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Isothermal methods, such as helicase-dependent amplification (HDA), have an advantage over polymerase chain reaction for DNA amplification owing to their ease of operation. Here, we developed a new HDA method that is nanoparticle-assisted, termed nanoHDA. This method uses gold nanoparticles (AuNPs) to improve the sensitivity and specificity of the isothermal method. In HDA, the denaturation of DNA templates is mediated by helicases, but this method is limited by the low denaturation efficiency of helicases. In this report, AuNPs with preferential affinity for single-stranded DNA (ssDNA) were utilized to improve the denaturation efficiency of helicases. The same affinity property of nanoparticles can also enhance specificity by suppressing primer-dimer formation. This nanoHDA method was employed to genotype the KRAS gene in genomic DNA samples from colorectal cancer patients, as achieved by the hybridization of nanoHDA amplicons using the NanoBioArray chip.
Saiki, R. K.; Scharf, S.; Faloona, F.; Mullis, K. B.; Horn, G. T.; Erlich, H. A.; Arnheim, N. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science 1985, 230, 1350–1354.
Notomi, T.; Okayama, H.; Masubuchi, H.; Yonekawa, T.; Watanabe, K.; Amino, N.; Hase, T. Loop-mediated isothermal amplification of DNA. Nucleic Acids Res. 2000, 28, e63.
Lizardi, P. M.; Huang, X. H.; Zhu, Z. R.; Bray-Ward, P.; Thomas, D. C.; Ward, D. C. Mutation detection and singlemolecule counting using isothermal rolling-circle amplification. Nat. Genet. 1998, 19, 225–232.
Kievits, T.; van Gemen, B.; van Strijp, D.; Schukkink, R.; Dircks, M.; Adriaanse, H.; Malek, L.; Sooknanan, R.; Lens, P. NASBATM isothermal enzymatic in vitro nucleic acid amplification optimized for the diagnosis of HIV-1 infection. J. Virol. Methods 1991, 35, 273–286.
Walker, G. T.; Fraiser, M. S.; Schram, J. L.; Little, M. C.; Nadeau, J. G.; Malinowski, D. P. Strand displacement amplification—An isothermal, in vitro DNA amplification technique. Nucleic Acids Res. 1992, 20, 1691–1696.
Vincent, M.; Xu, Y.; Kong, H. M. Helicase-dependent isothermal DNA amplification. EMBO Rep. 2004, 5, 795–800.
Hicke, B.; Pasko, C.; Groves, B.; Ager, E.; Corpuz, M.; Frech, G.; Munns, D.; Smith, W.; Warcup, A.; Denys, G. et al. Automated detection of toxigenic Clostridium difficile in clinical samples: Isothermal tcdB amplification coupled to array-based detection. J. Clin. Microbiol. 2012, 50, 2681–2687.
Andresen, D.; von Nickisch-Rosenegk, M.; Bier, F. F. Helicase dependent OnChip-amplification and its use in multiplex pathogen detection. Clin. Chim. Acta 2009, 403, 244–248.
Chow, W. H. A.; McCloskey, C.; Tong, Y. H.; Hu, L.; You, Q. M.; Kelly, C. P.; Kong, H. M.; Tang, Y.-W.; Tang, W. Application of isothermal helicase-dependent amplification with a disposable detection device in a simple sensitive stool test for toxigenic Clostridium difficile. J. Mol. Diagn. 2008, 10, 452–458.
Gill, P.; Alvandi, A.-H.; Abdul-Tehrani, H.; Sadeghizadeh, M. Colorimetric detection of Helicobacter pylori DNA using isothermal helicase-dependent amplification and gold nanoparticle probes. Diagn. Microbiol. Infect. Dis. 2008, 62, 119–124.
