메뉴 건너뛰기




Volumn 53, Issue 6, 2012, Pages 357-364

Directed evolution of nucleotide-based libraries using lambda exonuclease

Author keywords

Antibody; Diversity; Lambda exonuclease; Mutagenesis; Nucleotide based libraries

Indexed keywords

DOUBLE STRANDED DNA; EXONUCLEASE; LAMBDA EXONUCLEASE; SINGLE CHAIN FRAGMENT VARIABLE ANTIBODY; SINGLE STRANDED DNA; UNCLASSIFIED DRUG;

EID: 84871352798     PISSN: 07366205     EISSN: 19409818     Source Type: Journal    
DOI: 10.2144/000113964     Document Type: Review
Times cited : (13)

References (54)
  • 1
    • 48249098990 scopus 로고    scopus 로고
    • Protein design by directed evolution
    • Jäckel, C., P. Kast, and D. Hilvert. 2008. Protein design by directed evolution. Annu Rev. Biophys. 37:153-173.
    • (2008) Annu Rev. Biophys , vol.37 , pp. 153-173
    • Jäckel, C.1    Kast, P.2    Hilvert, D.3
  • 2
    • 0028816556 scopus 로고
    • Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction
    • Fromant, M., S. Blanquet, and P. Plateau. 1995. Direct random mutagenesis of gene-sized DNA fragments using polymerase chain reaction. Anal. Biochem. 224:347-353.
    • (1995) AnaL. Biochem , vol.224 , pp. 347-353
    • Fromant, M.1    Blanquet, S.2    Plateau, P.3
  • 3
    • 0028110130 scopus 로고
    • DNA shuffling by random fragmentation and reassembly: In vitro recombination for molecular evolution
    • Stemmer, W. P. 1994. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution. Proc. Natl. Acad. Sci. USA 91:10747-10751.
    • (1994) Proc. Natl. Acad. Sci. USA , vol.91 , pp. 10747-10751
    • Stemmer, W.P.1
  • 4
    • 0028050350 scopus 로고
    • Rapid evolution of a protein in vitro by DNA shuffling
    • Stemmer, W. P. 1994. Rapid evolution of a protein in vitro by DNA shuffling. Nature 370:389-391.
    • (1994) Nature , vol.370 , pp. 389-391
    • Stemmer, W.P.1
  • 5
    • 33344465082 scopus 로고    scopus 로고
    • Directed evolution of extradiol dioxygenase by a novel in vivo DNA shuffling
    • Xu, S., J. Ju, H. Misono, and K. Ohnishi. 2006. Directed evolution of extradiol dioxygenase by a novel in vivo DNA shuffling. Gene 368:126-137.
    • (2006) Gene , vol.368 , pp. 126-137
    • Xu, S.1    Ju, J.2    Misono, H.3    Ohnishi, K.4
  • 6
    • 0033987925 scopus 로고    scopus 로고
    • Exploiting recombination in single bacteria to make large phage antibody libraries
    • Sblattero, D. and A. Bradbury. 2000. Exploiting recombination in single bacteria to make large phage antibody libraries. Nat. Biotechnol. 18:75-80.
    • (2000) Nat. Biotechnol , vol.18 , pp. 75-80
    • Sblattero, D.1    Bradbury, A.2
  • 7
    • 2342510292 scopus 로고    scopus 로고
    • Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display
    • Swers, J.S., B.A. Kellogg, and K.D. Wittrup. 2004. Shuffled antibody libraries created by in vivo homologous recombination and yeast surface display. Nucleic Acids Res. 32:e36.
    • (2004) Nucleic Acids Res , vol.32
    • Swers, J.S.1    Kellogg, B.A.2    Wittrup, K.D.3
  • 8
    • 0027175018 scopus 로고
    • Combinatorial infection andin vivo recombination: A strategy for making large phage antibody repertoires
    • Waterhouse, P., A.D. Grifths, K.S. Johnson, and G. Winter. 1993. Combinatorial infection andin vivo recombination: a strategy for making large phage antibody repertoires. Nucleic Acids Res. 21:2265-2266.
