Nanomaterials-based polymerase chain reactions for DNA detection

Current Organic Chemistry

Volumn 15, Issue 4, 2011, Pages 486-497

  Pan, Dun ^a   Wen, Yangqin ^a   Mi, Lijuan ^a   Fan, Chunhai ^a   Hu, Jun ^a  

^a SHANGHAI INSTITUTE OF APPLIED PHYSICS   (China)

Author keywords

Carbon nanomaterial; DNA; DNA detection; Extend rate; Hot start; Mechanism; Metal nanoparticle; Metal oxide nanostructure; Nanomaterial; Optimization; PCR; Polymer; Polymerase; QDs; Sensitivity; Specificity; Yields

Indexed keywords

CARBON; CHAINS; DNA; METALLIC COMPOUNDS; NANOSTRUCTURED MATERIALS; POLYMERASE CHAIN REACTION; SEMICONDUCTOR QUANTUM DOTS;

CARBON NANO-MATERIALS; DNA DETECTION; EXTEND RATE; HOT-START; METAL OXIDE NANOSTRUCTURE; METAL-OXIDE; OPTIMISATIONS; OXIDE NANOSTRUCTURES; POLYMERASE; QD; SENSITIVITY; SPECIFICITY; YIELD;

METAL NANOPARTICLES;

EID: 79551675070     PISSN: 13852728     EISSN: None     Source Type: Journal    
DOI: 10.2174/138527211794474447     Document Type: Review

References (84)

