMAN SPECTROSCOPY; REUSABILITY; SILVER; TRACE ANALYSIS;

5-HYDROXYMETHYLCYTOSINE; DIRECT INTERACTIONS; DNA METHYLATION; EFFECTIVE COUPLING; LIMIT OF DETECTION; REPRODUCIBILITIES; SERS; SURFACE ENHANCED RAMAN SPECTROSCOPY;

SUBSTRATES;

5 CARBOXYLCYTOSINE; 5 HYDROXYMETHYLCYTOSINE; 5 METHYLCYTOSINE; CYTOSINE DERIVATIVE; GOLD NANOPARTICLE; GRAPHENE; SILVER; UNCLASSIFIED DRUG; 5-CARBOXYLCYTOSINE; 5-HYDROXYMETHYLCYTOSINE; CYTOSINE; DNA; GOLD; GRAPHITE; IMMOBILIZED ANTIBODY; METAL NANOPARTICLE;

ANTIBODY AFFINITY; ANTIGEN BINDING; ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; DNA METHYLATION; ELECTROMAGNETISM; HUMAN; HUMAN CELL; LASER; LIMIT OF DETECTION; MEASUREMENT ACCURACY; NANOARRAY; PARAMETERS; RAMAN SPECTROMETRY; REPRODUCIBILITY; REUSABILITY; SENSITIVITY ANALYSIS; SENSOR; SYNTHESIS; ANALOGS AND DERIVATIVES; CHEMISTRY; DEVICES; EQUIPMENT DESIGN; GENETIC PROCEDURES; PROCEDURES; TUMOR CELL LINE; ULTRASTRUCTURE;

5-METHYLCYTOSINE; ANTIBODIES, IMMOBILIZED; BIOSENSING TECHNIQUES; CELL LINE, TUMOR; CYTOSINE; DNA; DNA METHYLATION; EQUIPMENT DESIGN; GOLD; GRAPHITE; HUMANS; METAL NANOPARTICLES; REPRODUCIBILITY OF RESULTS; SILVER; SPECTRUM ANALYSIS, RAMAN;

EID: 85008234815     PISSN: 09565663     EISSN: 18734235     Source Type: Journal    
DOI: 10.1016/j.bios.2016.09.072     Document Type: Article

References (51)

