DNA polymerases engineered by directed evolution to incorporate non-standard nucleotides

被引：48
作者：
Laos, Roberto [1 ]
Thomson, J. Michael [1 ]
Benner, Steven A. [1 ]
机构：
[1] Fdn Appl Mol Evolut, Gainesville, FL 32601 USA
来源：
FRONTIERS IN MICROBIOLOGY | 2014年 / 5卷
关键词：
DNA polymerases; non-standard nucleotides; AEGIS; directed evolution; CSR; protein engineering; UNNATURAL BASE-PAIR; THERMUS-AQUATICUS; CRYSTAL-STRUCTURE; EXTREME THERMOPHILE; PROTEIN EVOLUTION; GENETIC ALPHABET; STRUCTURAL BASIS; LARGE FRAGMENT; IN-VITRO; ENZYMATIC INCORPORATION;
D O I：
10.3389/fmicb.2014.00565
中图分类号：
Q93 [微生物学];
学科分类号：
071005 ; 100705 ;
摘要：
DNA polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. However, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. The focus of this review is on non-standard nucleotides that expand the genetic "alphabet." This review focuses on experiments that, by directed evolution, have created variants of DNA polymerases that are better able to accept unnatural nucleotides. In many cases, an analysis of past evolution of these polymerases (as inferred by examining multiple sequence alignments) can help explain some of the mutations delivered by directed evolution.
引用
收藏
页数：14
相关论文
共 121 条
[1]   Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries [J].
Aird, Daniel ;
Ross, Michael G. ;
Chen, Wei-Sheng ;
Danielsson, Maxwell ;
Fennell, Timothy ;
Russ, Carsten ;
Jaffe, David B. ;
Nusbaum, Chad ;
Gnirke, Andreas .
GENOME BIOLOGY, 2011, 12 (02)
[2]  
Amitai G, 2007, HFSP J, V1, P67, DOI [10.2976/1.2739115, 10.2976/1.2739115/10.2976/1]
[3]   Optimal conditions to use Pfu exo- DNA polymerase for highly efficient ligation-mediated polymerase chain reaction protocols [J].
Angers, M ;
Cloutier, JF ;
Castonguay, A ;
Drouin, R .
NUCLEIC ACIDS RESEARCH, 2001, 29 (16)
[4]   Replisome-mediated DNA replication [J].
Benkovic, SJ ;
Valentine, AM ;
Salinas, F .
ANNUAL REVIEW OF BIOCHEMISTRY, 2001, 70 :181-208
[5]   Understanding nucleic acids using synthetic chemistry [J].
Benner, SA .
ACCOUNTS OF CHEMICAL RESEARCH, 2004, 37 (10) :784-797
[6]   PREDICTED SECONDARY STRUCTURE FOR THE SRC HOMOLOGY-3 DOMAIN [J].
BENNER, SA ;
COHEN, MA ;
GERLOFF, D .
JOURNAL OF MOLECULAR BIOLOGY, 1993, 229 (02) :295-305
[7]  
Berdis AJ, 2014, NUCLEIC ACIDS MOL BI, V30, P109, DOI 10.1007/978-3-642-39796-7_5
[8]   Low-fidelity Pyrococcus furiosus DNA polymerase mutants useful in error-prone PCR -: art. no. e176 [J].
Biles, BD ;
Connolly, BA .
NUCLEIC ACIDS RESEARCH, 2004, 32 (22) :e176
[9]   Neutral genetic drift can alter promiscuous protein functions, potentially aiding functional evolution [J].
Bloom, Jesse D. ;
Romero, Philip A. ;
Lu, Zhongyi ;
Arnold, Frances H. .
BIOLOGY DIRECT, 2007, 2
[10]   Evolution favors protein mutational robustness in sufficiently large populations [J].
Bloom, Jesse D. ;
Lu, Zhongyi ;
Chen, David ;
Raval, Alpan ;
Venturelli, Ophelia S. ;
Arnold, Frances H. .
BMC BIOLOGY, 2007, 5
12345678910