Detection of Single-Nucleotide Polymorphism on uidA Gene of Escherichia coli by a Multiplexed Electrochemical DNA Biosensor with Oligonucleotide-Incorporated Nonfouling Surface
We report here a practical application of a multiplexed electrochemical DNA sensor for highly specific single-nucleotide polymorphism (SNP) detection. In this work, a 16-electrode array was applied with an oligonucleotide-incorporated nonfouling surfaces (ONS) on each electrode for the resistance of unspecific absorption. The fully matched target DNA templated the ligation between the capture probe assembled on gold electrodes and the tandem signal probe with a biotin moiety, which could be transduced to peroxidase-based catalyzed amperometric signals. A mutant site (T93G) in uidA gene of E. coli was analyzed in PCR amplicons. 10% percentage of single mismatched mutant gene was detected, which clearly proved the selectivity of the multiplexed electrochemical DNA biosensor when practically applied.
References
[1]
Vignal, A; Milan, D; SanCristobal, M; Eggen, A. A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol 2002, 34, 275–305, doi:10.1186/1297-9686-34-3-275. 12081799
[2]
Frazer, KA; Ballinger, DG; Cox, DR; Hinds, DA; Stuve, LL; Gibbs, RA; Belmont, JW; Boudreau, A; Hardenbol, P; Leal, SM; et al. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449, 851–861, doi:10.1038/nature06258. 17943122
[3]
Scuteri, A; Sanna, S; Chen, WM; Uda, M; Albai, G; Strait, J; Najjar, S; Nagaraja, R; Orru, M; Usala, G; et al. Genome-wide association scan shows genetic variants in the FTO gene are associated with obesity-related traits. PLoS Genet 2007, 3, e115, doi:10.1371/journal.pgen.0030115. 17658951
[4]
He, Y; Zeng, K; Gurung, AS; Baloda, M; Xu, H; Zhang, X; Liu, G. Visual detection of single-nucleotide polymorphism with hairpin oligonucleotide-functionalized gold nanoparticles. Anal. Chem 2010, 82, 7169–7177, doi:10.1021/ac101275s. 20681563
[5]
Shabo, A. Integrating genomics into clinical practice: Standards and regulatory challenges. Curr. Opin. Mol. Ther 2008, 10, 267–272. 18535934
Taton, TA; Mirkin, CA; Letsinger, RL. Scanometric DNA array detection with nanoparticle probes. Science 2000, 289, 1757–1760, doi:10.1126/science.289.5485.1757. 10976070
[8]
Duan, X; Liu, L; Wang, S. Homogeneous and one-step fluorescent allele-specific PCR for SNP genotyping assays using conjugated polyelectrolytes. Biosens. Bioelectron 2009, 24, 2095–2099, doi:10.1016/j.bios.2008.10.027. 19070477
[9]
Gaunt, TR; Hinks, LJ; Rassoulian, H; Day, IN. Manual 768 or 384 well microplate gel “dry” electrophoresis for PCR checking and SNP genotyping. Nucleic Acids Res 2003, 31, e48, doi:10.1093/nar/gng048. 12711693
[10]
Pastinen, T; Raitio, M; Lindroos, K; Tainola, P; Peltonen, L; Syvanen, AC. A system for specific, high-throughput genotyping by allele-specific primer extension on microarrays. Genome Res 2000, 10, 1031–1042, doi:10.1101/gr.10.7.1031. 10899152
[11]
Okamoto, A; Ichiba, T; Saito, I. Pyrene-labeled oligodeoxynucleotide probe for detecting base insertion by excimer fluorescence emission. J. Am. Chem. Soc 2004, 126, 8364–8365, doi:10.1021/ja049061d. 15237978
[12]
Fei, Z; Smith, LM. Analysis of single nucleotide polymorphisms by primer extension and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Rapid Commun. Mass Spectrom 2000, 14, 950–959, doi:10.1002/(SICI)1097-0231(20000615)14:11<950::AID-RCM971>3.0.CO;2-3. 10844731
[13]
Tost, J; Gut, IG. Genotyping single nucleotide polymorphisms by mass spectrometry. Mass Spectrom. Rev 2002, 21, 388–418, doi:10.1002/mas.1009. 12666148