1. Bailey, V.J., Easwaran, H., Zhang, Y., Griffiths, E., Belinsky, S.A., Herman, J.G., Baylin, S.B., Carraway, H.E., Wang, T.-H., MS-qFRET: a quantum dot-based method for analysis of DNA methylation. Genome Res. 19:8 (2009), 1455–1461.
2. Baylin, S.B., Jones, P.A., A decade of exploring the cancer epigenome—biological and translational implications. Nat. Rev. Cancer 11:10 (2011), 726–734.
3. Cao, A., Zhang, C.-y, Sensitive and label-free DNA methylation detection by ligation-mediated hyperbranched rolling circle amplification. Anal. Chem. 84:14 (2012), 6199–6205.
4. Chowdhury, B., Cho, I.-H., Hahn, N., Irudayaraj, J., Quantification of 5-methylcytosine, 5-hydroxymethylcytosine and 5-carboxylcytosine from the blood of cancer patients by an enzyme-based immunoassay. Anal. Chim. Acta 852 (2014), 212–217.
5. Chowdhury, B., Seetharam, A., Wang, Z., Liu, Y., Lossie, A.C., Thimmapuram, J., Irudayaraj, J., A study of alterations in DNA epigenetic modifications (5mC and 5hmC) and gene expression influenced by simulated microgravity in human lymphoblastoid cells. PLoS One, 11(1), 2016, e0147514.
6. Du, Y., Zhao, Y., Qu, Y., Chen, C.-H., Chen, C.-M., Chuang, C.-H., Zhu, Y., Enhanced light–matter interaction of graphene–gold nanoparticle hybrid films for high-performance SERS detection. J. Mater. Chem. C 2:23 (2014), 4683–4691.
7. Feinberg, A.P., Vogelstein, B., Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature 301:5895 (1983), 89–92.
8. Feng, F., Wang, H., Han, L., Wang, S., Fluorescent conjugated polyelectrolyte as an indicator for convenient detection of DNA methylation. J. Am. Chem. Soc. 130:34 (2008), 11338–11343.
9. Frommer, M., McDonald, L.E., Millar, D.S., Collis, C.M., Watt, F., Grigg, G.W., Molloy, P.L., Paul, C.L., A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc. Natl. Acad. Sci. USA 89:5 (1992), 1827–1831.
10. Gama-Sosa, M.A., Slagel, V.A., Trewyn, R.W., Oxenhandler, R., Kuo, K.C., Gehrke, C.W., Ehrlich, M., The 5-methylcytosine content of DNA from human tumors. Nucleic Acids Res. 11:19 (1983), 6883–6894.
11. Gao, H., Hu, Y., Xuan, Y., Li, J., Yang, Y., Martinez, R.V., Li, C., Luo, J., Qi, M., Cheng, G.J., Large-scale nanoshaping of ultrasmooth 3D crystalline metallic structures. Science 346:6215 (2014), 1352–1356.
12. Garcia-Leis, A., Garcia-Ramos, J.V., Sanchez-Cortes, S., Silver nanostars with high SERS performance. J. Phys. Chem. C 117:15 (2013), 7791–7795.
13. Haynes, C.L., McFarland, A.D., Duyne, R.P.V., Surface-enhanced Raman spectroscopy. Anal. Chem. 77:17 (2005), 338A–346A.
14. Herman, J.G., Graff, J.R., Myöhänen, S., Nelkin, B.D., Baylin, S.B., Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 93:18 (1996), 9821–9826.
15. Hu, J., Zhang, C.-y, Single base extension reaction-based surface enhanced Raman spectroscopy for DNA methylation assay. Biosens. Bioelectron. 31:1 (2012), 451–457.
16. Hu, Y., Lee, S., Kumar, P., Nian, Q., Wang, W., Irudayaraj, J., Cheng, G.J., Water flattens graphene wrinkles: laser shock wrapping of graphene onto substrate-supported crystalline plasmonic nanoparticle arrays. Nanoscale 7:47 (2015), 19885–19893.
17. Huang, W., Qi, C.-B., Lv, S.-W., Xie, M., Feng, Y.-Q., Huang, W.-H., Yuan, B.-F., Determination of DNA and RNA methylation in circulating tumor cells by mass spectrometry. Anal. Chem. 88:2 (2016), 1378–1384.
18. Ito, S., Shen, L., Dai, Q., Wu, S.C., Collins, L.B., Swenberg, J.A., He, C., Zhang, Y., Tet proteins can convert 5-methylcytosine to 5-formylcytosine and 5-carboxylcytosine. Science 333:6047 (2011), 1300–1303.
19. Jones, P.A., Taylor, S.M., Cellular differentiation, cytidine analogs and DNA methylation. Cell 20:1 (1980), 85–93.
20. Kato, D., Goto, K., Fujii, S.-i, Takatsu, A., Hirono, S., Niwa, O., Electrochemical DNA methylation detection for enzymatically digested CpG oligonucleotides. Anal. Chem. 83:20 (2011), 7595–7599.
21. Laird, P.W., Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet. 11:3 (2010), 191–203.
22. Le, T., Kim, K.-P., Fan, G., Faull, K.F., A sensitive mass spectrometry method for simultaneous quantification of DNA methylation and hydroxymethylation levels in biological samples. Anal. Biochem. 412:2 (2011), 203–209.
23. Lee, S., Kumar, P., Hu, Y., Cheng, G.J., Irudayaraj, J., Graphene laminated gold bipyramids as sensitive detection platforms for antibiotic molecules. Chem. Commun. 51:85 (2015), 15494–15497.
24. Li, C., Sun, L., Sun, Y., Teranishi, T., One-Pot controllable synthesis of Au@ Ag heterogeneous nanorods with highly tunable plasmonic absorption. Chem. Mater. 25:13 (2013), 2580–2590.
25. Oda, M., Glass, J.L., Thompson, R.F., Mo, Y., Olivier, E.N., Figueroa, M.E., Selzer, R.R., Richmond, T.A., Zhang, X., Dannenberg, L., High-resolution genome-wide cytosine methylation profiling with simultaneous copy number analysis and optimization for limited cell numbers. Nucleic Acids Res. 37:12 (2009), 3829–3839.
