Reviews:Directed evolution/Library construction/bibliography

Introduction

This is the bibliography page for the Openwetware Review Reviews:Directed evolution/Library construction. This review uses the Biblio extension as described here. If you wish to add a reference to the review please place it at the bottom of the list and give it the next available reference number. If possible link the paper via the PubMed ID as this keeps the formatting consistent.

References

1. Farinas ET, Bulter T, and Arnold FH. Directed enzyme evolution. Curr Opin Biotechnol. 2001 Dec;12(6):545-51. DOI:10.1016/s0958-1669(01)00261-0 |

2. Reetz MT, Rentzsch M, Pletsch A, Maywald M, Towards the Directed Evolution of Hybrid Catalysts, Chimia 2002, 56, 721-723

3. Taylor SV, Kast P, and Hilvert D. Investigating and Engineering Enzymes by Genetic Selection. Angew Chem Int Ed Engl. 2001 Sep 17;40(18):3310-3335. DOI:10.1002/1521-3773(20010917)40:18<3310::aid-anie3310>3.0.co;2-p |
4. Waldo GS. Genetic screens and directed evolution for protein solubility. Curr Opin Chem Biol. 2003 Feb;7(1):33-8. DOI:10.1016/s1367-5931(02)00017-0 |
5. Tao H and Cornish VW. Milestones in directed enzyme evolution. Curr Opin Chem Biol. 2002 Dec;6(6):858-64. DOI:10.1016/s1367-5931(02)00396-4 |
6. Lin H and Cornish VW. Screening and selection methods for large-scale analysis of protein function. Angew Chem Int Ed Engl. 2002 Dec 2;41(23):4402-25. DOI:10.1002/1521-3773(20021202)41:23<4402::AID-ANIE4402>3.0.CO;2-H |
7. ISBN:158829286X
8. ISBN:1588292851
9. Stemmer WP. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc Natl Acad Sci U S A. 1994 Oct 25;91(22):10747-51. DOI:10.1073/pnas.91.22.10747 |
10. Stemmer WP. Rapid evolution of a protein in vitro by DNA shuffling. Nature. 1994 Aug 4;370(6488):389-91. DOI:10.1038/370389a0 |
11. Zhao H, Giver L, Shao Z, Affholter JA, and Arnold FH. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat Biotechnol. 1998 Mar;16(3):258-61. DOI:10.1038/nbt0398-258 |
12. Ostermeier M, Shim JH, and Benkovic SJ. A combinatorial approach to hybrid enzymes independent of DNA homology. Nat Biotechnol. 1999 Dec;17(12):1205-9. DOI:10.1038/70754 |
13. Bornscheuer UT, Altenbuchner J, and Meyer HH. Directed evolution of an esterase: screening of enzyme libraries based on pH-indicators and a growth assay. Bioorg Med Chem. 1999 Oct;7(10):2169-73. DOI:10.1016/s0968-0896(99)00147-9 |
14. Alexeeva M, Enright A, Dawson MJ, Mahmoudian M, and Turner NJ. Deracemization of alpha-methylbenzylamine using an enzyme obtained by in vitro evolution. Angew Chem Int Ed Engl. 2002 Sep 2;41(17):3177-80. DOI:10.1002/1521-3773(20020902)41:17<3177::AID-ANIE3177>3.0.CO;2-P |
15. Nguyen AW and Daugherty PS. Production of randomly mutated plasmid libraries using mutator strains. Methods Mol Biol. 2003;231:39-44. DOI:10.1385/1-59259-395-X:39 |
16. Cadwell RC and Joyce GF. Mutagenic PCR. PCR Methods Appl. 1994 Jun;3(6):S136-40. DOI:10.1101/gr.3.6.s136 |
17. Cirino PC, Mayer KM, and Umeno D. Generating mutant libraries using error-prone PCR. Methods Mol Biol. 2003;231:3-9. DOI:10.1385/1-59259-395-X:3 |
