-
1
-
-
0027159254
-
The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments
-
Winkler F.K., Banner D.W., Oefner C., Tsernoglou D., Brown R.S., Heathman S.P., Bryan R.K., Martin P.D., Petratos K., Wilson K.S. The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments. EMBO J. 12:1993;1781-1795.
-
(1993)
EMBO J
, vol.12
, pp. 1781-1795
-
-
Winkler, F.K.1
Banner, D.W.2
Oefner, C.3
Tsernoglou, D.4
Brown, R.S.5
Heathman, S.P.6
Bryan, R.K.7
Martin, P.D.8
Petratos, K.9
Wilson, K.S.10
-
2
-
-
0032538280
-
Towards the design of rare cutting restriction endonucleases: Using directed evolution to generate variants of EcoRV differing in their substrate specificity by two orders of magnitude
-
This paper describes one of the very few modifications of DNA recognition in an enzyme using a non-α-helical recognition motif. DNA shuffling was used to evolve the specificity of the enzyme to a longer sequence than its native target. Extension of the sequence specificity of restriction enzymes to longer sequences promises many practical applications in cloning and recombination.
-
Lanio T., Jeltsch A., Pingoud A. Towards the design of rare cutting restriction endonucleases: using directed evolution to generate variants of EcoRV differing in their substrate specificity by two orders of magnitude. J Mol Biol. 283:1998;59-69. This paper describes one of the very few modifications of DNA recognition in an enzyme using a non-α-helical recognition motif. DNA shuffling was used to evolve the specificity of the enzyme to a longer sequence than its native target. Extension of the sequence specificity of restriction enzymes to longer sequences promises many practical applications in cloning and recombination.
-
(1998)
J Mol Biol
, vol.283
, pp. 59-69
-
-
Lanio, T.1
Jeltsch, A.2
Pingoud, A.3
-
3
-
-
0025182484
-
Design of DNA-binding peptides based on the leucine zipper motif
-
O'Neil K.T., Hoess R.H., DeGrado W.F. Design of DNA-binding peptides based on the leucine zipper motif. Science. 249:1990;774-778.
-
(1990)
Science
, vol.249
, pp. 774-778
-
-
O'Neil, K.T.1
Hoess, R.H.2
Degrado, W.F.3
-
4
-
-
0027049805
-
The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α-helices: Crystal structure of the protein-DNA complex
-
Ellenberger T.E., Brandl C.J., Struhl K., Harrison S.C. The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α-helices: crystal structure of the protein-DNA complex. Cell. 71:1992;1223-1237.
-
(1992)
Cell
, vol.71
, pp. 1223-1237
-
-
Ellenberger, T.E.1
Brandl, C.J.2
Struhl, K.3
Harrison, S.C.4
-
5
-
-
0029863983
-
In vivo selection of basic region-leucine zipper proteins with altered DNA-binding specificities
-
Sera T., Schultz P.G. In vivo selection of basic region-leucine zipper proteins with altered DNA-binding specificities. Proc Natl Acad Sci USA. 93:1996;2920-2925.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 2920-2925
-
-
Sera, T.1
Schultz, P.G.2
-
6
-
-
0033612729
-
Highly specific DNA recognition by a designed miniature protein
-
This study demonstrates minimalist design at its best. Simple grafting of the recognition residues of GCN4 onto the well-studied avian pancreatic polypeptide and a little fine-tuning provided a small 42-residue protein with exquisite affinity and specificity for the target DNA, much greater than the native protein.
-
Zondlo N.J., Schepartz A. Highly specific DNA recognition by a designed miniature protein. J Am Chem Soc. 121:1999;6938-6939. This study demonstrates minimalist design at its best. Simple grafting of the recognition residues of GCN4 onto the well-studied avian pancreatic polypeptide and a little fine-tuning provided a small 42-residue protein with exquisite affinity and specificity for the target DNA, much greater than the native protein.
-
(1999)
J Am Chem Soc
, vol.121
, pp. 6938-6939
-
-
Zondlo, N.J.1
Schepartz, A.2
-
7
-
-
0027365669
-
The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: How receptors discriminate between their response elements
-
Schwabe J.W., Chapman L., Finch J.T., Rhodes D. The crystal structure of the estrogen receptor DNA-binding domain bound to DNA: how receptors discriminate between their response elements. Cell. 75:1993;567-578.