26. Ouyang, L., Zhu, L., Ruan, Y., Tang, H., Preparation of a native β-cyclodextrin modified plasmonic hydrogel substrate and its use as a surface-enhanced Raman scattering scaffold for antibiotics identification. J. Mater. Chem. C 3:29 (2015), 7575–7582.
27. Shames, D.S., Minna, J.D., Gazdar, A.F., Methods for detecting DNA methylation in tumors: from bench to bedside. Cancer Lett. 251:2 (2007), 187–198.
28. Shanmuganathan, R., Basheer, N.B., Amirthalingam, L., Muthukumar, H., Kaliaperumal, R., Shanmugam, K., Conventional and nanotechniques for DNA methylation profiling. J. Mol. Diagn. 15:1 (2013), 17–26.
29. Singer-Sam, J., LeBon, J.M., Tanguay, R.L., Riggs, A.D., A quantitative HpaII-PCR assay to measure methylation of DNA from a small number of cells. Nucleic Acids Res., 18(3), 1990, 687.
30. Song, C.-X., He, C., Balance of DNA methylation and demethylation in cancer development. Genome Biol., 13(10), 2012, 1.
31. Song, C.-X., He, C., Potential functional roles of DNA demethylation intermediates. Trends Biochem. Sci. 38:10 (2013), 480–484.
32. Stiles, P.L., Dieringer, J.A., Shah, N.C., Van Duyne, R.P., Surface-enhanced Raman spectroscopy. Annu. Rev. Anal. Chem. 1 (2008), 601–626.
33. Sun, L., Yu, C., Irudayaraj, J., Surface-enhanced Raman scattering based nonfluorescent probe for multiplex DNA detection. Anal. Chem. 79:11 (2007), 3981–3988.
34. Sun, L., Yu, C., Irudayaraj, J., Raman multiplexers for alternative gene splicing. Anal. Chem. 80:9 (2008), 3342–3349.
35. Taleat, Z., Mathwig, K., Sudhölter, E.J., Rassaei, L., Detection strategies for methylated and hypermethylated DNA. TrAC Trends Anal. Chem. 66 (2015), 80–89.
36. Timp, W., Feinberg, A.P., Cancer as a dysregulated epigenome allowing cellular growth advantage at the expense of the host. Nat. Rev. Cancer 13:7 (2013), 497–510.
37. Umezu, T., Ohyashiki, K., Ohyashiki, J.H., Detection method for quantifying global DNA methylation by fluorescence correlation spectroscopy. Anal. Biochem. 415:2 (2011), 145–150.
38. Wang, M., Xu, Z., Chen, L., Yin, H., Ai, S., Electrochemical immunosensing platform for DNA methyltransferase activity analysis and inhibitor screening. Anal. Chem. 84:21 (2012), 9072–9078.
39. Wang, P., Chen, H., Tian, J., Dai, Z., Zou, X., Electrochemical evaluation of DNA methylation level based on the stoichiometric relationship between purine and pyrimidine bases. Biosens. Bioelectron. 45 (2013), 34–39.
40. Wang, X., Cui, M., Zhou, H., Zhang, S., DNA-hybrid-gated functional mesoporous silica for sensitive DNA methyltransferase SERS detection. Chem. Commun. 51:73 (2015), 13983–13985.
41. Wang, X., Cui, Y., Irudayaraj, J., Single-cell quantification of cytosine modifications by hyperspectral dark-field imaging. ACS nano 9:12 (2015), 11924–11932.
42. Wang, Y., Wee, E.J., Trau, M., Accurate and sensitive total genomic DNA methylation analysis from sub-nanogram input with embedded SERS nanotags. Chem. Commun. 52:17 (2016), 3560–3563.
43. Wang, Y., Zhang, C.-H., Tang, L.-J., Jiang, J.-H., Enzymatic control of plasmonic coupling and surface enhanced Raman scattering transduction for sensitive detection of DNA demethylation. Anal. Chem. 84:20 (2012), 8602–8606.
44. Wu, Y., Zhang, B., Guo, L.-H., Label-free and selective photoelectrochemical detection of chemical DNA methylation damage using DNA repair enzymes. Anal. Chem. 85:14 (2013), 6908–6914.
45. Xu, S., Jiang, S., Wang, J., Wei, J., Yue, W., Ma, Y., Graphene isolated Au nanoparticle arrays with high reproducibility for high-performance surface-enhanced Raman scattering. Sens. Actuators B: Chem. 222 (2016), 1175–1183.
46. Yin, H., Zhou, Y., Xu, Z., Chen, L., Zhang, D., Ai, S., An electrochemical assay for DNA methylation, methyltransferase activity and inhibitor screening based on methyl binding domain protein. Biosens. Bioelectron. 41 (2013), 492–497.
47. Yu, Y., Blair, S., Gillespie, D., Jensen, R., Myszka, D., Badran, A.H., Ghosh, I., Chagovetz, A., Direct DNA methylation profiling using methyl binding domain proteins. Anal. Chem. 82:12 (2010), 5012–5019.
48. Zhang, H., Li, M., Fan, M., Gu, J., Wu, P., Cai, C., Electrochemiluminescence signal amplification combined with a conformation-switched hairpin DNA probe for determining the methylation level and position in the Hsp53 tumor suppressor gene. Chem. Commun. 50:22 (2014), 2932–2934.
49. Zhou, H., Lin, S., Nie, Y., Yang, D., Wang, Q., Chen, W., Huang, N., Jiang, Z., Chen, S., Surface-enhanced resonance Raman scattering (SERRS) simulates PCR for sensitive DNA detection. Analyst 140:22 (2015), 7518–7521.
50. Zhou, W., Gao, X., Liu, D., Chen, X., Gold nanoparticles for in vitro diagnostics. Chem. Rev. 115:19 (2015), 10575–10636.
51. Zhou, Z., Cho, I.-H., Shan, Z., Irudayaraj, J., Cross-platform detection of epigenetic modifications from extracted chromatin in leucocytes from blood. Anal. Chem. Res. 4 (2015), 39–44.