    • (1993) Nucleic Acids Res , vol.21 , pp. 2265-2266
    • Waterhouse, P.1    Grifths, A.D.2    Johnson, K.S.3    Winter, G.4
  • 9
    • 0034718615 scopus 로고    scopus 로고
    • Directed evolution of antibody fragments with monovalent femtomolar antigen-binding afinity
    • Boder, E.T., K.S. Midelfort, and K.D. Wittrup. 2000. Directed evolution of antibody fragments with monovalent femtomolar antigen-binding afinity. Proc. Natl. Acad. Sci. USA 97:10701-10705.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 10701-10705
    • Boder, E.T.1    Midelfort, K.S.2    Wittrup, K.D.3
  • 10
    • 0030832921 scopus 로고    scopus 로고
    • Use of mutator cells as a means for increasing production levels of a recom-binant antibody directed against Hepatitis B
    • Coia, G., A. Ayres, G.G. Lilley, P. J. Hudson, and R.A. Irving. 1997. Use of mutator cells as a means for increasing production levels of a recom-binant antibody directed against Hepatitis B. Gene 201:203-209.
    • (1997) Gene , vol.201 , pp. 203-209
    • Coia, G.1    Ayres, A.2    Lilley, G.G.3    Hudson, P.J.4    Irving, R.A.5
  • 12
    • 0029869449 scopus 로고    scopus 로고
    • An approach to random mutagenesis of DNA using mixtures of triphos-phate derivatives of nucleoside analogues
    • Zaccolo, M., D.M. Williams, D.M. Brown, and E. Gherardi. 1996. An approach to random mutagenesis of DNA using mixtures of triphos-phate derivatives of nucleoside analogues. J. Mol. Biol. 255:589-603.
    • (1996) J. Mol. Biol , vol.255 , pp. 589-603
    • Zaccolo, M.1    Williams, D.M.2    Brown, D.M.3    Gherardi, E.4
  • 14
    • 0033056238 scopus 로고    scopus 로고
    • Improving antibody afinity by mimicking somatic hyper-mutation in vitro
    • Chowdhury, P. S. and I. Pastan. 1999. Improving antibody afinity by mimicking somatic hyper-mutation in vitro. Nat. Biotechnol. 17:568-572.
    • (1999) Nat. Biotechnol , vol.17 , pp. 568-572
    • Chowdhury, P.S.1    Pastan, I.2
  • 15
    • 0027761151 scopus 로고
    • Antibody engineering by parsimonious mutagenesis
    • Balint, R.F. and J.W. Larrick. 1993. Antibody engineering by parsimonious mutagenesis. Gene 137:109-118.
    • (1993) Gene , vol.137 , pp. 109-118
    • Balint, R.F.1    Larrick, J.W.2
  • 17
    • 0031909113 scopus 로고    scopus 로고
    • Molecular evolution by staggered extension process (StEP) in vitro recombination
    • Zhao, H., L. Giver, Z. Shao, J.A. Afolter, and F.H. Arnold. 1998. Molecular evolution by staggered extension process (StEP) in vitro recombination. Nat. Biotechnol. 16:258-261.
    • (1998) Nat. Biotechnol , vol.16 , pp. 258-261
    • Zhao, H.1    Giver, L.2    Shao, Z.3    Afolter, J.A.4    Arnold, F.H.5
  • 18
    • 0033964975 scopus 로고    scopus 로고
    • An effective family shuffling method using single-stranded DNA
    • Kikuchi, M., K. Ohnishi, and S. Harayama. 2000. An effective family shuffling method using single-stranded DNA. Gene 243:133-137.
    • (2000) Gene , vol.243 , pp. 133-137
    • Kikuchi, M.1    Ohnishi, K.2    Harayama, S.3
  • 19
    • 79958028224 scopus 로고    scopus 로고
    • QuikChange Shuffling: A Convenient and Robust Method for Site-directed Mutagenesis and Random Recombination of Homologous Genes
    • An, Y., L. Chen, S. Sun, A. Lv, and W. Wu. 2011. QuikChange Shuffling: a Convenient and Robust Method for Site-directed Mutagenesis and Random Recombination of Homologous Genes. New Biotechnology.
    • (2011) New Biotechnology
    • An, Y.1    Chen, L.2    Sun, S.3    Lv, A.4    Wu, W.5
  • 20
    • 1542263494 scopus 로고    scopus 로고
    • Family shuffling with single-stranded DNA
    • Zha, W., T. Zhu, and H. Zhao. 2003. Family shuffling with single-stranded DNA. Methods Mol. Biol. 231: 91-97.
    • (2003) Methods Mol. Biol , vol.231 , pp. 91-97
    • Zha, W.1    Zhu, T.2    Zhao, H.3
  • 21
    • 0037716688 scopus 로고    scopus 로고
    • Synthetic gene libraries: In search of the optimal diversity
    • Ostermeier, M. 2003. Synthetic gene libraries: in search of the optimal diversity. Trends Biotechnol. 21:244-247.