-
(1993)
Cell
, vol.75
, pp. 567-578
-
-
Schwabe, J.W.1
Chapman, L.2
Finch, J.T.3
Rhodes, D.4
-
8
-
-
0025780755
-
Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA
-
Luisi B.F., Xu W.X., Otwinski Z., Freedman L.P., Yamamoto K.R., Sigler P.B. Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA. Nature. 352:1991;497-505.
-
(1991)
Nature
, vol.352
, pp. 497-505
-
-
Luisi, B.F.1
Xu, W.X.2
Otwinski, Z.3
Freedman, L.P.4
Yamamoto, K.R.5
Sigler, P.B.6
-
10
-
-
0028138773
-
Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices
-
Ogata K., Morikawa S., Nakamura H., Sekikawa A., Inoue T., Kanai H., Sarai A., Ishii S., Nishimura Y. Solution structure of a specific DNA complex of the Myb DNA-binding domain with cooperative recognition helices. Cell. 79:1994;639-648.
-
(1994)
Cell
, vol.79
, pp. 639-648
-
-
Ogata, K.1
Morikawa, S.2
Nakamura, H.3
Sekikawa, A.4
Inoue, T.5
Kanai, H.6
Sarai, A.7
Ishii, S.8
Nishimura, Y.9
-
11
-
-
0031024680
-
Differences between plant and animal Myb domains are fundamental for DNA binding activity, and chimeric Myb domains have novel DNA binding specificities
-
Williams C.E., Grotewold E. Differences between plant and animal Myb domains are fundamental for DNA binding activity, and chimeric Myb domains have novel DNA binding specificities. J Biol Chem. 272:1997;563-571.
-
(1997)
J Biol Chem
, vol.272
, pp. 563-571
-
-
Williams, C.E.1
Grotewold, E.2
-
12
-
-
0033584468
-
Construction of an artificial tandem protein of the c-Myb DNA-binding domain and analysis of its DNA binding specificity
-
Oda M., Furukawa K., Sarai A., Nakamura H. Construction of an artificial tandem protein of the c-Myb DNA-binding domain and analysis of its DNA binding specificity. Biochem Biophys Res Commun. 262:1999;94-97.
-
(1999)
Biochem Biophys Res Commun
, vol.262
, pp. 94-97
-
-
Oda, M.1
Furukawa, K.2
Sarai, A.3
Nakamura, H.4
-
13
-
-
0025773296
-
Zinc finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å
-
Pavletich N.P., Pabo C.O. Zinc finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å Science. 252:1991;809-817.
-
(1991)
Science
, vol.252
, pp. 809-817
-
-
Pavletich, N.P.1
Pabo, C.O.2
-
14
-
-
0032981699
-
Toward controlling gene expression at will: Selection and design of zinc finger domains recognizing each of the 5′-GNN-3′ DNA target sequences
-
••], this paper describes a system by which any laboratory can build a zinc finger protein capable, perhaps, of uniquely targeting any gene in a complex genome.
-
••], this paper describes a system by which any laboratory can build a zinc finger protein capable, perhaps, of uniquely targeting any gene in a complex genome.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 2758-2763
-
-
Segal, D.J.1
Dreier, B.2
Beerli, R.R.3
Barbas C.F. III4
-
15
-
-
0028046895
-
Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions
-
Choo Y., Klug A. Selection of DNA binding sites for zinc fingers using rationally randomized DNA reveals coded interactions. Proc Natl Acad Sci USA. 91:1994;11168-11172.
-
(1994)
Proc Natl Acad Sci USA
, vol.91
, pp. 11168-11172
-
-
Choo, Y.1
Klug, A.2
-
16
-
-
0027401045
-
Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins
-
Desjarlais J.R., Berg J.M. Use of a zinc-finger consensus sequence framework and specificity rules to design specific DNA binding proteins. Proc Natl Acad Sci USA. 90:1993;2256-2260.
-
(1993)
Proc Natl Acad Sci USA
, vol.90
, pp. 2256-2260
-
-
Desjarlais, J.R.1
Berg, J.M.2
-
18
-
-
0033524954
-
Analysis of zinc fingers optimized via phage display: Evaluating the utility of a recognition code
-
This paper reports the specificity of the proteins constructed by sequential selection (see [22]). The authors also argue that many of the interactions they observed were not predicted by a recognition code.
-
Wolfe S.A., Greisman H.A., Ramm E.I., Pabo C.O. Analysis of zinc fingers optimized via phage display: evaluating the utility of a recognition code. J Mol Biol. 285:1999;1917-1934. This paper reports the specificity of the proteins constructed by sequential selection (see [22]). The authors also argue that many of the interactions they observed were not predicted by a recognition code.