1. Mullis, K.B; Faloona, F.A. Specific synthesis of DNA in vitro via a polymerase- catalyzed chain reaction. Methods Enzymol., 1987, 155, 335-350.
2. Saiki, R.K.; Charf, S., Faloona, F.; Mullis, K.B. Enzymatic amplification of beta-globin genomic sequences and restriction site analysis for diagnosis of sickle cell anemia. Science, 1985, 230, 1350-1354.
3. McPherson, M.; Quirke, P.; Taylor, G. PCR, a practical approach, (Eds.: Rickwood, D.; Hames, B. D.), Oxford University Press, Oxford, 1991.
4. Shizuya, H.; Birren, B.; Kim, U-J.; Mancino, V.; Slepak, T.; Tachiiri, Y.; Simon, M. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc. Natl. Acad. Sci. U. S. A., 1992, 89, 8794-8797.
5. Rubin, W.M.; Andrews, K.A.; Kan, Y.W. Newborn screening by DNA analysis of dried blood spots. Hum. Genet.,1989, 82, 134-136.
6. Williams, C.; Williamson, R.; Coutelle, C.; Loeffler, F.; Smith, J.; Ivinson, A. Same-day, first-trimester antenatal diagnosis for cystic fibrosis by gene amplification. Lancet, 1988, 332, 102-103.
7. Jiang, X.; Huang, P.W.; Zhong, W. M.; Farkas, T.; Cubitt, D. W.; Matson, D. O. Design and evaluation of a primer pair that detects both Norwalk- and Sapporo-like caliciviruses by RT-PCR. J. Virol. Methods, 1999, 83, 145-154.
8. Paran, I.; Michelmore, R.W. Development of reliable PCR-based markers linked to downy mildew resistance genes in lettuce. Ther. Appl. Genet., 1993, 85, 985-993.
9. Reed, J. Z.; Tollit, D. J.; Thompson, P.M.; Amos, W. Molecular scatology: the use of molecular genetic analysis to assign species, sex and individual identity to seal faeces. Mol. Ecol., 1997, 6, 225-234.
10. Belkum, A. DNA fingerprinting of medically important microorganisms by use of PCR. Clin. Microbiol. Rev., 1994, 7, 174-184.
11. Jobling, M. A.; Gill, P. Encoded evidence: DNA in forensic analysis. Nat. Rev. Genet., 2004, 5, 739-754.
12. Walsh, P.; Metzger, D.; Higuchi, R. Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques, 1991, 10, 506-513.
13. LavalliÉE, F.; Salvas, Y.; Lamy, S.; Thomas, D. Y.; Degré, R.; Dulau, L. PCR and DNA fingerprinting used as quality control in the production of wine yeast strains. Am. J. Enol. Vitic., 1994, 45, 86-91.
14. DiDomenico, N.; Link, H.; Knobel, R.; Caratsch, T.; Weschler, W.; Loewy, Z.; Rosenstraus, M. Cobas amplicor: fully automated RNA and DNA amplification and detection system for routine diagnostic PCR. Clin. Chem., 1996, 42, 1915-1923.
15. Chien, A.; Edgar, D.B.; Trela, J. M. Deoxyribonucleic acid polymerase from the extreme thermophile thermus aquaticus. J. Bacteriol., 1976, 127, 1550-1557.
16. Daniel, M-C.; Astruc, D. Gold nanoparticles: assembly, supramolecular chemistry, quantum-size-related properties, and applications toward biology, catalysis, and nanotechnology. Chem. Rev. 2004, 104, 293-346.
17. Rao, C.N.R.; Cheetham, A. K. Science and technology of nanomaterials: current status and future prospects. J. Mater. Chem., 2001, 11, 2887-2894.
18. Salata, O.V. Applications of nanoparticles in biology and medicine. J. Nanobiotechnology, 2004, 2.
19. De, M.; Ghosh, P.S.; Rotello, V.M. Applications of nanoparticles in biology. Adv. Mater., 2008, 20, 4225-4241.
20. Brigger, I.; Dubernet, C.; Couvreur, P. Nanoparticles in cancer therapy and diagnosis. Adv. Drug Deliv. Rev., 2002, 54, 631-651.
21. Xu, Z.P.; Zeng, Q.H.; Lu, G.Q.; Yu, A.B. Inorganic nanoparticles as carriers for efficient cellular delivery. Chem. Eng. Sci., 2006, 61, 1027-1040.