    • (2003) Trends Biotechnol , vol.21 , pp. 244-247
    • Ostermeier, M.1
  • 22
    • 0033167916 scopus 로고    scopus 로고
    • Single-molecule DNA digestion by lambda-exonuclease
    • Dapprich, J. 1999. Single-molecule DNA digestion by lambda-exonuclease. Cytometry 36:163-168.
    • (1999) Cytometry , vol.36 , pp. 163-168
    • Dapprich, J.1
  • 23
    • 0014216084 scopus 로고
    • An exonuclease induced by bacteriophage
    • Little, J.W. 1967. An exonuclease induced by bacteriophage. J. Biol. Chem. 242:679.
    • (1967) J. Biol. Chem , vol.242 , pp. 679
    • Little, J.W.1
  • 24
    • 0015239451 scopus 로고
    • The role of exonuclease and protein of phage in genetic recombination. II. Substrate specificity and the mode of action of exonuclease
    • Carter, D.M. and C.M. Radding. 1971. The role of exonuclease and protein of phage in genetic recombination. II. Substrate specificity and the mode of action of exonuclease. J. Biol. Chem. 246:2502-2512.
    • (1971) J. Biol. Chem , vol.246 , pp. 2502-2512
    • Carter, D.M.1    Radding, C.M.2
  • 25
    • 0017840194 scopus 로고
    • Proces-sivity of DNA exonucleases
    • Tomas, K.R. and B.M. Olivera. 1978. Proces-sivity of DNA exonucleases. J. Biol. Chem. 253:424.
    • (1978) J. Biol. Chem , vol.253 , pp. 424
    • Tomas, K.R.1    Olivera, B.M.2
  • 27
    • 77956902264 scopus 로고    scopus 로고
    • Lamb da exonuclease pre-treatment for improved DNA-chip performance depends on the relative probe-target position
    • Brinker, A., H. Schulze, T. Bachmann, and R. Möller. 2010. La mb d a exonuc lease pre-treatment for improved DNA-chip performance depends on the relative probe-target position. Biosensors and Bioelectronics.
    • (2010) Biosensors and Bioelectronics
    • Brinker, A.1    Schulze, H.2    Bachmann, T.3    Möller, R.4
  • 28
    • 75749139323 scopus 로고    scopus 로고
    • Upgrading SE L E X technolog y by using la mbda exonuclease digestion for single-stranded DNA generation
    • Avci-Adali, M., A. Paul, N. Wilhelm, G. Ziemer, and H. P. Wendel. 2009. Upgrading SE L E X technolog y by using la mbda exonuclease digestion for single-stranded DNA generation. Molecules 15:1.
    • (2009) Molecules , vol.15 , pp. 1
    • Avci-Adali, M.1    Paul, A.2    Wilhelm, N.3    Ziemer, G.4    Wendel, H.P.5
  • 29
    • 0035881538 scopus 로고    scopus 로고
    • Lambda Exonuclease-Based Subtractive Hybridization Approach to Isolate Differentially Expressed Genes from Leaf Cultures of Paulownia kawakamii
    • R.K.W. Low, A.P. Prakash, S. Swarup, C.J. Goh, and P.P. Kumar. 2001. Lambda Exonuclease-Based Subtractive Hybridization Approach to Isolate Differentially Expressed Genes from Leaf Cultures of Paulownia kawakamii. Anal. Biochem. 295:240-247.
    • (2001) Anal. Biochem , vol.295 , pp. 240-247
    • Low, R.K.W.1    Prakash, A.P.2    Swarup, S.3    Goh, C.J.4    Kumar, P.P.5
  • 30
    • 0034000091 scopus 로고    scopus 로고
    • Preparation of single-stranded PCR products for electrospray ionization mass spectrometry using the DNA repair enzyme lambda exonuclease
    • Null, A. P., J.C. Hannis, and D.C. Muddiman. 2000. Preparation of single-stranded PCR products for electrospray ionization mass spectrometry using the DNA repair enzyme lambda exonuclease. Analyst (Lond.) 125:619-626.
    • (2000) Analyst (Lond.) , vol.125 , pp. 619-626
    • Null, A.P.1    Hannis, J.C.2    Muddiman, D.C.3
  • 31
    • 0033209590 scopus 로고    scopus 로고
    • Enzyme-free cloning: A rapid method to clone PCR products independent of vector restriction enzyme sites
    • Tillett, D. and B.A. Neilan. 1999. Enzyme-free cloning: a rapid method to clone PCR products independent of vector restriction enzyme sites. Nucleic Acids Res. 27:e26.
