Electrochemical and Optical Biosensing Strategies for DNA Methylation Analysis

Author(s): Shu Zhang, Jian Huang, Jingrun Lu, Min Liu, Xi Chen, Shasha Su, Fei Mo*, Junsong Zheng*

Journal Name: Current Medicinal Chemistry

Volume 27 , Issue 36 , 2020


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Abstract:

DNA methylation is considered as a crucial part of epigenetic modifications and a popular research topic in recent decades. It usually occurs with a methyl group adding to the fifth carbon atom of cytosine while the base sequence of DNA remains unchanged. DNA methylation has significant influences on maintaining cell functions, genetic imprinting, embryonic development and tumorigenesis procedures and hence the analysis of DNA methylation is of great medical significance. With the development of analytical techniques and further research on DNA methylation, numerous DNA methylation detection strategies based on biosensing technology have been developed to fulfill various study requirements. This article reviewed the development of electrochemistry and optical biosensing analysis of DNA methylation in recent years; in addition, we also reviewed some recent advances in the detection of DNA methylation using new techniques, such as nanopore biosensors, and highlighted the key technical and biological challenges involved in these methods. We hope this paper will provide useful information for the selection and establishment of analysis of DNA methylation.

Keywords: DNA methylation, methylation assays, electrochemical biosensors, optical biosensors, cancer diagnosis, epigenetics.

[1]
Reik, W.; Dean, W.; Walter, J. Epigenetic reprogramming in mammalian development. Science, 2001, 293(5532), 1089-1093.
[http://dx.doi.org/10.1126/science.1063443] [PMID: 11498579]
[2]
Moore, L.D.; Le, T.; Fan, G. DNA methylation and its basic function. Neuropsychopharmacology, 2013, 38(1), 23-38.
[http://dx.doi.org/10.1038/npp.2012.112] [PMID: 22781841]
[3]
Verschure, P.J.; Visser, A.E.; Rots, M.G. Step out of the groove: epigenetic gene control systems and engineered transcription factors. Adv. Genet., 2006, 56(56), 163-204.
[http://dx.doi.org/10.1016/S0065-2660(06)56005-5] [PMID: 16735158]
[4]
Jones, P.A.; Baylin, S.B. The epigenomics of cancer. Cell, 2007, 128(4), 683-692.
[http://dx.doi.org/10.1016/j.cell.2007.01.029] [PMID: 17320506]
[5]
Rodriguez, J.; Frigola, J.; Vendrell, E.; Risques, R.A.; Fraga, M.F.; Morales, C.; Moreno, V.; Esteller, M.; Capellà, G.; Ribas, M.; Peinado, M.A. Chromosomal instability correlates with genome-wide DNA demethylation in human primary colorectal cancers. Cancer Res., 2006, 66(17), 8462-9468.
[http://dx.doi.org/10.1158/0008-5472.CAN-06-0293] [PMID: 16951157]
[6]
Chen, R.Z.; Pettersson, U.; Beard, C.; Jackson-Grusby, L.; Jaenisch, R. DNA hypomethylation leads to elevated mutation rates. Nature, 1998, 395(6697), 89-93.
[http://dx.doi.org/10.1038/25779] [PMID: 9738504]
[7]
Jones, P.A.; Laird, P.W. Cancer epigenetics comes of age. Nat. Genet., 1999, 21(2), 163-167.
[http://dx.doi.org/10.1038/5947] [PMID: 9988266]
[8]
Mastroeni, D.; Grover, A.; Delvaux, E.; Whiteside, C.; Coleman, P.D.; Rogers, J. Epigenetic changes in Alzheimer’s disease: decrements in DNA methylation. Neurobiol. Aging, 2010, 31(12), 2025-2037.
[http://dx.doi.org/10.1016/j.neurobiolaging.2008.12.005] [PMID: 19117641]
[9]
Udali, S.; Guarini, P.; Moruzzi, S.; Choi, S.W.; Friso, S. Cardiovascular epigenetics: from DNA methylation to microRNAs. Mol. Aspects Med., 2013, 34(4), 883-901.
[http://dx.doi.org/10.1016/j.mam.2012.08.001] [PMID: 22981780]
[10]
Trasler, J.M. Gamete imprinting: setting epigenetic patterns for the next generation. Reprod. Fertil. Dev., 2006, 18(1-2), 63-69.
[http://dx.doi.org/10.1071/RD05118] [PMID: 16478603]
[11]
Issa, J.P. CpG island methylator phenotype in cancer. Nat. Rev. Cancer, 2004, 4(12), 988-993.
[http://dx.doi.org/10.1038/nrc1507] [PMID: 15573120]
[12]
Zardo, G.; Tiirikainen, M.I.; Hong, C.; Misra, A.; Feuerstein, B.G.; Volik, S.; Collins, C.C.; Lamborn, K.R.; Bollen, A.; Pinkel, D.; Albertson, D.G.; Costello, J.F. Integrated genomic and epigenomic analyses pinpoint biallelic gene inactivation in tumors. Nat. Genet., 2002, 32(3), 453-458.
[http://dx.doi.org/10.1038/ng1007] [PMID: 12355068]
[13]
Feinberg, A.P.; Vogelstein, B. Hypomethylation distinguishes genes of some human cancers from their normal counterparts. Nature, 1983, 301(5895), 89-92.
[http://dx.doi.org/10.1038/301089a0] [PMID: 6185846]
[14]
Herman, J.G.; Latif, F.; Weng, Y.; Lerman, M.I.; Zbar, B.; Liu, S.; Samid, D.; Duan, D.S.; Gnarra, J.R.; Linehan, W.M. Silencing of the VHL tumor-suppressor gene by DNA methylation in renal carcinoma. Proc. Natl. Acad. Sci. USA, 1994, 91(21), 9700-9704.
[http://dx.doi.org/10.1073/pnas.91.21.9700] [PMID: 7937876]
[15]
Baylin, S.B.; Ohm, J.E. Epigenetic gene silencing in cancer - a mechanism for early oncogenic pathway addiction? Nat. Rev. Cancer, 2006, 6(2), 107-116.
[http://dx.doi.org/10.1038/nrc1799] [PMID: 16491070]
[16]
Zhu, J.; Yao, X. Use of DNA methylation for cancer detection: promises and challenges. Int. J. Biochem. Cell Biol., 2009, 41(1), 147-154.
[http://dx.doi.org/10.1016/j.biocel.2008.09.003] [PMID: 18834953]
[17]
Moore, L.E.; Pfeiffer, R.M.; Poscablo, C.; Real, F.X.; Kogevinas, M.; Silverman, D.; García-Closas, R.; Chanock, S.; Tardón, A.; Serra, C.; Carrato, A.; Dosemeci, M.; García-Closas, M.; Esteller, M.; Fraga, M.; Rothman, N.; Malats, N. Genomic DNA hypomethylation as a biomarker for bladder cancer susceptibility in the Spanish bladder cancer study: a case-control study. Lancet Oncol., 2008, 9(4), 359-366.
[http://dx.doi.org/10.1016/S1470-2045(08)70038-X] [PMID: 18339581]
[18]
Ibanez de Caceres, I.; Battagli, C.; Esteller, M.; Herman, J.G.; Dulaimi, E.; Edelson, M.I.; Bergman, C.; Ehya, H.; Eisenberg, B.L.; Cairns, P. Tumor cell-specific BRCA1 and RASSF1A hypermethylation in serum, plasma, and peritoneal fluid from ovarian cancer patients. Cancer Res., 2004, 64(18), 6476-6481.