Goldmeyer, J.; Li, H. J.; McCormac, M.; Cook, S.; Stratton, C.; Lemieux, B.; Kong, H. M.; Tang, W.; Tang, Y.-W. Identification of Staphylococcus aureus and determination of methicillin resistance directly from positive blood cultures by isothermal amplification and a disposable detection device. J. Clin. Microbiol. 2008, 46, 1534–1536.
Kivlehan, F.; Mavré, F.; Talini, L.; Limoges, B.; Marchal, D. Real-time electrochemical monitoring of isothermal helicase-dependent amplification of nucleic acids. Analyst 2011, 136, 3635–3642.
Mahalanabis, M.; Do, J.; ALMuayad, H.; Zhang, J. Y.; Klapperich, C. M. An integrated disposable device for DNA extraction and helicase dependent amplification. Biomed. Microdevices 2010, 12, 353–359.
Motré, A.; Li, Y.; Kong, H. M. Enhancing helicase-dependent amplification by fusing the helicase with the DNA polymerase. Gene 2008, 420, 17–22.
Torres-Chavolla, E.; Alocilja, E. C. Nanoparticle based DNA biosensor for tuberculosis detection using thermophilic helicase-dependent isothermal amplification. Biosens. Bioelectron. 2011, 26, 4614–4618.
Ramalingam, N.; San, T. C.; Kai, T. J.; Mak, M. Y. M.; Gong, H.-Q. Microfluidic devices harboring unsealed reactors for real-time isothermal helicase-dependent amplification. Microfluid. Nanofluid. 2009, 7, 325–336.
Li, Y.; Jortani, S. A.; Ramey-Hartung, B.; Hudson, E.; Lemieux, B.; Kong, H. M. Genotyping three SNPs affecting warfarin drug response by isothermal real-time HDA assays. Clin. Chim. Acta 2011, 412, 79–85.
Zhou, W.; Gao, X.; Liu, D.; Chen, X. Gold nanoparticles for in vitro diagnostics. Chem. Rev. 2015, 115, 10575–10636.
Saha, K.; Agasti, S. S.; Kim, C.; Li, X. N.; Rotello, V. M. Gold nanoparticles in chemical and biological sensing. Chem. Rev. 2012, 112, 2739–2779.
Sedighi, A.; Li, P. C. H.; Pekcevik, I. C.; Gates, B. D. A proposed mechanism of the influence of gold nanoparticles on DNA hybridization. ACS Nano 2014, 8, 6765–6777.
Sedighi, A.; Li, P. C. H. KRAS gene codon 12 mutation detection enabled by gold nanoparticles conducted in a nanobioarray chip. Anal. Biochem. 2014, 448, 58–64.
Sedighi, A.; Whitehall, V.; Li, P. C. H. Enhanced destabilization of mismatched DNA using gold nanoparticles offers specificity without compromising sensitivity for nucleic acid analyses. Nano Res. 2015, 8, 3922–3933.
Yuce, M.; Kurt, H.; Mokkapati, V. R. S. S.; Budak, H. Employment of nanomaterials in polymerase chain reaction: Insight into the impacts and putative operating mechanisms of nano-additives in PCR. RSC Adv. 2014, 4, 36800–36814.
Lou, X. H.; Zhang, Y. Mechanism studies on nanoPCR and applications of gold nanoparticles in genetic analysis. ACS Appl. Mater. Interfaces 2013, 5, 6276–6284.
Li, H. K.; Huang, J. H.; Lv, J. H.; An, H. J.; Zhang, X. D.; Zhang, Z. Z.; Fan, C. H.; Hu, J. Nanoparticle PCR: Nanogold-assisted PCR with enhanced specificity. Angew. Chem. Int. Ed. 2005, 44, 5100–5103.
Li, M.; Lin, Y.-C.; Wu, C.-C.; Liu, H.-S. Enhancing the efficiency of a PCR using gold nanoparticles. Nucleic Acids Res. 2005, 33, e184.