    • (1999) Nucleic Acids Res , vol.27
    • Tillett, D.1    Neilan, B.A.2
  • 33
    • 0037418551 scopus 로고    scopus 로고
    • Interaction of DNA polymerase I (Klenow fragment) with the single-stranded template beyond the site of synthesis
    • Turner, R.M., Jr., N.D.F. Grindley, and C.M. Joyce. 2003. Interaction of DNA polymerase I (Klenow fragment) with the single-stranded template beyond the site of synthesis. Biochemistry 42:2373-2385.
    • (2003) Biochemistry , vol.42 , pp. 2373-2385
    • Turner Jr., R.M.1    Grindley, N.D.F.2    Joyce, C.M.3
  • 34
    • 0022479114 scopus 로고
    • Cloning of random-sequence oligodeoxy-nucleotides
    • Oliphant, A.R., A.L. Nussbaum, and K. Struhl. 1986. Cloning of random-sequence oligodeoxy-nucleotides. Gene 44:177-183.
    • (1986) Gene , vol.44 , pp. 177-183
    • Oliphant, A.R.1    Nussbaum, A.L.2    Struhl, K.3
  • 35
    • 0033559532 scopus 로고    scopus 로고
    • Low temperature cycled PCR protocol for Klenow fragment of DNA polymerase I in the presence of proline
    • Iakobashvili, R. and A. Lapidot. 1999. Low temperature cycled PCR protocol for Klenow fragment of DNA polymerase I in the presence of proline. Nucleic Acids Res. 27:1566.
    • (1999) Nucleic Acids Res , vol.27 , pp. 1566
    • Iakobashvili, R.1    Lapidot, A.2
  • 36
    • 0032761672 scopus 로고    scopus 로고
    • DN A cloning without restrict ion enzyme and ligase
    • Tseng, H. 1999. DN A cloning without restrict ion enzyme and ligase. Biotechniques 27:1240-1244.
    • (1999) Biotechniques , vol.27 , pp. 1240-1244
    • Tseng, H.1
  • 37
    • 0028926814 scopus 로고
    • Selection and application of human single chain Fv antibody fragments from a semi-synthetic phage antibody display library with designed CDR3 regions
    • de Kruif, J., E. Boel, and T. Logtenberg. 1995. Selection and application of human single chain Fv antibody fragments from a semi-synthetic phage antibody display library with designed CDR3 regions. J. Mol. Biol. 248:97-105.
    • (1995) J. Mol. Biol , vol.248 , pp. 97-105
    • de Kruif, J.1    Boel, E.2    Logtenberg, T.3
  • 38
    • 0034244316 scopus 로고    scopus 로고
    • By-passing selection: Direct screening for a ntibody-antigen interact ions using protein arrays
    • Holt, L.J., K. Büssow, G. Walter, and I.M. Tomlinson. 2000. By-passing selection: direct screening for a ntibody-antigen interact ions using protein arrays. Nucleic Acids Res. 28:E72.
    • (2000) Nucleic Acids Res , vol.28
    • Holt, L.J.1    Büssow, K.2    Walter, G.3    Tomlinson, I.M.4
  • 39
    • 0033711628 scopus 로고    scopus 로고
    • Diversity in the CDR3 region of VH is sufficient for most antibody specificities
    • Xu, J.L. and M.M. Davis. 2000. Diversity in the CDR3 region of VH is sufficient for most antibody specificities. Immunity 13:37-45.
    • (2000) Immunity , vol.13 , pp. 37-45
    • Xu, J.L.1    Davis, M.M.2
  • 40
    • 0004700486 scopus 로고    scopus 로고
    • Afinity Maturation by Chain Shuffling and Site Directed Mutagenesis
    • Lou, J. and J.D. Marks. 2010. Afinity Maturation by Chain Shuffling and Site Directed Mutagenesis. Antibody Engineering:377-396.
    • (2010) Antibody Engineering , pp. 377-396
    • Lou, J.1    Marks, J.D.2
  • 41
    • 77957306871 scopus 로고    scopus 로고
    • Polymerization behavior of Klenow fragment and Taq DNA polymerase in short primer extension reactions
    • Zhao, G. and Y. Guan. 2010. Polymerization behavior of Klenow fragment and Taq DNA polymerase in short primer extension reactions. Acta Biochim. Biophys. Sin. (Shanghai) 42:722.
    • (2010) Acta Biochim. Biophys. Sin. (Shanghai) , vol.42 , pp. 722
    • Zhao, G.1    Guan, Y.2
  • 42
    • 77952243807 scopus 로고    scopus 로고
    • V-gene amplification revisited-An optimised procedure for amplification of rearranged human antibody genes of different isotypes
    • Lim, T. S., S. Mollova, F. Rubelt, V. Sievert, S. Dubel, H. Lehrach, and Z. Konthur. 2010. V-gene amplification revisited-An optimised procedure for amplification of rearranged human antibody genes of different isotypes. New Biotechnology.