[http://dx.doi.org/10.1158/0008-5472.CAN-04-1529] [PMID: 15374957]
[19]
Balgkouranidou, I.; Matthaios, D.; Karayiannakis, A.; Bolanaki, H.; Michailidis, P.; Xenidis, N.; Amarantidis, K.; Chelis, L.; Trypsianis, G.; Chatzaki, E.; Lianidou, E.S.; Kakolyris, S. Prognostic role of APC and RASSF1A promoter methylation status in cell free circulating DNA of operable gastric cancer patients. Mutat. Res., 2015, 778, 46-51.
[http://dx.doi.org/10.1016/j.mrfmmm.2015.05.002] [PMID: 26073472]
[20]
Milani, L.; Lundmark, A.; Kiialainen, A.; Nordlund, J.; Flaegstad, T.; Forestier, E.; Heyman, M.; Jonmundsson, G.; Kanerva, J.; Schmiegelow, K.; Söderhäll, S.; Gustafsson, M.G.; Lönnerholm, G.; Syvänen, A.C. DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia. Blood, 2010, 115(6), 1214-1225.
[http://dx.doi.org/10.1182/blood-2009-04-214668] [PMID: 19965625]
[21]
Teodoridis, J.M.; Hall, J.; Marsh, S.; Kannall, H.D.; Smyth, C.; Curto, J.; Siddiqui, N.; Gabra, H.; McLeod, H.L.; Strathdee, G.; Brown, R. CpG island methylation of DNA damage response genes in advanced ovarian cancer. Cancer Res., 2005, 65(19), 8961-8967.
[http://dx.doi.org/10.1158/0008-5472.CAN-05-1187] [PMID: 16204069]
[22]
Shanmuganathan, R.; Basheer, N.B.; Amirthalingam, L.; Muthukumar, H.; Kaliaperumal, R.; Shanmugam, K. Conventional and nanotechniques for DNA methylation profiling. J. Mol. Diagn., 2013, 15(1), 17-26.
[http://dx.doi.org/10.1016/j.jmoldx.2012.06.007] [PMID: 23127612]
[23]
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, 1992, 89(5), 1827-1831.
[http://dx.doi.org/10.1073/pnas.89.5.1827] [PMID: 1542678]
[24]
Clark, S.J.; Harrison, J.; Paul, C.L.; Frommer, M. High sensitivity mapping of methylated cytosines. Nucleic Acids Res., 1994, 22(15), 2990-2997.
[http://dx.doi.org/10.1093/nar/22.15.2990] [PMID: 8065911]
[25]
Herman, J.G.; Graff, J.R.; Myöhänen, S.; Nelkin, B.D.; Baylin, S.B.; Methylation-specific, P.C.R. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA, 1996, 93(18), 9821-9826.
[http://dx.doi.org/10.1073/pnas.93.18.9821] [PMID: 8790415]
[26]
Hibi, K.; Goto, T.; Shirahata, A.; Saito, M.; Kigawa, G.; Nemoto, H.; Sanada, Y. Detection of TFPI2 methylation in the serum of colorectal cancer patients. Cancer Lett., 2011, 311(1), 96-100.
[http://dx.doi.org/10.1016/j.canlet.2011.07.006] [PMID: 21820798]
[27]
Eads, C.A.; Danenberg, K.D.; Kawakami, K.; Saltz, L.B.; Blake, C.; Shibata, D.; Danenberg, P.V.; Laird, P.W. MethyLight: a high-throughput assay to measure DNA methylation. Nucleic Acids Res., 2000, 28(8),E32.
[http://dx.doi.org/10.1093/nar/28.8.e32] [PMID: 10734209]
[28]
Wojdacz, T.K.; Dobrovic, A. Methylation-sensitive high resolution melting (MS-HRM): a new approach for sensitive and high-throughput assessment of methylation. Nucleic Acids Res., 2007, 35(6),e41.
[http://dx.doi.org/10.1093/nar/gkm013] [PMID: 17289753]
[29]
Tost, J.; Gut, I.G. DNA methylation analysis by pyrosequencing. Nat. Protoc., 2007, 2(9), 2265-2275.
[http://dx.doi.org/10.1038/nprot.2007.314] [PMID: 17853883]
[30]
Krejcova, L.; Richtera, L.; Hynek, D.; Labuda, J.; Adam, V. Current trends in electrochemical sensing and biosensing of DNA methylation. Biosens. Bioelectron., 2017, 97, 384-399.
[http://dx.doi.org/10.1016/j.bios.2017.06.004] [PMID: 28641203]
[31]
Singer, J.; Roberts-Ems, J.; Riggs, A.D. Methylation of mouse liver DNA studied by means of the restriction enzymes msp I and hpa II. Science, 1979, 203(4384), 1019-1021.
[http://dx.doi.org/10.1126/science.424726] [PMID: 424726]
[32]
Hiraoka, D.; Yoshida, W.; Abe, K.; Wakeda, H.; Hata, K.; Ikebukuro, K. Development of a method to measure DNA methylation levels by using methyl CpG-binding protein and luciferase-fused zinc finger protein. Anal. Chem., 2012, 84(19), 8259-8264.
[http://dx.doi.org/10.1021/ac3015774] [PMID: 22924825]
[33]
Wang, X.; Song, Y.; Song, M.; Wang, Z.; Li, T.; Wang, H. Fluorescence polarization combined capillary electrophoresis immunoassay for the sensitive detection of genomic DNA methylation. Anal. Chem., 2009, 81(19), 7885-7891.
[http://dx.doi.org/10.1021/ac901681k] [PMID: 19788313]
[34]
Shiraishi, M.; Sekiguchi, A.; Oates, A.J.; Terry, M.J.; Miyamoto, Y.; Sekiya, T. Methyl-CpG binding domain column chromatography as a tool for the analysis of genomic DNA methylation. Anal. Biochem., 2004, 329(1), 1-10.
[http://dx.doi.org/10.1016/j.ab.2004.02.024] [PMID: 15136161]
[35]
Friso, S.; Choi, S.W.; Dolnikowski, G.G.; Selhub, J. A method to assess genomic DNA methylation using high-performance liquid chromatography/electrospray ionization mass spectrometry. Anal. Chem., 2002, 74(17), 4526-4531.
[http://dx.doi.org/10.1021/ac020050h] [PMID: 12236365]
[36]
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., 2011, 412(2), 203-209.
[http://dx.doi.org/10.1016/j.ab.2011.01.026] [PMID: 21272560]
[37]
Li, Y.; Yu, C.; Han, H.; Zhao, C.; Zhang, X. Sensitive SERS detection of DNA methyltransferase by target triggering primer generation-based multiple signal amplification strategy. Biosens. Bioelectron., 2016, 81, 111-116.
[http://dx.doi.org/10.1016/j.bios.2016.02.057] [PMID: 26926592]
[38]
Gitan, R.S.; Shi, H.; Chen, C.M.; Yan, P.S.; Huang, T.H. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res., 2002, 12(1), 158-164.
