-
1
-
-
0026682657
-
Transcription factors: Structural families and principles of DNA recognition
-
Pabo,C.O. and Sauer,R.T. (1992) Transcription factors: Structural families and principles of DNA recognition. Annu. Rev. Biochem., 61, 1053-1095.
-
(1992)
Annu. Rev. Biochem
, vol.61
, pp. 1053-1095
-
-
Pabo, C.O.1
Sauer, R.T.2
-
2
-
-
0004204457
-
-
Garland Publishing, Inc, New York, USA
-
Branden,C. and Tooze,J. (1999) Introduction to Protein Structure Garland Publishing, Inc., New York, USA.
-
(1999)
Introduction to Protein Structure
-
-
Branden, C.1
Tooze, J.2
-
3
-
-
0033647653
-
An overview of the structures of protein-DNA complexes
-
Luscombe,N.M., Austin,S.M., Berman,H.M. and Thornton,J.M. (2000) An overview of the structures of protein-DNA complexes. Genome Biol., 1, 1-37.
-
(2000)
Genome Biol
, vol.1
, pp. 1-37
-
-
Luscombe, N.M.1
Austin, S.M.2
Berman, H.M.3
Thornton, J.M.4
-
4
-
-
0035393302
-
Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level
-
Luscombe,N.M., Laskowski,R.A. and Thornton,J.M. (2001) Amino acid-base interactions: A three-dimensional analysis of protein-DNA interactions at an atomic level. Nucleic Acids Res., 29, 2860-2874.
-
(2001)
Nucleic Acids Res
, vol.29
, pp. 2860-2874
-
-
Luscombe, N.M.1
Laskowski, R.A.2
Thornton, J.M.3
-
5
-
-
20544460658
-
Protein-DNA recognition patterns and predictions
-
Sarai,A. and Kono,H. (2005) Protein-DNA recognition patterns and predictions. Annu. Rev. Biophys. Biomol. Struct., 34, 379-398.
-
(2005)
Annu. Rev. Biophys. Biomol. Struct
, vol.34
, pp. 379-398
-
-
Sarai, A.1
Kono, H.2
-
6
-
-
17044403057
-
Type II restriction endonucleases: Structure and mechanism
-
Pingoud,A., Fuxreiter,M., Pingoud,V. and Wende,W. (2005) Type II restriction endonucleases: Structure and mechanism. Cell. Mol. Life Sci., 62, 685-707.
-
(2005)
Cell. Mol. Life Sci
, vol.62
, pp. 685-707
-
-
Pingoud, A.1
Fuxreiter, M.2
Pingoud, V.3
Wende, W.4
-
8
-
-
0030812487
-
Homing endonucleases - keeping the house in order
-
Beffort,M. and Roberts,R. (1997) Homing endonucleases - keeping the house in order. Nucleic Acids Res., 25, 3379-3388.
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 3379-3388
-
-
Beffort, M.1
Roberts, R.2
-
9
-
-
34047150780
-
-
Springer, Berlin
-
Belfort,M., Derbyshire,V., Stoddard,B.L. and Wood,D.W. (2005) Homing Endonucleases and Inteins Springer, Berlin.
-
(2005)
Homing Endonucleases and Inteins
-
-
Belfort, M.1
Derbyshire, V.2
Stoddard, B.L.3
Wood, D.W.4
-
10
-
-
33644756595
-
Homing endonuclease structure and function
-
Stoddard,B.L. (2005) Homing endonuclease structure and function. Quarterly Rev. Biophys., 38, 1-47.
-
(2005)
Quarterly Rev. Biophys
, vol.38
, pp. 1-47
-
-
Stoddard, B.L.1
-
11
-
-
23444441147
-
Gene targeting using zinc finger nucleases
-
Porteus,M.H. and Carroll,D. (2005) Gene targeting using zinc finger nucleases. Nat. Biotechnol., 23, 967-973.
-
(2005)
Nat. Biotechnol
, vol.23
, pp. 967-973
-
-
Porteus, M.H.1
Carroll, D.2
-
12
-
-
0034656221
-
Invasion of a multitude of genetic niches by mobile endonuclease genes
-
Gimble,F.S. (2000) Invasion of a multitude of genetic niches by mobile endonuclease genes. FEMS Microbiol. Lett., 185, 99-107.