18. Matsumura I and Ellington AD. In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates. J Mol Biol. 2001 Jan 12;305(2):331-9. DOI:10.1006/jmbi.2000.4259 |
19. Lingen B, Grötzinger J, Kolter D, Kula MR, and Pohl M. Improving the carboligase activity of benzoylformate decarboxylase from Pseudomonas putida by a combination of directed evolution and site-directed mutagenesis. Protein Eng. 2002 Jul;15(7):585-93. DOI:10.1093/protein/15.7.585 |
20. Bessler C, Schmitt J, Maurer KH, and Schmid RD. Directed evolution of a bacterial alpha-amylase: toward enhanced pH-performance and higher specific activity. Protein Sci. 2003 Oct;12(10):2141-9. DOI:10.1110/ps.0384403 |
21. Zaccolo M, Williams DM, Brown DM, and Gherardi E. An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J Mol Biol. 1996 Feb 2;255(4):589-603. DOI:10.1006/jmbi.1996.0049 |
22. Zaccolo M and Gherardi E. The effect of high-frequency random mutagenesis on in vitro protein evolution: a study on TEM-1 beta-lactamase. J Mol Biol. 1999 Jan 15;285(2):775-83. DOI:10.1006/jmbi.1998.2262 |
23. Patrick WM, Firth AE, and Blackburn JM. User-friendly algorithms for estimating completeness and diversity in randomized protein-encoding libraries. Protein Eng. 2003 Jun;16(6):451-7. DOI:10.1093/protein/gzg057 |
24. Rowe LA, Geddie ML, Alexander OB, and Matsumura I. A comparison of directed evolution approaches using the beta-glucuronidase model system. J Mol Biol. 2003 Sep 26;332(4):851-60. DOI:10.1016/s0022-2836(03)00972-0 |
25. Miyazaki K and Arnold FH. Exploring nonnatural evolutionary pathways by saturation mutagenesis: rapid improvement of protein function. J Mol Evol. 1999 Dec;49(6):716-20. DOI:10.1007/pl00006593 |
26. Murakami H, Hohsaka T, and Sisido M. Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs. Nat Biotechnol. 2002 Jan;20(1):76-81. DOI:10.1038/nbt0102-76 |
27. Murakami H, Hohsaka T, and Sisido M. Random insertion and deletion mutagenesis. Methods Mol Biol. 2003;231:53-64. DOI:10.1385/1-59259-395-X:53 |
28. Hayes F and Hallet B. Pentapeptide scanning mutagenesis: encouraging old proteins to execute unusual tricks. Trends Microbiol. 2000 Dec;8(12):571-7. DOI:10.1016/s0966-842x(00)01857-6 |
29. Pikkemaat MG and Janssen DB. Generating segmental mutations in haloalkane dehalogenase: a novel part in the directed evolution toolbox. Nucleic Acids Res. 2002 Apr 15;30(8):E35-5. DOI:10.1093/nar/30.8.e35 |
30. Ward B and Juehne T. Combinatorial library diversity: probability assessment of library populations. Nucleic Acids Res. 1998 Feb 15;26(4):879-86. DOI:10.1093/nar/26.4.879 |
31. Palfrey D, Picardo M, and Hine AV. A new randomization assay reveals unexpected elements of sequence bias in model 'randomized' gene libraries: implications for biopanning. Gene. 2000 Jun 13;251(1):91-9. DOI:10.1016/s0378-1119(00)00206-7 |
32. Virnekäs B, Ge L, Plückthun A, Schneider KC, Wellnhofer G, and Moroney SE. Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis. Nucleic Acids Res. 1994 Dec 25;22(25):5600-7. DOI:10.1093/nar/22.25.5600 |