[http://dx.doi.org/10.1101/gr.202801] [PMID: 11779841]
[39]
Jelen, F.; Tomschik, M.; Paleček, E. Adsorptive stripping square-wave voltammetry of DNA. J. Electroanal. Chem. (Lausanne Switz.), 1997, 423(1-2), 141-148.
[http://dx.doi.org/10.1016/S0022-0728(96)04954-6]
[40]
Jing, X.; Cao, X.; Wang, L.; Lan, T.; Li, Y.; Xie, G. DNA-AuNPs based signal amplification for highly sensitive detection of DNA methylation, methyltransferase activity and inhibitor screening. Biosens. Bioelectron., 2014, 58, 40-47.
[http://dx.doi.org/10.1016/j.bios.2014.02.035] [PMID: 24613968]
[41]
Labib, M.; Sargent, E.H.; Kelley, S.O. electrochemical methods for the analysis of clinically relevant biomolecules. Chem. Rev., 2016, 116(16), 9001-9090.
[http://dx.doi.org/10.1021/acs.chemrev.6b00220] [PMID: 27428515]
[42]
Mulchandani, A.; Bassi, A.S. Principles and applications of biosensors for bioprocess monitoring and control. Crit. Rev. Biotechnol., 1995, 15(2), 105-124.
[http://dx.doi.org/10.3109/07388559509147402] [PMID: 7641291]
[43]
Clark, L.C., Jr; Lyons, C. Electrode systems for continuous monitoring in cardiovascular surgery. Ann. N. Y. Acad. Sci., 1962, 102(1), 29-45.
[http://dx.doi.org/10.1111/j.1749-6632.1962.tb13623.x] [PMID: 14021529]
[44]
Goode, J.A.; Rushworth, J.V.; Millner, P.A. Biosensor regeneration: a review of common techniques and outcomes. Langmuir, 2015, 31(23), 6267-6276.
[http://dx.doi.org/10.1021/la503533g] [PMID: 25402969]
[45]
Vargas-Bernal, R.; Rodrguez-Miranda, E.; Herrera-Prez, G. Evolution and expectations of enzymatic biosensors for pesticides; Pesticides - Advances in Chemical and Botanical Pesticides, 2012, pp. 331-354.
[http://dx.doi.org/10.5772/46227]
[46]
Grieshaber, D.; MacKenzie, R.; Vörös, J.; Reimhult, E. Electrochemical biosensors - sensor principles and architectures. Sensors (Basel), 2008, 8(3), 1400-1458.
[http://dx.doi.org/10.3390/s80314000] [PMID: 27879772]
[47]
Kasemo, B. Biological surface science. Surf. Sci., 2002, 500(1-3), 656-677.
[http://dx.doi.org/10.1016/S0039-6028(01)01809-X]
[48]
Rawson, F.J.; Yeung, C.L.; Jackson, S.K.; Mendes, P.M. Tailoring 3D single-walled carbon nanotubes anchored to indium tin oxide for natural cellular uptake and intracellular sensing. Nano Lett., 2013, 13(1), 1-8.
[http://dx.doi.org/10.1021/nl203780d] [PMID: 22268573]
[49]
Ge, C.; Miao, W.; Ji, M.; Gu, N. Glutaraldehyde-modified electrode for nonlabeling voltammetric detection of p16 INK4A gene. Anal. Bioanal. Chem., 2005, 383(4), 651-659.
[http://dx.doi.org/10.1007/s00216-005-0032-7] [PMID: 16132144]
[50]
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., 2013, 41, 492-497.
[http://dx.doi.org/10.1016/j.bios.2012.09.010] [PMID: 23021851]
[51]
Yin, H.; Zhou, Y.; Yang, Z.; Guo, Y.; Wang, X.; Ai, S.; Zhang, X. Electrochemical immunosensor for N6-methyladenosine RNA modification detection. Sens. Actuators B Chem., 2015, 221, 1-6.
[http://dx.doi.org/10.1016/j.snb.2015.06.045]
[52]
Zhou, Y.; Li, B.; Wang, M.; Yang, Z.; Yin, H.; Ai, S. Enzyme-based electrochemical biosensor for sensitive detection of DNA demethylation and the activity of DNA demethylase. Anal. Chim. Acta, 2014, 840, 28-32.
[http://dx.doi.org/10.1016/j.aca.2014.06.020] [PMID: 25086890]
[53]
Saheb, A.; Patterson, S.; Josowicz, M. Probing for DNA methylation with a voltammetric DNA detector. Analyst (Lond.), 2014, 139(4), 786-792.
[http://dx.doi.org/10.1039/C3AN02154H] [PMID: 24358460]
[54]
Daneshpour, M.; Moradi, L.S.; Izadi, P.; Omidfar, K. Femtomolar level detection of RASSF1A tumor suppressor gene methylation by electrochemical nano-genosensor based on Fe3O4/TMC/Au nanocomposite and PT-modified electrode. Biosens. Bioelectron., 2016, 77, 1095-1103.
[http://dx.doi.org/10.1016/j.bios.2015.11.007] [PMID: 26562330]
[55]
Brotons, A.; Arán-Ais, R.M.; Feliu, J.M.; Montiel, V.; Iniesta, J.; Vidal-Iglesias, F.J.; Solla-Gullón, J. Electrochemical detection of cytosine and 5-methylcytosine on Au(111) surfaces. Electrochem. Commun., 2016, 65, 27-30.
[http://dx.doi.org/10.1016/j.elecom.2016.02.008]
[56]
Wang, G.L.; Zhou, L.Y.; Luo, H.Q.; Li, N.B.G.L. Electrochemical strategy for sensing DNA methylation and DNA methyltransferase activity. Anal. Chim. Acta, 2013, 768, 76-81.
[http://dx.doi.org/10.1016/j.aca.2013.01.026] [PMID: 23473252]
[57]
Kato, D.; Sekioka, N.; Ueda, A.; Kurita, R.; Hirono, S.; Suzuki, K.; Niwa, O. A nanocarbon film electrode as a platform for exploring DNA methylation. J. Am. Chem. Soc., 2008, 130(12), 3716-3717.
[http://dx.doi.org/10.1021/ja710536p] [PMID: 18314986]
[58]
Xu, Z.; Wang, M.; Yin, H.; Ai, S.; Wang, L.; Pang, J. A sensitive electrochemical method for DNA methyltransferase assay and inhibitor screening based on DNA methylation-sensitive cleavage. Electrochim. Acta, 2013, 112(12), 596-602.
[http://dx.doi.org/10.1016/j.electacta.2013.09.037]
[59]
Hossain, T.; Mahmudunnabi, G.; Masud, M.K.; Islam, M.N.; Ooi, L.; Konstantinov, K.; Hossain, M.S.A.; Martinac, B.; Alici, G.; Nguyen, N.T.; Shiddiky, M.J.A. Electrochemical biosensing strategies for DNA methylation analysis. Biosens. Bioelectron., 2017, 94, 63-73.
[http://dx.doi.org/10.1016/j.bios.2017.02.026] [PMID: 28259051]
[60]
Bartosik, M.; Fojta, M.; Palecek, E. Electrochemical detection of 5-methylcytosine in bisulfite-treated DNA. Electrochim. Acta, 2012, 78(9), 75-81.
[http://dx.doi.org/10.1016/j.electacta.2012.05.115]
[61]
Wang, P.; Wu, H.; Dai, Z.; Zou, X. Picomolar level profiling of the methylation status of the p53 tumor suppressor gene by a label-free electrochemical biosensor. Chem. Commun. (Camb.), 2012, 48(87), 10754-10756.