[14]
Zhang, S; Wu, Z; Shen, G; Yu, R. A label-free strategy for SNP detection with high fidelity and sensitivity based on ligation-rolling circle amplification and intercalating of methylene blue. Biosens. Bioelectron 2009, 24, 3201–3207, doi:10.1016/j.bios.2009.03.012. 19481921
[15]
Di Giusto, DA; Wlassoff, WA; Giesebrecht, S; Gooding, JJ; King, GC. Multipotential electrochemical detection of primer extension reactions on DNA self-assembled monolayers. J. Am. Chem. Soc 2004, 126, 4120–4121, doi:10.1021/ja0319036. 15053597
[16]
Sipova, H; Springer, T; Homola, J. Streptavidin-enhanced assay for sensitive and specific detection of single nucleotide polymorphism in TP53. Anal. Bioanal. Chem 2011, 399, 2343–2350, doi:10.1007/s00216-010-3863-9. 20532484
[17]
Fan, C; Plaxco, KW; Heeger, AJ. Electrochemical interrogation of conformational changes as a reagentless method for the sequence-specific detection of DNA. Proc. Natl. Acad. Sci. USA 2003, 100, 9134–9137, doi:10.1073/pnas.1633515100. 12867594
[18]
Zhang, J; Song, S; Zhang, L; Wang, L; Wu, H; Pan, D; Fan, C. Sequence-specific detection of femtomolar DNA via a chronocoulometric DNA sensor (CDS): Effects of nanoparticle-mediated amplification and nanoscale control of DNA assembly at electrodes. J. Am. Chem. Soc 2006, 128, 8575–8580, doi:10.1021/ja061521a. 16802824
[19]
Zhang, J; Song, S; Wang, L; Pan, D; Fan, C. A gold nanoparticle-based chronocoulometric DNA sensor for amplified detection of DNA. Nat. Protoc 2007, 2, 2888–2895, doi:10.1038/nprot.2007.419. 18007624
[20]
Akagi, Y; Makimura, M; Yokoyama, Y; Fukazawa, M; Fujiki, S; Kadosaki, M; Tanino, K. Development of a ligation-based impedimetric DNA sensor for single-nucleotide polymorphism associated with metabolic syndrome. Electrochim. Acta 2006, 51, 6367–6372, doi:10.1016/j.electacta.2006.04.053.
[21]
Li, D; Song, S; Fan, C. Target-responsive structural switching for nucleic acid-based sensors. Acc. Chem. Res 2010, 43, 631–641, doi:10.1021/ar900245u. 20222738
[22]
Liu, G; Wan, Y; Gau, V; Zhang, J; Wang, L; Song, S; Fan, C. An enzyme-based E-DNA sensor for sequence-specific detection of femtomolar DNA targets. J. Am. Chem. Soc 2008, 130, 6820–6825, doi:10.1021/ja800554t. 18459781
Zhang, J; Lao, R; Song, S; Yan, Z; Fan, C. Design of an oligonucleotide-incorporated nonfouling surface and its application in electrochemical DNA sensors for highly sensitive and sequence-specific detection of target DNA. Anal. Chem 2008, 80, 9029–9033, doi:10.1021/ac801424y. 19551931
[25]
Wan, Y; Zhang, J; Liu, G; Pan, D; Wang, L; Song, S; Fan, C. Ligase-based multiple DNA analysis by using an electrochemical sensor array. Biosens. Bioelectron 2009, 24, 1209–1212, doi:10.1016/j.bios.2008.07.004. 18701273
[26]
Wan, Y; Lao, R; Liu, G; Song, S; Wang, L; Li, D; Fan, C. Multiplexed electrochemical DNA sensor for single-nucleotide polymorphism typing by using oligonucleotide-incorporated nonfouling surfaces. J. Phys. Chem. B 2010, 114, 6703–6706, doi:10.1021/jp100871u. 20415492
[27]
Lai, RY; Lagally, ET; Lee, SH; Soh, HT; Plaxco, KW; Heeger, AJ. Rapid, sequence-specific detection of unpurified PCR amplicons via a reusable, electrochemical sensor. Proc. Natl. Acad. Sci. USA 2006, 103, 4017–4021, doi:10.1073/pnas.0511325103. 16537478
[28]
Poddar, SK. Symmetric vs. asymmetric PCR and molecular beacon probe in the detection of a target gene of adenovirus. Mol. Cell. Probes 2000, 14, 25–32, doi:10.1006/mcpr.1999.0278. 10722789