    • (2010) New Biotechnology
    • Lim, T.S.1    Mollova, S.2    Rubelt, F.3    Sievert, V.4    Dubel, S.5    Lehrach, H.6    Konthur, Z.7
  • 44
    • 77953421267 scopus 로고    scopus 로고
    • Real-ti me observation of a single DNA d igestion by lambda exonuclease under a fuorescence microscope field
    • Matsuura, S., J. Komatsu, K. Hirano, H. Yasuda, K. Takashima, S. Katsura, and A. Mizuno. 2001. Real-ti me observation of a single DNA d igestion by lambda exonuclease under a fuorescence microscope field. Nucleic Acids Res. 29:E79.
    • (2001) Nucleic Acids Res , vol.29
    • Matsuura, S.1    Komatsu, J.2    Hirano, K.3    Yasuda, H.4    Takashima, K.5    Katsura, S.6    Mizuno, A.7
  • 45
    • 0016720497 scopus 로고
    • Chain length determination of small double-and single-stranded DNA molecules by polyacrylamide gel electrophoresis
    • Maniatis, T., A. Jefrey, and H. Van de Sande. 1975. Chain length determination of small double-and single-stranded DNA molecules by polyacrylamide gel electrophoresis. Biochemistry 14:3787-3794.
    • (1975) Biochemistry , vol.14 , pp. 3787-3794
    • Maniatis, T.1    Jefrey, A.2    Van de Sande, H.3
  • 47
    • 33646144457 scopus 로고    scopus 로고
    • Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA
    • Datta, K., A.J. Wowor, A.J. Richard, and V.J. LiCata. 2006. Temperature dependence and thermodynamics of Klenow polymerase binding to primed-template DNA. Biophys. J. 90:1739-1751.
    • (2006) Biophys. J , vol.90 , pp. 1739-1751
    • Datta, K.1    Wowor, A.J.2    Richard, A.J.3    Licata, V.J.4
  • 48
    • 0029829054 scopus 로고    scopus 로고
    • DNA end joining by the Klenow fragment of DNA polymerase I
    • King, J.S., C. F. Fairley, and W. F. Morgan. 1996. DNA end joining by the Klenow fragment of DNA polymerase I. J. Biol. Chem. 271:20450.
    • (1996) J. Biol. Chem , vol.271 , pp. 20450
    • King, J.S.1    Fairley, C.F.2    Morgan, W.F.3
  • 49
  • 50
    • 77954658425 scopus 로고    scopus 로고
    • A convenient and robust method for construction of combinatoria l and random mutant libraries
    • An, Y., W. Wu, and A. Lv. 2010. A convenient and robust method for construction of combinatoria l and random mutant libraries. Biochimie 92:1081-1084.
    • (2010) Biochimie , vol.92 , pp. 1081-1084
    • An, Y.1    Wu, W.2    Lv, A.3
  • 51
    • 0008844470 scopus 로고    scopus 로고
    • Bacteriophage library construction and selection of recombinant antibod ies
    • Galanis M., R.A. Irving, and P. J. Hudson. 2001. Bacteriophage library construction and selection of recombinant antibod ies. Current Protocols in Immunology:1711-17118.
    • (2001) Current Protocols In Immunology , pp. 1711-17118
    • Galanis, M.1    Irving, R.A.2    Hudson, P.J.3
  • 52
    • 33750372541 scopus 로고    scopus 로고
    • Direct measurement of T-cell receptor repertoire diversity with AmpliCot
    • Baum, P. D. and J.M. McCune. 2006. Direct measurement of T-cell receptor repertoire diversity with AmpliCot. Nat. Methods 3:895-901.
    • (2006) Nat. Methods , vol.3 , pp. 895-901
    • Baum, P.D.1    McCune, J.M.2
  • 53
    • 79951580671 scopus 로고    scopus 로고
    • Diversity visualization by endonuclease: A rapid assay to monitor diverse nucleotide libraries
    • Lim, T. S., T. Schütze, H. Lehrach, J. Glökler, and Z. Konthur. 2011. Diversity visualization by endonuclease: A rapid assay to monitor diverse nucleotide libraries. Anal. Biochem. 411:16-21.
    • (2011) Anal. Biochem , vol.411 , pp. 16-21
    • Lim, T.S.1    Schütze, T.2    Lehrach, H.3    Glökler, J.4    Konthur, Z.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.