[http://dx.doi.org/10.1039/c2cc35615e] [PMID: 23010984]
[62]
Haque, M.H.; Gopalan, V.; Yadav, S.; Islam, M.N.; Eftekhari, E.; Li, Q.; Carrascosa, L.G.; Nguyen, N.T.; Lam, A.K.; Shiddiky, M.J.A. Detection of regional DNA methylation using DNA-graphene affinity interactions. Biosens. Bioelectron., 2017, 87, 615-621.
[http://dx.doi.org/10.1016/j.bios.2016.09.016] [PMID: 27616287]
[63]
Liu, S.; Zhang, X.; Zhao, K. Methylation-specific electrochemical biosensing strategy for highly sensitive and quantitative analysis of promoter methylation of tumor-suppressor gene in real sample. Electroanal. Chem., 2016, 773, 63-68.
[http://dx.doi.org/10.1016/j.jelechem.2016.03.001]
[64]
Kurita, R.; Yanagisawa, H.; Kamata, T.; Kato, D.; Niwa, O. On-chip evaluation of DNA methylation with electrochemical combined bisulfite restriction analysis utilizing a carbon film containing a nanocrystalline structure. Anal. Chem., 2017, 89(11), 5976-5982.
[http://dx.doi.org/10.1021/acs.analchem.7b00533] [PMID: 28466637]
[65]
Yanagisawa, H.; Kurita, R.; Yoshida, T.; Kamata, T.; Niwa, O. Electrochemical assessment of local cytosine methylation in genomic DNA on a nanocarbon film electrode fabricated by unbalanced magnetron sputtering. Sens. Actuators B Chem., 2015, 221, 816-822.
[http://dx.doi.org/10.1016/j.snb.2015.07.030]
[66]
Liu, H.; Luo, J.; Fang, L.; Huang, H.; Deng, J.; Huang, J.; Zhang, S.; Li, Y.; Zheng, J. An electrochemical strategy with tetrahedron rolling circle amplification for ultrasensitive detection of DNA methylation. Biosens. Bioelectron., 2018, 121, 47-53.
[http://dx.doi.org/10.1016/j.bios.2018.07.055] [PMID: 30196047]
[67]
Chen, C.; Li, B. Chemiluminescence resonance energy transfer biosensing platform for site-specific determination of DNA methylation and assay of DNA methyltransferase activity using exonuclease III-assisted target recycling amplification. Biosens. Bioelectron., 2014, 54, 48-54.
[http://dx.doi.org/10.1016/j.bios.2013.10.050] [PMID: 24240168]
[68]
Koo, K.M.; Wee, E.J.; Rauf, S.; Shiddiky, M.J.; Trau, M. Microdevices for detecting locus-specific DNA methylation at CpG resolution. Biosens. Bioelectron., 2014, 56, 278-285.
[http://dx.doi.org/10.1016/j.bios.2014.01.029] [PMID: 24514080]
[69]
Dai, Z.; Cai, T.; Zhu, W.; Gao, X.; Zou, X. Simultaneous profiling of multiple gene-methylation loci by electrochemical methylation-specific ligase detection reaction. Chem. Commun. (Camb.), 2013, 49(19), 1939-1941.
[http://dx.doi.org/10.1039/c3cc38942a] [PMID: 23364409]
[70]
Xu, Y.; Gao, X.; Li, Z.; Chen, D.; Zong, D.; Zou, X. Simultaneous detection of double gene-specific methylation loci based on hairpin probes tagged with electrochemical quantum dots barcodes. Electroanal. Chem., 2016, 781, 356-362.
[http://dx.doi.org/10.1016/j.jelechem.2016.06.042]
[71]
Shin, Y.; Perera, A.P.; Kee, J.S.; Song, J.; Fang, Q.; Lo, G.Q.; Park, M.K. Label-free methylation specific sensor based on silicon microring resonators for detection and quantification of DNA methylation biomarkers in bladder cancer. Sens. Actuators B Chem., 2013, 177(2), 404-411.
[http://dx.doi.org/10.1016/j.snb.2012.11.058]
[72]
Yoon, J.; Park, M.K.; Lee, T.Y.; Yoon, Y.J.; Shin, Y. LoMA-B: a simple and versatile lab-on-a-chip system based on single-channel bisulfite conversion for DNA methylation analysis. Lab Chip, 2015, 15(17), 3530-3539.
[http://dx.doi.org/10.1039/C5LC00458F] [PMID: 26194344]
[73]
Khulan, B.; Thompson, R.F.; Ye, K.; Fazzari, M.J.; Suzuki, M.; Stasiek, E.; Figueroa, M.E.; Glass, J.L.; Chen, Q.; Montagna, C.; Hatchwell, E.; Selzer, R.R.; Richmond, T.A.; Green, R.D.; Melnick, A.; Greally, J.M. Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res., 2006, 16(8), 1046-1055.
[http://dx.doi.org/10.1101/gr.5273806] [PMID: 16809668]
[74]
Ferrin, L.J.; Camerini-Otero, R.D. Selective cleavage of human DNA: recA-assisted restriction endonuclease (RARE) cleavage. Science, 1991, 254(5037), 1494-1497.
[http://dx.doi.org/10.1126/science.1962209] [PMID: 1962209]
[75]
Li, X.; Xie, Z.; Wang, W.; Zhou, Y.; Yin, H.; Yang, Z.; Ai, S. Rapid detection of Dam methyltransferase activity based on the exonuclease III-assisted isothermal amplification cycle. Anal. Methods, 2016, 8(13), 2771-2777.
[http://dx.doi.org/10.1039/C5AY03397G]
[76]
Dai, Z.; Hu, X.; Wu, H.; Zou, X. A label-free electrochemical assay for quantification of gene-specific methylation in a nucleic acid sequence. Chem. Commun. (Camb.), 2012, 48(12), 1769-1771.
[http://dx.doi.org/10.1039/c2cc15398j] [PMID: 22218332]
[77]
Hou, P.; Ji, M.; Ge, C.; Shen, J.; Li, S.; He, N.; Lu, Z. Detection of methylation of human p16(Ink4a) gene 5′-CpG islands by electrochemical method coupled with linker-PCR. Nucleic Acids Res., 2003, 31(16),e92.
[http://dx.doi.org/10.1093/nar/gng092] [PMID: 12907744]
[78]
Hashimoto, K.; Kokubun, S.; Itoi, E.; Roach, H.I. Improved quantification of DNA methylation using methylation-sensitive restriction enzymes and real-time PCR. Epigenetics, 2007, 2(2), 86-91.
[http://dx.doi.org/10.4161/epi.2.2.4203] [PMID: 17965602]
[79]
Yin, H.; Yang, Z.; Li, B.; Zhou, Y.; Ai, S. Electrochemical biosensor for DNA demethylase detection based on demethylation triggered endonuclease BstUI and Exonuclease III digestion. Biosens. Bioelectron., 2015, 66, 266-270.
[http://dx.doi.org/10.1016/j.bios.2014.11.026] [PMID: 25437362]
[80]
Muren, N.B.; Barton, J.K. Electrochemical assay for the signal-on detection of human DNA methyltransferase activity. J. Am. Chem. Soc., 2013, 135(44), 16632-16640.