22. Penn, S.G.; He, L.; Natan, M.J. Nanoparticles for bioanalysis. Curr. Opin. Chem. Biol., 2003, 7, 609-615.
23. Menintz, I.; Uyeda, H.T.; Goldman, E. R.; Mattoussi, H. Quantum dot bioconjugates for imaging, labelling and sensing. Nat. Mater, 2005, 4, 435-446.
24. Cui, D.; Tian, F.; Kong, Y.; Titushikin, I.; Gao, H. Effects of single-walled carbon nanotubes on the polymerase chain reaction. Nanotechnology, 2004, 15, 154-157.
25. Li, H.; Huang, J.; Lv, J.; An, H.; Zhang, X.; Zhang, Z.; Fan, C.; Hu, J. Nanoparticle PCR: nanogold-assisted PCR with enhanced specificity. Angew. Chem. Int. Ed., 2005, 44, 2-5.
26. Li, M.; Lin, Y-C.; Wu, C-C. Enhancing the efficiency of a PCR using gold nanoparticles. Nucleic. Acids. Res., 2005, 33, e184.
27. Huang, S-H.; Yang, T-C.; Tsai, M-H.; Tsai, I-S.; Lu, H-C.; Chuang, P-H.; Wan, L.; Lin, Y-J.; Lai, C-H.; Lin, C-W. Gold nanoparticle-based RT-PCR and real-time quantitative RT-PCR assays for detection of Japanese encephalitis virus. Nanotechnology, 2008, 19, 405101-405108.
28. Mi, L.; Wen, Y.; Pan, D.; Wang, Y.; Fan, C.; Hu, J. Modulation of DNA polymerases with gold nanoparticles and their applications in hot-start PCR. Small, 2009, 22, 2597-2600.
29. Wang, Q.; Li, J.; Cao, X.; Wang, Z. Silver nanoparticles enhance the specificity of repeated long PCR amplification. J. Tianjin Univ. Sci. Technol. (Chinese), 2007, 22, 1-5.
30. Ma, L.; He, S.; Huang, J.; Cao, L.; Yang, F.; Li, L. Maximizing specificity and yield of PCR by the quamtum dot itself rather than property of the quantum dot surface. Biochimie, 2009, 91, 969-973.
31. Nie, L.; Gao, L.; Yan, X.; Wang, T. Functionalized tetrapod-like ZnO nanostructures for plasmid DNA purification, polymerase chain reaction and delivery. Nanotechnology, 2007, 18, 015101-015106.
32. Zhang, Z.; Shen, C.; Wang, M.; Han, H.; Cao, X. Aqueous suspension of carbon nanotubes enhances the specificity of long PCR. BioTechniques, 2008, 44, 537-545.
33. Zhang, Z.; Wang, M.; An, H. An aqueous suspension of carbon nanopowder enhances the efficiency of a polymerase chain reaction. Nanotechnology, 2007, 18, 355706-355711.
34. 60 affects DNA replication in vitro by decreasing the melting temperature of DNA templates. Carbon, 2009, 47, 1457-1465.
35. Zhang, L.; Meng, L.; Lu, X.; Liu, Y. Novel amphiphilic poly(Nvinylpyrrolidone) block copolymer: aggregative behavior and interaction with DNA. Macromol. Symp., 2008, 261, 182-189.
36. Cao, X.; Shi, X.; Yang, W.; Zhang, X.; Fan, C.; Hu, J. Enhanced specificity and efficiency of polymerase chain reactions using poly(amidoamine) dendrimers and derivatives. Analyst, 2009, 134, 87-92.
37. Murphy, C.J.; Gole, A.M.; Stone, J.W.; Sisco, P.N.; Alkilany, A.M.; Goldsmith, E.C.; Baxter, S. C. Gold nanoparticles in biology: beyond toxicity to cellular imaging. Acc. Chem. Res., 2008, 41, 1721-1730.
38. Brust, M.; Walker, M.; Bethell, D.; Schiffrin, D.J.; Whyman, R. Synthesis of thiol-derivatised gold nanoparticles in a two-phase liquid-liquid system. J. Chem. Soc., Chem. Commun., 1994, 801-802.
39. Spatz, J. P.; Möβmer, S.; Möiler, M. Mineralization of gold nanoparticles in a block copolymer microemulsion. Chem. Eur. J, 1996, 2, 1552-1555.
40. Hernández, J.; Solla-Gullón, J.; Herrero, E. Gold nanoparticles synthesized in a water-in-oil microemulsion: electrochemical characterization and effect of the surface structure on the oxygen reduction reaction. J. Electroanal. Chem., 2004, 574, 185-196.