Vu, B. V.; Litvinov, D.; Willson, R. C. Gold nanoparticle effects in polymerase chain reaction: Favoring of smaller products by polymerase adsorption. Anal. Chem. 2008, 80, 5462–5467.
Mi, L. J.; Wen, Y. Q.; Pan, D.; Wang, Y. H.; Fan, C. H.; Hu, J. Modulation of DNA polymerases with gold nanoparticles and their applications in hot-start PCR. Small 2009, 5, 2597–2600.
Jimeno, A.; Messersmith, W. A.; Hirsch, F. R.; Franklin, W. A.; Eckhardt, S. G. KRAS mutations and sensitivity to epidermal growth factor receptor inhibitors in colorectal cancer: Practical application of patient selection. J. Clin. Oncol. 2009, 27, 1130–1136.
Whitehall, V.; Tran, K.; Umapathy, A.; Grieu, F.; Hewitt, C.; Evans, T.-J.; Ismail, T.; Li, W. Q.; Collins, P.; Ravetto, P. et al. A multicenter blinded study to evaluate KRAS mutation testing methodologies in the clinical setting. J. Mol. Diagn. 2009, 11, 543–552.
Sedighi, A.; Li, P. C. H. Gold nanoparticle assists SNP detection at room temperature in the nanoBioArray chip. Int. J. Mater. Sci. Eng. 2013, 1, 45–49.
Wang, L.; Li, P. C. H. Flexible microarray construction and fast DNA hybridization conducted on a microfluidic chip for greenhouse plant fungal pathogen detection. J. Agric. Food Chem. 2007, 55, 10509–10516.
Wang, L.; Li, P. C. H. Optimization of a microfluidic microarray device for the fast discrimination of fungal pathogenic DNA. Anal. Biochem. 2010, 400, 282–288.
Wang, L.; Li, P. C. H. Gold nanoparticle-assisted single base-pair mismatch discrimination on a microfluidic microarray device. Biomicrofluidics 2010, 4, 032209.
Chim, W.; Li, P. C. H. Repeated capillary electrophoresis separations conducted on a commercial DNA chip. Anal. Methods 2012, 4, 864–868.
Tong, Y. H.; Lemieux, B.; Kong, H. M. Multiple strategies to improve sensitivity, speed and robustness of isothermal nucleic acid amplification for rapid pathogen detection. BMC Biotechnol. 2011, 11, 50.
Chen, C. L.; Wang, W. J.; Ge, J.; Zhao, X. S. Kinetics and thermodynamics of DNA hybridization on gold nanoparticles. Nucleic Acids Res. 2009, 37, 3756–3765.
Cho, K.; Lee, Y.; Lee, C.-H.; Lee, K.; Kim, Y.; Choi, H.; Ryu, P.-D.; Lee, S. Y.; Joo, S.-W. Selective aggregation mechanism of unmodified gold nanoparticles in detection of single nucleotide polymorphism. J. Phys. Chem. C 2008, 112, 8629–8633.
Wan, W. J.; Yeow, J. T. W. The effects of gold nanoparticles with different sizes on polymerase chain reaction efficiency. Nanotechnology 2009, 20, 325702.
Mandal, S.; Hossain, M.; Muruganandan, T.; Kumar, G. S.; Chaudhuri, K. Gold nanoparticles alter Taq DNA polymerase activity during polymerase chain reaction. RSC Adv. 2013, 3, 20793–20799.
An, L. X.; Tang, W.; Ranalli, T. A.; Kim, H.-J.; Wytiaz, J.; Kong, H. M. Characterization of a thermostable UvrD helicase and its participation in helicase-dependent amplification. J. Biol. Chem. 2005, 280, 28952–28958.
Zhao, W. T.; Lee, T. M. H.; Leung, S. S. Y.; Hsing, I.-M. Tunable stabilization of gold nanoparticles in aqueous solutions by mononucleotides. Langmuir 2007, 23, 7143–7147.
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