33. Zehl A, Starke A, Cech D, Hartsch T, Merkl R, Fritz HJ, Efficient and flexible access to fully protected trinucleotides suitable for DNA synthesis by automated phosphoramidite chemistryI, Chem Comm 1996, 23, 2677-2678

34. Kayushin AL, Korosteleva MD, Miroshnikov AI, Kosch W, Zubov D, and Piel N. A convenient approach to the synthesis of trinucleotide phosphoramidites--synthons for the generation of oligonucleotide/peptide libraries. Nucleic Acids Res. 1996 Oct 1;24(19):3748-55. DOI:10.1093/nar/24.19.3748 |
35. Kayushin A, Korosteleva M, and Miroshnikov A. Large-scale solid-phase preparation of 3'-unprotected trinucleotide phosphotriesters--precursors for synthesis of trinucleotide phosphoramidites. Nucleosides Nucleotides Nucleic Acids. 2000 Oct-Dec;19(10-12):1967-76. DOI:10.1080/15257770008045471 |
36. Gaytán P, Yáñez J, Sánchez F, and Soberón X. Orthogonal combinatorial mutagenesis: a codon-level combinatorial mutagenesis method useful for low multiplicity and amino acid-scanning protocols. Nucleic Acids Res. 2001 Feb 1;29(3):E9. DOI:10.1093/nar/29.3.e9 |
37. Gaytán P, Yañez J, Sánchez F, Mackie H, and Soberón X. Combination of DMT-mononucleotide and Fmoc-trinucleotide phosphoramidites in oligonucleotide synthesis affords an automatable codon-level mutagenesis method. Chem Biol. 1998 Sep;5(9):519-27. DOI:10.1016/s1074-5521(98)90007-2 |
38. Lahr SJ, Broadwater A, Carter CW Jr, Collier ML, Hensley L, Waldner JC, Pielak GJ, and Edgell MH. Patterned library analysis: a method for the quantitative assessment of hypotheses concerning the determinants of protein structure. Proc Natl Acad Sci U S A. 1999 Dec 21;96(26):14860-5. DOI:10.1073/pnas.96.26.14860 |
39. Glaser SM, Yelton DE, and Huse WD. Antibody engineering by codon-based mutagenesis in a filamentous phage vector system. J Immunol. 1992 Dec 15;149(12):3903-13.
40. Liebeton K, Zonta A, Schimossek K, Nardini M, Lang D, Dijkstra BW, Reetz MT, and Jaeger KE. Directed evolution of an enantioselective lipase. Chem Biol. 2000 Sep;7(9):709-18. DOI:10.1016/s1074-5521(00)00015-6 |
41. Sakamoto T, Joern JM, Arisawa A, and Arnold FH. Laboratory evolution of toluene dioxygenase to accept 4-picoline as a substrate. Appl Environ Microbiol. 2001 Sep;67(9):3882-7. DOI:10.1128/AEM.67.9.3882-3887.2001 |
42. Horsman GP, Liu AM, Henke E, Bornscheuer UT, and Kazlauskas RJ. Mutations in distant residues moderately increase the enantioselectivity of Pseudomonas fluorescens esterase towards methyl 3bromo-2-methylpropanoate and ethyl 3phenylbutyrate. Chemistry. 2003 May 9;9(9):1933-9. DOI:10.1002/chem.200204551 |
43. Leemhuis H, Rozeboom HJ, Wilbrink M, Euverink GJ, Dijkstra BW, and Dijkhuizen L. Conversion of cyclodextrin glycosyltransferase into a starch hydrolase by directed evolution: the role of alanine 230 in acceptor subsite +1. Biochemistry. 2003 Jun 24;42(24):7518-26. DOI:10.1021/bi034439q |
44. Wada M, Hsu CC, Franke D, Mitchell M, Heine A, Wilson I, and Wong CH. Directed evolution of N-acetylneuraminic acid aldolase to catalyze enantiomeric aldol reactions. Bioorg Med Chem. 2003 May 1;11(9):2091-8. DOI:10.1016/s0968-0896(03)00052-x |
45. Juillerat A, Gronemeyer T, Keppler A, Gendreizig S, Pick H, Vogel H, and Johnsson K. Directed evolution of O6-alkylguanine-DNA alkyltransferase for efficient labeling of fusion proteins with small molecules in vivo. Chem Biol. 2003 Apr;10(4):313-7. DOI:10.1016/s1074-5521(03)00068-1 |