41. Turkevich, J.; Stevenson, P.C.; Hillier, J. A study of the nucleation and growth processes in the synthesis of colloidal gold. Discuss. Faraday Soc., 1951, 11, 55-57.
42. Frens, G. Controlled nucleation for the regulation of the particle size in monodisperse gold suspensions. Nat. Phys. Sci., 1973, 241, 20-22.
43. Pan, J.; Li, H.; Cao, X.; Huang, J.; Zhang, X.; Fan, C.; Hu, J. Nanogoldassisted multi-round polymerase chain reaction (PCR). J. Nanosci. Nanotechnol., 2007, 7, 4428-4433.
44. Sumiyoshi, H.; Mori, C.; Fuke, I.; Morita, K.; Kuhara, S.; Kondou, J.; Kikuchi, Y.; Nagamatu, H.; Igarashi, A. Complete nucleotide sequence of the Japanese encephalitis virus genome RNA. Virology, 1987, 161, 497-510.
45. Alivisatos, A.P. Perspectives on the physical chemistry of semiconductor nanocrystals. J. Phys. Chem., 1996, 100, 13226-13239.
46. Sutherland, A.J. Quantum dots as luminescent probes in biological systems. Curr. Opin. Solid. State. Mater. Sci., 2002, 6, 365-370.
47. Alivisatos, A.P. Semiconductor clusters, nanocrystals, and quantum dots. Science, 1996, 271, 933-937.
48. Banin, U.; Cao, Y.; Katz, D.; Millo, O. Identification of atomic-like electronic states in indium arsenide nanocrystal quantum dots. Nature, 1999, 400, 542-544.
49. Nirmal, M.; Brus, L. Luminescence photophysics in semiconductor nanocrystals. Acc. Chem. Res., 1999, 32, 404-414.
50. Bailey, R.E.; Smith, A.M.; Nie, S. Quantum dots in biology and medicine. Physica E, 2004, 25, 1-12.
51. Wan, Q.; Yu, K.; Wang, T.H.; Lin, V. L. Low-field electron emission from tetrapod-like ZnO nanostructures synthesized by rapid evaporation. Appl. Phys. Lett., 2003, 83, 2253.
52. Vayssieres, L. Growth of arrayed nanorods and nanowires of ZnO from aqueous solutions. Adv. Mater., 2003, 13, 464-466.
53. 2 nanoparticles on DNA synthesis in vitro. Sci. Chin. Ser. B-Chem., 2008, 51, 367-372.
54. Ke, P. C.; Qiao, R. Carbon nanomaterials in biological systems. J. Phys. Condens. Matter., 2007, 19, 373101-373125.
55. Jia, G.; Wang, H.; Yan, L.; Wang, X.; Pei, R.; Yan, T.; Zhao, Y.; Wang, X. Cycotoxicity of carbon nanomaterials: single-wall nanotube, multi-wall nanotube, and fullerene. Environ. Sci. Technol., 2005, 39, 1378-1383.
56. 60: a new form of carbon. Nature, 1990, 347, 354-358.
57. Bachmann, B.; Luke, W.; Hunsmann, G. Improvement of PCR amplified DNA sequencing with the aid of detergents. Nucleic. Acids. Res., 1990, 18, 1309.
58. Sarkar, G.; Kapelner, S.; Sommer, S.S. Formamide can dramatically improve the specificity of PCR. Nucleic. Acids. Res., 1990, 18, 7465.
59. Seto, D. An improved method for sequencing double stranded plasmid DNA from minipreps using DMSO and modified template preparation. Nucleic. Acids. Res., 1990, 18, 5905-5906.
60. Chevet, E.; Lemaê, G.; Katinka, M.D. Low concentrations of tetramethylammonium chloride increase yield and specificity of PCR. Nucleic. Acids. Res., 1995, 23, 3343-3344.
61. Hengen, P.N. Methods and reagents: optimizing multiplex and LA-PCR with betaine. Trends Biochem. Sci., 1997, 22, 225-226.
62. Nagai, M.; Yoshida, A.; Sato, N. Additive effects of bovine serum albumin, dithiothreitol and glycerol on PCR. Biochem. Mol. Biol. Int., 1998, 44, 157-163.
63. Hébert, B.; Bergeron, J.; Potworowski, E.F.; Tijssen, P. Increased PCR sensitivity by using paraffin wax as a reaction mix overlay. Mol. Cell. Probes, 1993, 7, 249-252.