[http://dx.doi.org/10.1021/ja4085918] [PMID: 24164112]
[81]
Joda, H.; Moutsiopoulou, A.; Stone, G.; Daunert, S.; Deo, S. Design of Gaussia luciferase-based bioluminescent stem-loop probe for sensitive detection of HIV-1 nucleic acids. Analyst (Lond.), 2018, 143(14), 3374-3381.
[http://dx.doi.org/10.1039/C8AN00047F] [PMID: 29897056]
[82]
Liu, W.; Lai, H.; Huang, R.; Zhao, C.; Wang, Y.; Weng, X.; Zhou, X. DNA methyltransferase activity detection based on fluorescent silver nanocluster hairpin-shaped DNA probe with 5′-C-rich/G-rich-3′ tails. Biosens. Bioelectron., 2015, 68, 736-740.
[http://dx.doi.org/10.1016/j.bios.2015.02.005] [PMID: 25682501]
[83]
Zhang, H.; Zou, L.; Li, R.; Zhao, M.; Ling, L. Hairpin probe for sequence-specific recognition of double-stranded DNA on simian virus 40. Chem. Res. Chin. Univ., 2017, 34, 28-32.
[http://dx.doi.org/10.1007/s40242-017-7152-4]
[84]
Bonnet, G.; Tyagi, S.; Libchaber, A.; Kramer, F.R. Thermodynamic basis of the enhanced specificity of structured DNA probes. Proc. Natl. Acad. Sci. USA, 1999, 96(11), 6171-6176.
[http://dx.doi.org/10.1073/pnas.96.11.6171] [PMID: 10339560]
[85]
Su, J.; He, X.; Wang, Y.; Wang, K.; Chen, Z.; Yan, G. A sensitive signal-on assay for MTase activity based on methylation-responsive hairpin-capture DNA probe. Biosens. Bioelectron., 2012, 36(1), 123-128.
[http://dx.doi.org/10.1016/j.bios.2012.04.012] [PMID: 22560164]
[86]
Wu, H.; Liu, S.; Jiang, J.; Shen, G.; Yu, R. A sensitive electrochemical biosensor for detection of DNA methyltransferase activity by combining DNA methylation-sensitive cleavage and terminal transferase-mediated extension. Chem. Commun. (Camb.), 2012, 48(50), 6280-6282.
[http://dx.doi.org/10.1039/c2cc32397d] [PMID: 22610282]
[87]
Liu, P.; Wang, D.; Zhou, Y.; Wang, H.; Yin, H.; Ai, S. DNA methyltransferase detection based on digestion triggering the combination of poly adenine DNA with gold nanoparticles. Biosens. Bioelectron., 2016, 80, 74-78.
[http://dx.doi.org/10.1016/j.bios.2015.12.100] [PMID: 26807517]
[88]
Liu, P.; Liu, M.; Yin, H.; Zhou, Y.; Ai, S. Electrochemical biosensor for DNA methyltransferase detection based on DpnI digestion triggering the formation of G-quadruplex DNAzymes. Sens. Actuators B Chem., 2015, 220, 101-106.
[http://dx.doi.org/10.1016/j.snb.2015.05.058]
[89]
Li, J.; He, G.; Mu, C.; Wang, K.; Xiang, Y. Assay of DNA methyltransferase 1 activity based on uracil-specific excision reagent digestion induced G-quadruplex formation. Anal. Chim. Acta, 2017, 986, 131-137.
[http://dx.doi.org/10.1016/j.aca.2017.07.021] [PMID: 28870318]
[90]
Liu, K.; Xu, C.; Lei, M.; Yang, A.; Loppnau, P.; Hughes, T.R.; Min, J. Structural basis for the ability of MBD domains to bind methyl-CG and TG sites in DNA. J. Biol. Chem., 2018, 293(19), 7344-7354.
[http://dx.doi.org/10.1074/jbc.RA118.001785] [PMID: 29567833]
[91]
Yang, Z.; Jiang, W.; Liu, F.; Zhou, Y.; Yin, H.; Ai, S. A novel electrochemical immunosensor for 5-hydroxymethylcytosine quantitative detection in genomic DNA of breast cancer tissue. Chem. Commun. (Camb.), 2015, 51(78), 14671-14673.
[http://dx.doi.org/10.1039/C5CC05921F] [PMID: 26291430]
[92]
Haque, M.H.; Bhattacharjee, R.; Islam, M.N.; Gopalan, V.; Nguyen, N.T.; Lam, A.K.; Shiddiky, M.J.A. Colorimetric and electrochemical quantification of global DNA methylation using a methyl cytosine-specific antibody. Analyst (Lond.), 2017, 142(11), 1900-1908.
[http://dx.doi.org/10.1039/C7AN00526A] [PMID: 28516982]
[93]
Povedano, E.; Vargas, E.; Montiel, V.R.; Torrente-Rodríguez, R.M.; Pedrero, M.; Barderas, R.; Segundo-Acosta, P.S.; Peláez-García, A.; Mendiola, M.; Hardisson, D.; Campuzano, S.; Pingarrón, J.M. Electrochemical affinity biosensors for fast detection of gene-specific methylations with no need for bisulfite and amplification treatments. Sci. Rep., 2018, 8(1), 6418.
[http://dx.doi.org/10.1038/s41598-018-24902-1] [PMID: 29686400]
[94]
Bhattacharjee, R.; Moriam, S.; Nguyen, N.T.; Shiddiky, M.J.A. A bisulfite treatment and PCR-free global DNA methylation detection method using electrochemical enzymatic signal engagement. Biosens. Bioelectron., 2019, 126, 102-107.
[http://dx.doi.org/10.1016/j.bios.2018.10.020] [PMID: 30396016]
[95]
Gao, F.; Fan, T.; Ou, S.; Wu, J.; Zhang, X.; Luo, J.; Li, N.; Yao, Y.; Mou, Y.; Liao, X.; Geng, D. Highly efficient electrochemical sensing platform for sensitive detection DNA methylation, and methyltransferase activity based on Ag NPs decorated carbon nanocubes. Biosens. Bioelectron., 2018, 99, 201-208.
[http://dx.doi.org/10.1016/j.bios.2017.07.063] [PMID: 28759870]
[96]
Du, Q.; Luu, P.L.; Stirzaker, C.; Clark, S.J. Methyl-CpG-binding domain proteins: readers of the epigenome. Epigenomics, 2015, 7(6), 1051-1073.
[http://dx.doi.org/10.2217/epi.15.39] [PMID: 25927341]
[97]
Xu, Z.; Yin, H.; Tian, Z.; Zhou, Y.; Ai, S. Electrochemical immunoassays for the detection the activity of DNA methyltransferase by using the rolling circle amplification technique. Mikrochim. Acta, 2014, 181, 471-477.
[http://dx.doi.org/10.1007/s00604-013-1141-1]
[98]
Yin, H.; Zhou, Y.; Xu, Z.; Wang, M.; Ai, S. Ultrasensitive electrochemical immunoassay for DNA methyltransferase activity and inhibitor screening based on methyl binding domain protein of MeCP2 and enzymatic signal amplification. Biosens. Bioelectron., 2013, 49, 39-45.