46. Sio CF, Riemens AM, van der Laan JM, Verhaert RM, and Quax WJ. Directed evolution of a glutaryl acylase into an adipyl acylase. Eur J Biochem. 2002 Sep;269(18):4495-504. DOI:10.1046/j.1432-1033.2002.03143.x |
47. Georgescu R, Bandara G, and Sun L. Saturation mutagenesis. Methods Mol Biol. 2003;231:75-83. DOI:10.1385/1-59259-395-X:75 |
48. Miyazaki K and Takenouchi M. Creating random mutagenesis libraries using megaprimer PCR of whole plasmid. Biotechniques. 2002 Nov;33(5):1033-4, 1036-8. DOI:10.2144/02335st03 |
49. Miyazaki K. Creating random mutagenesis libraries by megaprimer PCR of whole plasmid (MEGAWHOP). Methods Mol Biol. 2003;231:23-8. DOI:10.1385/1-59259-395-X:23 |
50. Zha D, Eipper A, and Reetz MT. Assembly of designed oligonucleotides as an efficient method for gene recombination: a new tool in directed evolution. Chembiochem. 2003 Jan 3;4(1):34-9. DOI:10.1002/cbic.200390011 |
51. Ness JE, Kim S, Gottman A, Pak R, Krebber A, Borchert TV, Govindarajan S, Mundorff EC, and Minshull J. Synthetic shuffling expands functional protein diversity by allowing amino acids to recombine independently. Nat Biotechnol. 2002 Dec;20(12):1251-5. DOI:10.1038/nbt754 |
52. Hogrefe HH, Cline J, Youngblood GL, and Allen RM. Creating randomized amino acid libraries with the QuikChange Multi Site-Directed Mutagenesis Kit. Biotechniques. 2002 Nov;33(5):1158-60, 1162, 1164-5. DOI:10.2144/02335pf01 |
53. Hughes MD, Nagel DA, Santos AF, Sutherland AJ, and Hine AV. Removing the redundancy from randomised gene libraries. J Mol Biol. 2003 Aug 29;331(5):973-9. DOI:10.1016/s0022-2836(03)00833-7 |
54. Joern JM. DNA shuffling. Methods Mol Biol. 2003;231:85-9. DOI:10.1385/1-59259-395-X:85 |
55. Aguinaldo AM and Arnold FH. Staggered extension process (StEP) in vitro recombination. Methods Mol Biol. 2003;231:105-10. DOI:10.1385/1-59259-395-X:105 |
56. Coco WM, Levinson WE, Crist MJ, Hektor HJ, Darzins A, Pienkos PT, Squires CH, and Monticello DJ. DNA shuffling method for generating highly recombined genes and evolved enzymes. Nat Biotechnol. 2001 Apr;19(4):354-9. DOI:10.1038/86744 |
57. Coco WM. RACHITT: Gene family shuffling by Random Chimeragenesis on Transient Templates. Methods Mol Biol. 2003;231:111-27. DOI:10.1385/1-59259-395-X:111 |
58. Lutz S, Ostermeier M, and Benkovic SJ. Rapid generation of incremental truncation libraries for protein engineering using alpha-phosphothioate nucleotides. Nucleic Acids Res. 2001 Feb 15;29(4):E16. DOI:10.1093/nar/29.4.e16 |
59. Ostermeier M and Lutz S. The creation of ITCHY hybrid protein libraries. Methods Mol Biol. 2003;231:129-41. DOI:10.1385/1-59259-395-X:129 |
60. Lutz S and Ostermeier M. Preparation of SCRATCHY hybrid protein libraries: size- and in-frame selection of nucleic acid sequences. Methods Mol Biol. 2003;231:143-51. DOI:10.1385/1-59259-395-X:143 |
61. Dixon DP, McEwen AG, Lapthorn AJ, and Edwards R. Forced evolution of a herbicide detoxifying glutathione transferase. J Biol Chem. 2003 Jun 27;278(26):23930-5. DOI:10.1074/jbc.M303620200 |
62. Baik SH, Ide T, Yoshida H, Kagami O, and Harayama S. Significantly enhanced stability of glucose dehydrogenase by directed evolution. Appl Microbiol Biotechnol. 2003 May;61(4):329-35. DOI:10.1007/s00253-002-1215-1 |
63. Miyazaki K. Random DNA fragmentation with endonuclease V: application to DNA shuffling. Nucleic Acids Res. 2002 Dec 15;30(24):e139. DOI:10.1093/nar/gnf139 |