64. Kaijalainen, S.; Karhunen, P.J.; Lalu, K.; Lindström, K. An alternative hot start technique for PCR in small volumes using beads of wax-embedded reaction components dried in trehalose. Nucleic Acids Res., 1993, 21, 2959-2960.
65. Brich, D.E. Simplified hot start PCR. Nature, 1996, 381, 445-446.
66. Kermekchiev, M.B.; Tzekov, A.; Barnes, W.M. Cold-sensitive mutants of Taq DNA polymerase provide a hot start for PCR. Nucleic. Acids. Res., 2003, 31, 6139-6147.
67. Kellogg, D.E.; Rybalkin, I.; Chen, S.; Mukhamedova, N.; Vlasik, T.; Siebert, P.D.; Chenchik, A. TaqStart antibody: 'hot start' PCR facilitated by a neutralizing monoclonal antibody directed against Taq DNA polymerase. Biotechniques, 1994, 16, 1134-1137.
68. Scalice, E.R.; Sharkey, D.J.; Daiss, J.L. Monoclonal antibodies prepared against the DNA polymerase from Thermus aquaticus are potent inhibitors of enzyme activity. J. Immunol. Methods, 1994, 172, 147-163.
69. Sharkey, D.J.; Scalice, E.R.; Christy, K.G.; Atwood, S.M.; Daiss, J.L. Antibodies as thermolabile switches: high temperature triggering for the polymerase chain reaction. Biotechnology, 1994, 12, 506-509.
70. Lundberg, K.S.; Schoemaker, D.D.; Adems, M.W.W. High-fidelity amplification using a thermostable DNA polymerase isolated from Pyrococcus furiosus. Gene, 1991, 108, 1-6.
71. Barnes, W.M.; Rowlyk, K.R. Magnesium precipitate hot start method for PCR. Mol. Cell. Probes, 2002, 16, 167-171.
72. Ignatov, K.B.; Miroshnikov, A.I.; Kramarov, V.M. A new approach to enhanced PCR specificity. Russ. J. Bioorg. Chem., 2003, 29, 368-371.
73. Huang, J.; Zhang, X.; Wang, C.; Wang, L.; Li, H.; Cao, X.; Zhang, A.; Li, X.; Fan, C.; Hu, J. Size and surface of gold nanoparticles (AuNPs) in nanogold-assisted PCR. Surf. Revi. Lett., 2008, 15, 752-762.
74. Wan, W.; Yeow, J.T. The effects of gold nanoparticles with different sizes on polymerase chain reaction efficiency. Nanotechnology, 2009, 20, 325702-325706.
75. Chase, J. W, Williams, K.R. Single stranded DNA binding proteins required for DNA replication. Annu. Rev. Biochem., 1986, 55, 103-136.
76. Nielson, K.B.; Mathur, E. J. Method for producing primed nucleic acid templates. US Patent, 1997, No. 5646019.
77. Kumar, D.H.; Patel, H.E.; Kumar, V.R.R.; Sundararajan, T.; Pradeep, T.; Das, S.K. Model for Heat Conduction in Nanofluids. Phys. Rev. Lett., 2004, 93, 144301.
78. Keblinski, P.; Phillpot, S.R.; Choi, S. U. S. Mechanism of heat flow in suspension of nano-sized particles (nanofluids). Int. J. Heat Mass Transf., 2002, 45, 855-863.
79. Zhu, H.; Mi, L.; Chen, S.; Wang, W.; Yao, S. Study on the interaction of colloidal gold with Taq DNA polymerase. Chin. J. Chem., 2007, 25, 1233-1237.
80. Yi, C.; Fong, C-C.; Chen, W.; Qi, S.; Tzang, C-H.; Lee, S-T.; Yang, M. Interactions between carbon nanotubes and DNA polymerase and restriction endonucleases. Nanotechnology, 2007, 18, 025102-025107.
81. Binh, V.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.
82. Yi, C.; Fong, C-C.; Chen, W.; Qi, S.; Lee, S-T.; Yang, M. Inhibition of biochemical reactions by silicon nanowires through modulating enzyme activities. ChemBioChem., 2007, 8, 1225-1229.
83. Mi, L.; Zhu, H.; Zhang, X.; Hu, J.; Fan, C. Mechanism of the interaction between Au nanoparticles and polymerase in nanoparticle PCR. Chin. Sci. Bull., 2007, 52, 2345-2349.
84. Von-Hippel, P.H.; Fairfield, F.R.; Dolejsi, M.K. On the processivity of polymerases. Ann. N.Y. Acad. Sci., 1994, 726, 118-131.