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DNA聚合酶与引物/模板的相互作用对PCR效率的影响 |
杨奇奇1, 张俊威1, 朱坚1,2, 刘建平1, 黄强1 |
1 复旦大学遗传工程国家重点实验室 生命科学学院 上海 200433;
2 上海美迪西生物医药有限公司 上海 201299 |
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DNA Polymerase Binding to the Primer/template Duplex Affects the Efficiency of PCR |
YANG Qi-qi1, ZHANG Jun-wei1, ZHU Jian1,2, LIU Jian-ping1, HUANG Qiang1 |
1 State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai 200433, China;
2 Shanghai Medicilon Inc., Shanghai 201299, China |
引用本文:
杨奇奇, 张俊威, 朱坚, 刘建平, 黄强. DNA聚合酶与引物/模板的相互作用对PCR效率的影响[J]. 中国生物工程杂志, 2014, 34(5): 6-13.
YANG Qi-qi, ZHANG Jun-wei, ZHU Jian, LIU Jian-ping, HUANG Qiang. DNA Polymerase Binding to the Primer/template Duplex Affects the Efficiency of PCR. China Biotechnology, 2014, 34(5): 6-13.
链接本文:
https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20140502
或
https://manu60.magtech.com.cn/biotech/CN/Y2014/V34/I5/6
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[1] Saiki R K, Gelfand D H, Stoffel S, et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science, 1988, 239 (4839): 487-491.
[2] Terpe K, Overview of thermostable DNA polymerases for classical PCR applications: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biot, 2013, 97 (24): 10243-10254.
[3] Schochetman G, Ou C Y, Jones W K, Polymerase chain reaction. J Infect Dis, 1988, 158 (6): 1154-1157.
[4] Dieffenbach C, Lowe T, Dveksler G. General concepts for PCR primer design. Genome Res, 1993, 3 (3): S30-S37.
[5] Burpo F J. A critical review of PCR primer design algorithms and crosshybridization case study. Biochemistry, 2001, 218 1-12.
[6] Han J. Polymerase Preference Index. US Patent,A1,2012100089, 2012-07-26.
[7] Li Y, Korolev S, Waksman G, Crystal structures of open and closed forms of binary and ternary complexes of the large fragment of Thermus aquaticus DNA polymerase I: structural basis for nucleotide incorporation, EMBO J., 1998, 17 (24): 7514-7525.
[8] Eom S H, Wang J, Steitz T A. Structure of Taq polymerase with DNA at the polymerase active site. Nature, 1996, 382 (6588): 278-281.
[9] Eswar N, Webb B, Marti-Renom M A, et al. Comparative protein structure modeling using Modeller. Curr. Protoc. Bioinformatics, 2006, 15:561-563.
[10] SaIi A, Blundell T. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol, 1993, 234 (3): 779-815.
[11] Chu S W, Noyes M B, Christensen R G, et al. Exploring the DNA-recognition potential of homeodomains. Genome Res, 2012, 22 (10): 1889-1898.
[12] Case D A, Cheatham T E, Darden T, et al. The Amber biomolecular simulation programs. J Comput Chem, 2005, 26 (16): 1668-1688.
[13] Hornak V, Abel R, Okur A, et al. Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins, 2006, 65 (3): 712-725.
[14] Liu L A, Bradley P. Atomistic modeling of protein-DNA interaction specificity: progress and applications. Curr Opin Struc Biol, 2012, 22 (4): 397-405.
[15] Hou T, Wang J, Li Y, et al. Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model, 2010, 51 (1): 69-82.
[16] Huang Q, Korte T, Rachakonda PS, et al. Energetics of the loop-to-helix transition leading to the coiled-coil structure of influenza virus hemagglutinin HA2 subunits. Proteins, 2009, 74 (2): 291-303.
[17] Huang Q, Herrmann A. Calculating pH-dependent free energy of proteins by using Monte Carlo protonation probabilities of ionizable residues. Protein Cell, 2012, 3 (3): 230-238.
[18] Saito K, Hamano K, Nakagawa M, et al. Conformational analysis of human serum albumin and its non-enzymatic glycation products using monoclonal antibodies. J Biochem, 2011, 149 (5): 569-580.
[19] Arraiano C M, Cruz A A, Kushner S R. Analysis of the in vivo decay of the Escherichia coli dicistronic pyrF-orfF transcript: evidence for multiple degradation pathways. J Mol Biol, 1997, 268 (2): 261-272.
[20] Schneider C A, Rasband W S, Eliceiri K W. NIH Image to ImageJ: 25 years of image analysis. Nat Methods, 2012, 9 (7): 671-675.
[21] Golosov A A, Warren J J, Beese L S, et al. The mechanism of the translocation step in DNA replication by DNA polymerase I: a computer simulation analysis. Structure, 2010, 18 (1): 83-93.
[22] Steitz T A. DNA-and RNA-dependent DNA polymerases. Curr Opin Struc Biol, 1993, 3 (1): 31-38.
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