[http://dx.doi.org/10.1016/j.bios.2013.04.040] [PMID: 23708816]
[99]
Xu, Z.; Yin, H.; Huo, L.; Zhou, Y.; Ai, S. Electrochemical immunosensor for DNA methyltransferase activity assay based on methyl CpG-binding protein and dual gold nanoparticle conjugate-based signal amplification. Sens. Actuators B Chem., 2014, 192, 143-149.
[http://dx.doi.org/10.1016/j.snb.2013.10.099]
[100]
Lee, J.; Yoshida, W.; Abe, K.; Nakabayashi, K.; Wakeda, H.; Hata, K.; Marquette, C.A.; Blum, L.J.; Sode, K.; Ikebukuro, K. Development of an electrochemical detection system for measuring DNA methylation levels using methyl CpG-binding protein and glucose dehydrogenase-fused zinc finger protein. Biosens. Bioelectron., 2017, 93, 118-123.
[http://dx.doi.org/10.1016/j.bios.2016.09.060] [PMID: 27666367]
[101]
Gilboa, T.; Torfstein, C.; Juhasz, M.; Grunwald, A.; Ebenstein, Y.; Weinhold, E.; Meller, A. Single-molecule DNA methylation quantification using electro-optical sensing in solid-state nanopores. ACS Nano, 2016, 10(9), 8861-8870.
[http://dx.doi.org/10.1021/acsnano.6b04748] [PMID: 27580095]
[102]
Yang, Z.; Wang, F.; Wang, M.; Yin, H.; Ai, S. A novel signal-on strategy for M.SssI methyltransfease activity analysis and inhibitor screening based on photoelectrochemical immunosensor. Biosens. Bioelectron., 2015, 66, 109-114.
[http://dx.doi.org/10.1016/j.bios.2014.11.015] [PMID: 25460890]
[103]
Tanabe, K.; Yamada, H.; Ito, T.; Nishimoto, S. Photoelectrochemical identification of 5-methylcytosine modification in DNA: combination of photosensitization and enzymatic cleavage. Nucleic Acids Symp Ser (Oxf), 2009, 53(1), 205-206.
[http://dx.doi.org/10.1093/nass/nrp103]]
[104]
Hawk, R.M.; Armani, A.M. Label free detection of 5′ hydroxymethylcytosine within CpG islands using optical sensors. Biosens. Bioelectron., 2015, 65, 198-203.
[http://dx.doi.org/10.1016/j.bios.2014.10.041] [PMID: 25461158]
[105]
Wu, Y.; Zhang, B.; Guo, L.H. Label-free and selective photoelectrochemical detection of chemical DNA methylation damage using DNA repair enzymes. Anal. Chem., 2013, 85(14), 6908-6914.
[http://dx.doi.org/10.1021/ac401346x] [PMID: 23777269]
[106]
Wang, H.; Zhu, L.; Duan, J.; Wang, M.; Yin, H.; Wang, P.; Ai, S. Photoelectrochemical biosensor for HEN1 RNA methyltransferase detection using peroxidase mimics PtCu NFs and poly(U) polymerase-mediated RNA extension. Biosens. Bioelectron., 2018, 103, 32-38.
[http://dx.doi.org/10.1016/j.bios.2017.12.035] [PMID: 29277012]
[107]
Wang, H.; Liu, P.; Jiang, W.; Li, X.; Yin, H.; Ai, S. Photoelectrochemical immunosensing platform for M.SssI methyltransferase activity analysis and inhibitor screening based on g-C3N4 and CdS quantum dots. Sens. Actuators B Chem., 2017, 244, 458-465.
[http://dx.doi.org/10.1016/j.snb.2017.01.016]
[108]
Wang, Z.Y.; Wang, L.J.; Zhang, Q.; Tang, B.; Zhang, C.Y. Single quantum dot-based nanosensor for sensitive detection of 5-methylcytosine at both CpG and non-CpG sites. Chem. Sci. (Camb.), 2017, 9(5), 1330-1338.
[http://dx.doi.org/10.1039/C7SC04813K] [PMID: 29675180]
[109]
Shen, Q.; Han, L.; Fan, G.; Abdel-Halim, E.S.; Jiang, L.; Zhu, J.J. Highly sensitive photoelectrochemical assay for DNA methyltransferase activity and inhibitor screening by exciton energy transfer coupled with enzyme cleavage biosensing strategy. Biosens. Bioelectron., 2015, 64, 449-455.
[http://dx.doi.org/10.1016/j.bios.2014.09.044] [PMID: 25282398]
[110]
Dadmehr, M.; Hosseini, M.; Hosseinkhani, S.; Ganjali, M.R.; Khoobi, M.; Behzadi, H.; Hamedani, M.; Sheikhnejad, R. DNA methylation detection by a novel fluorimetric nanobiosensor for early cancer diagnosis. Biosens. Bioelectron., 2014, 60, 35-44.
[http://dx.doi.org/10.1016/j.bios.2014.03.033] [PMID: 24768860]
[111]
Ma, Y.; Bai, Y.; Mao, H.; Hong, Q.; Yang, D.; Zhang, H.; Liu, F.; Wu, Z.; Jin, Q.; Zhou, H.; Cao, J.; Zhao, J.; Zhong, X.; Mao, H. A panel of promoter methylation markers for invasive and noninvasive early detection of NSCLC using a quantum dots-based FRET approach. Biosens. Bioelectron., 2016, 85, 641-648.
[http://dx.doi.org/10.1016/j.bios.2016.05.067] [PMID: 27240011]
[112]
Wang, P.; Han, P.; Dong, L.; Miao, X. Direct potential resolution and simultaneous detection of cytosine and 5-methylcytosine based on the construction of polypyrrole functionalized graphene nanowall interface. Electrochem. Commun., 2015, 61, 36-39.
[http://dx.doi.org/10.1016/j.elecom.2015.09.025]
[113]
Kurita, R.; Arai, K.; Nakamoto, K.; Kato, D.; Niwa, O. Determination of DNA methylation using electrochemiluminescence with surface accumulable coreactant. Anal. Chem., 2012, 84(4), 1799-1803.
[http://dx.doi.org/10.1021/ac202692f] [PMID: 22263690]
[114]
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. (Camb.), 2014, 50(22), 2932-2934.
[http://dx.doi.org/10.1039/C3CC49719D] [PMID: 24501739]
[115]
Zhang, H.; Guo, Z.; Dong, H.; Chen, H.; Cai, C. An electrochemiluminescence assay for sensitive detection of methyltransferase activity in different cancer cells by hybridization chain reaction coupled with a G-quadruplex/hemin DNAzyme biosensing strategy. Analyst (Lond.), 2017, 142(11), 2013-2019.
[http://dx.doi.org/10.1039/C7AN00486A] [PMID: 28513652]
[116]
Sun, H.; Ma, S.; Li, Y.; Qi, H.; Ning, X.; Zheng, J. Electrogenerated chemiluminescence biosensing method for the discrimination of DNA hydroxymethylation and assay of the β-glucosyltransferase activity. Biosens. Bioelectron., 2016, 79, 92-97.
[http://dx.doi.org/10.1016/j.bios.2015.11.068] [PMID: 26700581]
[117]
Zhao, H.F.; Liang, R.P.; Wang, J.W.; Qiu, J.D. One-pot synthesis of GO/AgNPs/luminol composites with electrochemiluminescence activity for sensitive detection of DNA methyltransferase activity. Biosens. Bioelectron., 2015, 63, 458-464.