-
(1999)
J Mol Biol
, vol.285
, pp. 1917-1934
-
-
Wolfe, S.A.1
Greisman, H.A.2
Ramm, E.I.3
Pabo, C.O.4
-
19
-
-
0030940295
-
Synergy between adjacent zinc fingers in sequence-specific DNA recognition
-
Isalan M., Choo Y., Klug A. Synergy between adjacent zinc fingers in sequence-specific DNA recognition. Proc Natl Acad Sci USA. 94:1997;5617-5621.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 5617-5621
-
-
Isalan, M.1
Choo, Y.2
Klug, A.3
-
20
-
-
0032168890
-
Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers
-
By randomizing residues at the interface of two domains, the authors showed that they could select residues that would allow the recognition of sequences starting with any base. It is still not clear if these results can be generalized, however, and the authors have yet to show that they can apply their methods to make multi-finger proteins of high affinity and specificity or that purified rather than phage-bound proteins actually bind the target sequence.
-
Isalan M., Klug A., Choo Y. Comprehensive DNA recognition through concerted interactions from adjacent zinc fingers. Biochemistry. 37:1998;12026-12033. By randomizing residues at the interface of two domains, the authors showed that they could select residues that would allow the recognition of sequences starting with any base. It is still not clear if these results can be generalized, however, and the authors have yet to show that they can apply their methods to make multi-finger proteins of high affinity and specificity or that purified rather than phage-bound proteins actually bind the target sequence.
-
(1998)
Biochemistry
, vol.37
, pp. 12026-12033
-
-
Isalan, M.1
Klug, A.2
Choo, Y.3
-
21
-
-
0029822407
-
A zinc finger directory for high-affinity DNA recognition
-
Jamieson A.C., Wang H., Kim S-H. A zinc finger directory for high-affinity DNA recognition. Proc Natl Acad Sci USA. 93:1996;12834-12839.
-
(1996)
Proc Natl Acad Sci USA
, vol.93
, pp. 12834-12839
-
-
Jamieson, A.C.1
Wang, H.2
Kim, S.-H.3
-
22
-
-
0031053362
-
A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites
-
Greisman H.A., Pabo C.O. A general strategy for selecting high-affinity zinc finger proteins for diverse DNA target sites. Science. 275:1997;657-661.
-
(1997)
Science
, vol.275
, pp. 657-661
-
-
Greisman, H.A.1
Pabo, C.O.2
-
23
-
-
0032437591
-
Toward controlling gene expression at will: Specific regulation of the erbB-2/HER-2 promoter by using polydactyl zinc finger proteins constructed from modular building blocks
-
••]. Transcription factors recognizing an 18 base pair sequence are assembled and demonstrated to specifically control the erbB-2 promoter in human cells, the first time that transcription factors have been fashioned to regulate a specific promoter. Together, these papers provide the necessary tools by which any laboratory can build a zinc finger protein capable, perhaps, of uniquely targeting any gene in the human genome.
-
••]. Transcription factors recognizing an 18 base pair sequence are assembled and demonstrated to specifically control the erbB-2 promoter in human cells, the first time that transcription factors have been fashioned to regulate a specific promoter. Together, these papers provide the necessary tools by which any laboratory can build a zinc finger protein capable, perhaps, of uniquely targeting any gene in the human genome.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 14628-14633
-
-
Beerli, R.R.1
Segal, D.J.2
Dreier, B.3
Barbas C.F. III4
-
24
-
-
0030697441
-
Transcriptional repression by zinc finger peptides. Exploring the potential for applications in gene therapy
-
Kim J.S., Pabo C.O. Transcriptional repression by zinc finger peptides. Exploring the potential for applications in gene therapy. J Biol Chem. 272:1997;29795-29800.
-
(1997)
J Biol Chem
, vol.272
, pp. 29795-29800
-
-
Kim, J.S.1
Pabo, C.O.2
-
25
-
-
0032522662
-
High-resolution structures of variant Zif268-DNA complexes: Implications for understanding zinc finger-DNA recognition
-
This paper presents the structures of phage display selected mutants. The structures show interactions in cognate and non-cognate sites. The paper also describes the repositioning of the α-helix relative to the DNA. This is an excellent and necessary descriptive work, although the paucity of quantitative affinity and specificity data for these proteins allows for few conclusions regarding specific interactions that provide for binding one sequence while excluding others.