64. Glieder A, Farinas ET, and Arnold FH. Laboratory evolution of a soluble, self-sufficient, highly active alkane hydroxylase. Nat Biotechnol. 2002 Nov;20(11):1135-9. DOI:10.1038/nbt744 |
65. Sun L, Petrounia IP, Yagasaki M, Bandara G, and Arnold FH. Expression and stabilization of galactose oxidase in Escherichia coli by directed evolution. Protein Eng. 2001 Sep;14(9):699-704. DOI:10.1093/protein/14.9.699 |
66. Moore GL, Maranas CD, Lutz S, and Benkovic SJ. Predicting crossover generation in DNA shuffling. Proc Natl Acad Sci U S A. 2001 Mar 13;98(6):3226-31. DOI:10.1073/pnas.051631498 |
67. Moore GL and Maranas CD. eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments. Nucleic Acids Res. 2002 Jun 1;30(11):2407-16. DOI:10.1093/nar/30.11.2407 |
68. Joern JM, Meinhold P, and Arnold FH. Analysis of shuffled gene libraries. J Mol Biol. 2002 Feb 22;316(3):643-56. DOI:10.1006/jmbi.2001.5349 |
69. Kikuchi M, Ohnishi K, and Harayama S. Novel family shuffling methods for the in vitro evolution of enzymes. Gene. 1999 Aug 5;236(1):159-67. DOI:10.1016/s0378-1119(99)00240-1 |
70. Kikuchi M, Ohnishi K, and Harayama S. An effective family shuffling method using single-stranded DNA. Gene. 2000 Feb 8;243(1-2):133-7. DOI:10.1016/s0378-1119(99)00547-8 |
71. Zha W, Zhu T, and Zhao H. Family shuffling with single-stranded DNA. Methods Mol Biol. 2003;231:91-7. DOI:10.1385/1-59259-395-X:91 |
72. Gibbs MD, Nevalainen KM, and Bergquist PL. Degenerate oligonucleotide gene shuffling (DOGS): a method for enhancing the frequency of recombination with family shuffling. Gene. 2001 Jun 13;271(1):13-20. DOI:10.1016/s0378-1119(01)00506-6 |
73. Lutz S, Fast W, and Benkovic SJ. A universal, vector-based system for nucleic acid reading-frame selection. Protein Eng. 2002 Dec;15(12):1025-30. DOI:10.1093/protein/15.12.1025 |
74. Lutz S, Ostermeier M, Moore GL, Maranas CD, and Benkovic SJ. Creating multiple-crossover DNA libraries independent of sequence identity. Proc Natl Acad Sci U S A. 2001 Sep 25;98(20):11248-53. DOI:10.1073/pnas.201413698 |
75. Kawarasaki Y, Griswold KE, Stevenson JD, Selzer T, Benkovic SJ, Iverson BL, and Georgiou G. Enhanced crossover SCRATCHY: construction and high-throughput screening of a combinatorial library containing multiple non-homologous crossovers. Nucleic Acids Res. 2003 Nov 1;31(21):e126. DOI:10.1093/nar/gng126 |
76. O'Maille PE, Bakhtina M, and Tsai MD. Structure-based combinatorial protein engineering (SCOPE). J Mol Biol. 2002 Aug 23;321(4):677-91. DOI:10.1016/s0022-2836(02)00675-7 |
77. Hiraga K and Arnold FH. General method for sequence-independent site-directed chimeragenesis. J Mol Biol. 2003 Jul 4;330(2):287-96. DOI:10.1016/s0022-2836(03)00590-4 |
78. Voigt CA, Martinez C, Wang ZG, Mayo SL, and Arnold FH. Protein building blocks preserved by recombination. Nat Struct Biol. 2002 Jul;9(7):553-8. DOI:10.1038/nsb805 |
79. Meyer MM, Silberg JJ, Voigt CA, Endelman JB, Mayo SL, Wang ZG, and Arnold FH. Library analysis of SCHEMA-guided protein recombination. Protein Sci. 2003 Aug;12(8):1686-93. DOI:10.1110/ps.0306603 |
80. Moore JC, Jin HM, Kuchner O, and Arnold FH. Strategies for the in vitro evolution of protein function: enzyme evolution by random recombination of improved sequences. J Mol Biol. 1997 Sep 26;272(3):336-47. DOI:10.1006/jmbi.1997.1252 |

Up to here is the references for the original review. Below are new ones.

<biblio>

1. 81 pmid=15766704
2. 82 pmid=15707683
3. 83 pmid=17425805
4. 84 pmid=15507684
5. 85 pmid=17406496
6. 86 pmid=15857786