[http://dx.doi.org/10.1016/j.bios.2014.07.079] [PMID: 25129507]
[118]
Wang, P.; Mai, Z.; Dai, Z.; Zou, X. Investigation of DNA methylation by direct electrocatalytic oxidation. Chem. Commun. (Camb.), 2010, 46(41), 7781-7783.
[http://dx.doi.org/10.1039/c0cc00983k] [PMID: 20830331]
[119]
Meng, X.; Xu, Z.; Wang, M.; Yin, H.; Ai, S. Direct determination of 5-methylcytosine based on electrochemical activation of surfactant functionalized graphene modified pyrolytic graphite electrode. Electrochim. Acta, 2013, 95, 200-204.
[http://dx.doi.org/10.1016/j.electacta.2013.02.050]
[120]
Zheng, X.; Wang, L. Direct electrocatalytic oxidation and simultaneous determination of 5-methylcytosine and cytosine at electrochemically reduced graphene modified glassy carbon electrode. Electroanalysis, 2013, 25(7), 1697-1705.
[http://dx.doi.org/10.1002/elan.201300040]
[121]
Wang, J.; Kawde, A-N.; Musameh, M. Carbon-nanotube-modified glassy carbon electrodes for amplified label-free electrochemical detection of DNA hybridization. Analyst (Lond.), 2003, 128(7), 912-916.
[http://dx.doi.org/10.1039/b303282e] [PMID: 12894830]
[122]
Xu, Y.; Niu, C.; Xiao, X.; Zhu, W.; Dai, Z.; Zou, X. Chemical-oxidation cleavage triggered isothermal exponential amplification reaction for attomole gene-specific methylation analysis. Anal. Chem., 2015, 87(5), 2945-2951.
[http://dx.doi.org/10.1021/ac5044785] [PMID: 25635709]
[123]
Ma, S.; Sun, H.; Li, Y.; Qi, H.; Zheng, J. Discrimination between 5-hydroxymethylcytosine and 5-methylcytosine in DNA via selective electrogenerated chemiluminescence labeling. Anal. Chem., 2016, 88(20), 9934-9940.
[http://dx.doi.org/10.1021/acs.analchem.6b01265] [PMID: 27620533]
[124]
Zhou, Y.; Yang, Z.; Li, X.; Wang, Y.; Yin, H.; Ai, S. Electrochemical biosensor for detection of DNA hydroxymethylation based on glycosylation and alkaline phosphatase catalytic signal amplification. Electrochimica, 2015, 174, 647-652.
[http://dx.doi.org/10.1016/j.electacta.2015.06.043]
[125]
Fukuzawa, S.; Tachibana, K.; Tajima, S.; Suetake, I. Selective oxidation of 5-hydroxymethylcytosine with micelle incarcerated oxidants to determine it at single base resolution. Bioorg. Med. Chem. Lett., 2015, 25(24), 5667-5671.
[http://dx.doi.org/10.1016/j.bmcl.2015.11.017] [PMID: 26584880]
[126]
Chandran, S. Rapid assembly of DNA via ligase cycling reaction (LCR). Methods Mol. Biol., 2017, 1472, 105-110.
[http://dx.doi.org/10.1007/978-1-4939-6343-0_8] [PMID: 27671935]
[127]
Gibriel, A.A.; Adel, O. Advances in ligase chain reaction and ligation based amplifications for genotyping assays: detection and applications. Mutat. Res., 2017, 773, 66-90.
[http://dx.doi.org/10.1016/j.mrrev.2017.05.001]] [PMID: 28927538]
[128]
Wee, E.J.H.; Shiddiky, M.J.A.; Brown, M.A.; Trau, M. eLCR: electrochemical detection of single DNA base changes via ligase chain reaction. Chem. Commun. (Camb.), 2012, 48(98), 12014-12016.
[http://dx.doi.org/10.1039/c2cc35841g] [PMID: 23133830]
[129]
Wee, E.J.H.; Rauf, S.; Koo, K.M.; Shiddiky, M.J.A.; Trau, M. μ-eLCR: a microfabricated device for electrochemical detection of DNA base changes in breast cancer cell lines. Lab Chip, 2013, 13(22), 4385-4391.
[http://dx.doi.org/10.1039/c3lc50528f] [PMID: 24061339]
[130]
Su, F.; Wang, L.; Sun, Y.; Liu, C.; Duan, X.; Li, Z. Highly sensitive detection of CpG methylation in genomic DNA by AuNP-based colorimetric assay with ligase chain reaction. Chem. Commun. (Camb.), 2015, 51(16), 3371-3374.
[http://dx.doi.org/10.1039/C4CC07688E] [PMID: 25621431]
[131]
Wang, Y.; Wee, E.J.H.; Trau, M. Highly sensitive DNA methylation analysis at CpG resolution by surface-enhanced Raman scattering via ligase chain reaction. Chem. Commun. (Camb.), 2015, 51(54), 10953-10956.
[http://dx.doi.org/10.1039/C5CC03921E] [PMID: 26063626]
[132]
Erdem, A.; Meric, B.; Kerman, K.; Dalbasti, T.; Ozsoz, M. Detection of interaction between metal complex indicator and DNA by using electrochemical biosensor. Electroanalysis, 2015, 11(18), 1372-1376.
[http://dx.doi.org/10.1002/(SICI)1521-4109(199912)11:18<1372:AID-ELAN1372>3.0.CO;2-4]
[133]
Li, W.; Liu, X.; Hou, T.; Li, H.; Li, F. Ultrasensitive homogeneous electrochemical strategy for DNA methyltransferase activity assay based on autonomous exonuclease III-assisted isothermal cycling signal amplification. Biosens. Bioelectron., 2015, 70, 304-309.
[http://dx.doi.org/10.1016/j.bios.2015.03.060] [PMID: 25840015]
[134]
Furst, A.L.; Muren, N.B.; Hill, M.G.; Barton, J.K. Label-free electrochemical detection of human methyltransferase from tumors. Proc. Natl. Acad. Sci. USA, 2014, 111(42), 14985-14989.
[http://dx.doi.org/10.1073/pnas.1417351111] [PMID: 25288757]
[135]
Hong, L.; Wan, J.; Zhang, X.; Wang, G. DNA-gold nanoparticles network based electrochemical biosensors for DNA MTase activity. Talanta, 2016, 152, 228-235.
[http://dx.doi.org/10.1016/j.talanta.2016.01.026] [PMID: 26992515]
[136]
Bao, J.; Geng, X.; Hou, C.; Zhao, Y.; Huo, D.; Wang, Y.; Wang, Z.; Zeng, Y.; Yang, M.; Fa, H. A simple and universal electrochemical assay for sensitive detection of DNA methylation, methyltransferase activity and screening of inhibitors. J. Electroanal. Chem. (Lausanne Switz.), 2018, 814, 144-152.
[http://dx.doi.org/10.1016/j.jelechem.2018.02.060]
[137]
Sato, S.; Takenaka, S. Ferrocenyl naphthalene diimides as tetraplex DNA binders. J. Inorg. Biochem., 2017, 167, 21-26.
[http://dx.doi.org/10.1016/j.jinorgbio.2016.11.020] [PMID: 27893990]
[138]
Sato, S.; Tsueda, M.; Kanezaki, Y.; Takenaka, S. Detection of an aberrant methylation of CDH4 gene in PCR product by ferrocenylnaphthalene diimide-based electrochemical hybridization assay. Anal. Chim. Acta, 2012, 715, 42-48.