-
Elrod-Erickson M., Benson T.E., Pabo C.O. High-resolution structures of variant Zif268-DNA complexes: implications for understanding zinc finger-DNA recognition. Structure. 6:1998;451-464. This paper presents the structures of phage display selected mutants. The structures show interactions in cognate and non-cognate sites. The paper also describes the repositioning of the α-helix relative to the DNA. This is an excellent and necessary descriptive work, although the paucity of quantitative affinity and specificity data for these proteins allows for few conclusions regarding specific interactions that provide for binding one sequence while excluding others.
-
(1998)
Structure
, vol.6
, pp. 451-464
-
-
Elrod-Erickson, M.1
Benson, T.E.2
Pabo, C.O.3
-
26
-
-
0032539846
-
Differing roles for zinc fingers in DNA recognition: Structure of a six-finger transcription factor IIIA complex
-
Nolte R.T., Conlin R.M., Harrison S.C., Brown R.S. Differing roles for zinc fingers in DNA recognition: structure of a six-finger transcription factor IIIA complex. Proc Natl Acad Sci USA. 95:1998;2938-2943.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 2938-2943
-
-
Nolte, R.T.1
Conlin, R.M.2
Harrison, S.C.3
Brown, R.S.4
-
27
-
-
0031576363
-
Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: Determinants of affinity and sequence specificity
-
Wuttke D.S., Foster M.P., Case D.A., Gottesfeld J.M., Wright P.E. Solution structure of the first three zinc fingers of TFIIIA bound to the cognate DNA sequence: determinants of affinity and sequence specificity. J Mol Biol. 273:1997;183-206.
-
(1997)
J Mol Biol
, vol.273
, pp. 183-206
-
-
Wuttke, D.S.1
Foster, M.P.2
Case, D.A.3
Gottesfeld, J.M.4
Wright, P.E.5
-
28
-
-
0032004598
-
The role of zinc finger linkers in p43 and TFIIIA binding to 5S rRNA and DNA
-
Ryan R.F., Darby M.K. The role of zinc finger linkers in p43 and TFIIIA binding to 5S rRNA and DNA. Nucleic Acids Res. 26:1998;703-709.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 703-709
-
-
Ryan, R.F.1
Darby, M.K.2
-
29
-
-
0030903688
-
Design of polydactyl zinc-finger proteins for unique addressing within complex genomes
-
Liu Q., Segal D.J., Ghiara J.B., Barbas C.F. III Design of polydactyl zinc-finger proteins for unique addressing within complex genomes. Proc Natl Acad Sci USA. 94:1997;5525-5530.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 5525-5530
-
-
Liu, Q.1
Segal, D.J.2
Ghiara, J.B.3
Barbas C.F. III4
-
30
-
-
0032539902
-
Getting a handhold on DNA: Design of poly-zinc finger proteins with femtomolar dissociation constants
-
This work suggests that modifications to the framework of a zinc-finger protein can lead to dramatic improvements in binding. The authors state that by using a noncanonical linker between zinc fingers 3 and 4, a > 6000-fold increase in affinity can be obtained by a six-finger protein over that of its constituent three-fingers proteins. It remains to be seen if specificity is sacrificed, or if this effect can be reproduced with other proteins. To date, further application of this approach has failed. More importantly, it is not clear that the effect has anything to do with the noncanonical linker, as it appears that the canonical linker was never tested. Kinetic measurements are used to derive dissociation constants. As performed, these measurements can lead to very large errors. Therefore, the use of the term 'femtomolar' in the title and abstract of this paper is provocatively misleading. Normalizing the reported affinities to a more traditional value for Zif268 produces
-
Kim J.S., Pabo C.O. Getting a handhold on DNA: design of poly-zinc finger proteins with femtomolar dissociation constants. Proc Natl Acad Sci USA. 95:1998;2812-2817. This work suggests that modifications to the framework of a zinc-finger protein can lead to dramatic improvements in binding. The authors state that by using a noncanonical linker between zinc fingers 3 and 4, a > 6000-fold increase in affinity can be obtained by a six-finger protein over that of its constituent three-fingers proteins. It remains to be seen if specificity is sacrificed, or if this effect can be reproduced with other proteins. To date, further application of this approach has failed. More importantly, it is not clear that the effect has anything to do with the noncanonical linker, as it appears that the canonical linker was never tested. Kinetic measurements are used to derive dissociation constants. As performed, these measurements can lead to very large errors. Therefore, the use of the term 'femtomolar' in the title and abstract of this paper is provocatively misleading. Normalizing the reported affinities to a more traditional value for Zif268 produces dissociation constants in the picomolar range. Such affinities are still impressive, but are achievable with canonical linkers.