[http://dx.doi.org/10.1016/j.aca.2011.12.010] [PMID: 22244165]
[139]
Haraguchi, K.; Sato, S.; Habu, M.; Yada, N.; Hayakawa, M.; Takahashi, O.; Yoshioka, I.; Matsuo, K.; Tominaga, K.; Takenaka, S. Oral cancer screening based on methylation frequency detection in hTERT gene using electrochemical hybridization assay via a multi-electrode chip coupled with ferrocenylnaphthalene diimide. Electroanalysis, 2017, 29(6), 1596-1601.
[http://dx.doi.org/10.1002/elan.201700028]
[140]
Zhang, Z.; Sheng, S.; Cao, X.; Li, Y.; Yao, J.; Wang, T.; Xie, G. Proximity-based electrochemical biosensor for highly sensitive determination of methyltransferase activity using gold nanoparticle-based cooperative signal amplification. Mikrochim. Acta, 2015, 182, 2329-2336.
[http://dx.doi.org/10.1007/s00604-015-1564-y]
[141]
Hasegawa, Y.; Takada, T.; Nakamura, M.; Yamana, K. Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch. Bioorg. Med. Chem. Lett., 2017, 27(15), 3555-3557.
[http://dx.doi.org/10.1016/j.bmcl.2017.05.049] [PMID: 28583799]
[142]
Shen, Q.; Fan, M.; Yang, Y.; Zhang, H. Electrochemical DNA sensor-based strategy for sensitive detection of DNA demethylation and DNA demethylase activity. Anal. Chim. Acta, 2016, 934, 66-71.
[http://dx.doi.org/10.1016/j.aca.2016.06.037] [PMID: 27506345]
[143]
Cui, W.R.; Li, Z.J.; Chi, B.Z.; Li, Z.M.; Liang, R.P.; Qiu, J.D. Ultrasensitively electrochemical detection activity of DNA methyltransferase using an autocatalytic and recycling amplification strategy. J. Electroanal. Chem. (Lausanne Switz.), 2018, 808, 329-334.
[http://dx.doi.org/10.1016/j.jelechem.2017.12.011]
[144]
Sina, A.A.I.; Howell, S.; Carrascosa, L.G.; Rauf, S.; Shiddiky, M.J.A.; Trau, M. eMethylsorb: electrochemical quantification of DNA methylation at CpG resolution using DNA-gold affinity interactions. Chem. Commun. (Camb.), 2014, 50(86), 13153-13156.
[http://dx.doi.org/10.1039/C4CC06732K] [PMID: 25227312]
[145]
Sina, A.A.I.; Foster, M.T.; Korbie, D.; Carrascosa, L.G.; Shiddiky, M.J.A.; Gao, J.; Dey, S.; Trau, M. A multiplex microplatform for the detection of multiple DNA methylation events using gold-DNA affinity. Analyst (Lond.), 2017, 142(19), 3573-3578.
[http://dx.doi.org/10.1039/C7AN00611J] [PMID: 28861578]
[146]
Haque, M.H.; Gopalan, V.; Islam, M.N.; Masud, M.K.; Bhattacharjee, R.; Hossain, M.S.A.; Nguyen, N.T.; Lam, A.K.; Shiddiky, M.J.A. Quantification of gene-specific DNA methylation in oesophageal cancer via electrochemistry. Anal. Chim. Acta, 2017, 976, 84-93.
[http://dx.doi.org/10.1016/j.aca.2017.04.034] [PMID: 28576321]
[147]
Huang, Z.; Liu, J. Length-dependent diblock DNA with poly-cytosine (Poly-C) as high-affinity anchors on graphene oxide. Langmuir, 2018, 34(3), 1171-1177.
[http://dx.doi.org/10.1021/acs.langmuir.7b02812] [PMID: 28946748]
[148]
Špaček, J.; Daňhel, A.; Hasoň, S.; Fojta, M. Label-free detection of canonical DNA bases, uracil and 5-methylcytosine in DNA oligonucleotides using linear sweep voltammetry at a pyrolytic graphite electrode. Electrochem. Commun., 2017, 82, 34-38.
[http://dx.doi.org/10.1016/j.elecom.2017.07.013]
[149]
Wei, W.; Gao, C.; Xiong, Y.; Zhang, Y.; Liu, S.; Pu, Y. A fluorescence method for detection of DNA and DNA methylation based on graphene oxide and restriction endonuclease HpaII. Talanta, 2015, 131, 342-347.
[http://dx.doi.org/10.1016/j.talanta.2014.07.094] [PMID: 25281112]
[150]
Le, X.; Li, X.; Chuan, G.; Yulin, Z.; Qunfeng, Y.; Guo-Jun, Z.A. MoS2 nanosheet-based fluorescence biosensor for simple and quantitative analysis of DNA methylation. Sensors (Basel), 2016, 16(10), 1561.
[http://dx.doi.org/10.3390/s16101561] [PMID: 27669248]
[151]
Taleat, Z.; Mathwig, K.; Sudhölter, E.J.R.; Rassaei, L. Detection strategies for methylated and hypermethylated DNA. Trends Analyt. Chem., 2015, 66, 80-89.
[http://dx.doi.org/10.1016/j.trac.2014.11.013]
[152]
Mirsaidov, U.; Timp, W.; Zou, X.; Dimitrov, V.; Schulten, K.; Feinberg, A.P.; Timp, G. Nanoelectromechanics of methylated DNA in a synthetic nanopore. Biophys. J., 2009, 96(4), L32-L34.
[http://dx.doi.org/10.1016/j.bpj.2008.12.3760] [PMID: 19217843]
[153]
Timp, G.; Timp, W.; Feinberg, A.; Mirsaidov, U.; University, T.J.H. Detecting and sorting methylated DNA using a synthetic nanopore U.S. Patent 8394584, 2009.
[154]
Wang, Y.; Zhang, Y.; Guo, Y.; Kang, X.F. Fast and precise detection of DNA methylation with tetramethylammonium-filled nanopore. Sci. Rep., 2017, 7(1), 183.
[http://dx.doi.org/10.1038/s41598-017-00317-2] [PMID: 28298646]
[155]
Laszlo, A.H.; Derrington, I.M.; Brinkerhoff, H.; Langford, K.W.; Nova, I.C.; Samson, J.M.; Bartlett, J.J.; Pavlenok, M.; Gundlach, J.H. Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA. Proc. Natl. Acad. Sci. USA, 2013, 110(47), 18904-18909.
[http://dx.doi.org/10.1073/pnas.1310240110] [PMID: 24167255]
[156]
Wang, R.; Dejian, G.U.; Liu, Q. Research progress in nanopores-based sensing technology for nucleic acid detection. Materials China, 2018, 1, 059-067.
[157]
Kang, I.; Wang, Y.; Reagan, C.; Fu, Y.; Wang, M.X.; Gu, L.Q. Designing DNA interstrand lock for locus-specific methylation detection in a nanopore. Sci. Rep., 2013, 3, 2381.
[http://dx.doi.org/10.1038/srep02381] [PMID: 24135881]


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Article Details

VOLUME: 27
ISSUE: 36
Year: 2020
Published on: 04 November, 2020
Page: [6159 - 6187]
Pages: 29
DOI: 10.2174/0929867326666190903161750
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