-
(1998)
Proc Natl Acad Sci USA
, vol.95
, pp. 2812-2817
-
-
Kim, J.S.1
Pabo, C.O.2
-
31
-
-
0033594535
-
Genetic selection of short peptides that support protein oligomerization in vivo
-
In this study a genetic selection is devised to select novel peptides that result in dimerization or multimerization of the λ repressor. Effective peptide motifs allow cell survival following assault with the lytic phage. An amazingly diverse selection of novel functional peptides results from this.
-
Zhang Z., Murphy A., Hu J.C., Kodadek T. Genetic selection of short peptides that support protein oligomerization in vivo. Curr Biol. 9:1999;417-420. In this study a genetic selection is devised to select novel peptides that result in dimerization or multimerization of the λ repressor. Effective peptide motifs allow cell survival following assault with the lytic phage. An amazingly diverse selection of novel functional peptides results from this.
-
(1999)
Curr Biol
, vol.9
, pp. 417-420
-
-
Zhang, Z.1
Murphy, A.2
Hu, J.C.3
Kodadek, T.4
-
32
-
-
0032029590
-
Targeting a truncated HO-endonuclease of yeast to novel DNA sites with foreign zinc fingers
-
Nahon E., Raveh D. Targeting a truncated HO-endonuclease of yeast to novel DNA sites with foreign zinc fingers. Nucleic Acids Res. 26:1998;1233-1239.
-
(1998)
Nucleic Acids Res
, vol.26
, pp. 1233-1239
-
-
Nahon, E.1
Raveh, D.2
-
33
-
-
0032876974
-
Chimeric restriction enzymes: What is next?
-
This review describes fusions of zinc finger proteins and the gal4 DBD with the endonuclease domain of FokI. The zinc finger proteins were constructed entirely by rational design. The fusions exhibit activity, though their ability to catalyze multiple DNA cleavages is not assessed. Efficient site-specific enzymes may be only an evolutionary selection away.
-
Chandrasegaran S., Smith J. Chimeric restriction enzymes: what is next? Biol Chem. 380:1999;841-848. This review describes fusions of zinc finger proteins and the gal4 DBD with the endonuclease domain of FokI. The zinc finger proteins were constructed entirely by rational design. The fusions exhibit activity, though their ability to catalyze multiple DNA cleavages is not assessed. Efficient site-specific enzymes may be only an evolutionary selection away.
-
(1999)
Biol Chem
, vol.380
, pp. 841-848
-
-
Chandrasegaran, S.1
Smith, J.2
-
34
-
-
84984766752
-
Cytosine methylation targetted to pre-determined sequences
-
Xu G-L., Bestor T.H. Cytosine methylation targetted to pre-determined sequences. Nat Genet. 17:1997;376-378.
-
(1997)
Nat Genet
, vol.17
, pp. 376-378
-
-
Xu, G.-L.1
Bestor, T.H.2
-
35
-
-
0033179386
-
Tethering a type IB topoisomerase to a DNA site by enzyme fusion to a heterologous site-selective DNA-binding protein domain
-
Beretta G.L., Binaschi M., Zagni E., Capuani L., Capranico G. Tethering a type IB topoisomerase to a DNA site by enzyme fusion to a heterologous site-selective DNA-binding protein domain. Cancer Res. 59:1999;3689-3697.
-
(1999)
Cancer Res
, vol.59
, pp. 3689-3697
-
-
Beretta, G.L.1
Binaschi, M.2
Zagni, E.3
Capuani, L.4
Capranico, G.5
-
36
-
-
0031060377
-
Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites
-
Bushman F.D., Miller M.D. Tethering human immunodeficiency virus type 1 preintegration complexes to target DNA promotes integration at nearby sites. J Virol. 71:1997;458-464.
-
(1997)
J Virol
, vol.71
, pp. 458-464
-
-
Bushman, F.D.1
Miller, M.D.2
-
37
-
-
0034652141
-
Selective positive and negative regulation of endogenous genes by designed transcription factors
-
in press.
-
Beerli R.B., Dreier B., Barbas C.F. III Selective positive and negative regulation of endogenous genes by designed transcription factors. Proc Natl Acad Sci USA. 2000;. in press.
-
(2000)
Proc Natl Acad Sci USA
-
-
Beerli, R.B.1
Dreier, B.2
Barbas C.F. III3
|