-
(2000)
FEMS Microbiol. Lett
, vol.185
, pp. 99-107
-
-
Gimble, F.S.1
-
13
-
-
8644255915
-
Homing endonuclease genes: The rise and fall and rise again of a selfish element
-
Burt,A. and Koufopanou,V. (2004) Homing endonuclease genes: The rise and fall and rise again of a selfish element. Curr. Opin. Genet. Dev, 14, 609-615.
-
(2004)
Curr. Opin. Genet. Dev
, vol.14
, pp. 609-615
-
-
Burt, A.1
Koufopanou, V.2
-
14
-
-
0024966071
-
A mobile Group I intron in the nuclear rDNA of Physarum polycephalum
-
Muscarella,D.E. and Vogt,V.M. (1989) A mobile Group I intron in the nuclear rDNA of Physarum polycephalum. Cell, 56, 443-454.
-
(1989)
Cell
, vol.56
, pp. 443-454
-
-
Muscarella, D.E.1
Vogt, V.M.2
-
15
-
-
0033459467
-
Structural parsimony in endonuclease active sites: Should the number of homing endonuclease families be redefined?
-
Kuhlmann,U.C., Moore,G.R., James,R., Kleanthous,C. and Hemmings,A.M. (1999) Structural parsimony in endonuclease active sites: Should the number of homing endonuclease families be redefined? FEBS Lett., 463, 1-2.
-
(1999)
FEBS Lett
, vol.463
, pp. 1-2
-
-
Kuhlmann, U.C.1
Moore, G.R.2
James, R.3
Kleanthous, C.4
Hemmings, A.M.5
-
16
-
-
33644782864
-
His-Cys box homing endonucleases
-
Belfort,M, Derbyshire,V, Stoddard,B.L. and Wood,D.W, eds, Springer-Verlag, Berlin
-
Galburt,E.A. and Jurica,M.S. (2005) His-Cys box homing endonucleases. In Belfort,M., Derbyshire,V., Stoddard,B.L. and Wood,D.W. (eds), Homing Endonucleases and Inteins, Springer-Verlag, Berlin, Vol. 16, pp. 85-102.
-
(2005)
Homing Endonucleases and Inteins
, vol.16
, pp. 85-102
-
-
Galburt, E.A.1
Jurica, M.S.2
-
17
-
-
0025375161
-
Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum
-
Muscarella,D.E., Ellison,E.L., Ruoff,B.M. and Vogt,V.M. (1990) Characterization of I-Ppo, an intron-encoded endonuclease that mediates homing of a group I intron in the ribosomal DNA of Physarum polycephalum. Mol. Cell. Biol., 10, 3386-3396.
-
(1990)
Mol. Cell. Biol
, vol.10
, pp. 3386-3396
-
-
Muscarella, D.E.1
Ellison, E.L.2
Ruoff, B.M.3
Vogt, V.M.4
-
18
-
-
0027424120
-
Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site
-
Ellison,E.L. and Vogt,V.M. (1993) Interaction of the intron-encoded mobility endonuclease I-PpoI with its target site. Mol. Cell. Biol. 13, 7531-7539.
-
(1993)
Mol. Cell. Biol
, vol.13
, pp. 7531-7539
-
-
Ellison, E.L.1
Vogt, V.M.2
-
19
-
-
0345120902
-
Generation of highly site-specific DNA double-strand breaks in human cells by the homing endonucleases I-PpoI and I-CreI
-
Monnat,R.J., Hackmann,A.F.M. and Cantrell,M.A. (1999) Generation of highly site-specific DNA double-strand breaks in human cells by the homing endonucleases I-PpoI and I-CreI. Biochem. Biophys. Res. Commun., 255, 88-93.
-
(1999)
Biochem. Biophys. Res. Commun
, vol.255
, pp. 88-93
-
-
Monnat, R.J.1
Hackmann, A.F.M.2
Cantrell, M.A.3
-
20
-
-
34447551681
-
Roles of ATM and NBSI in chromatin structure modulation and DNA double-strand break repair
-
Berkovich,E., Monnat,R.J. and Kastan,M.B. (2007) Roles of ATM and NBSI in chromatin structure modulation and DNA double-strand break repair. Nat. Cell Biol., 9, 683-690.
-
(2007)
Nat. Cell Biol
, vol.9
, pp. 683-690
-
-
Berkovich, E.1
Monnat, R.J.2
Kastan, M.B.3
-
21
-
-
0032474760
-
DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI
-
Flick,K.E., Jurica,M.S., Monnat,R.J., Jr and Stoddard,B.L. (1998) DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature, 394, 96-101.
-
(1998)
Nature
, vol.394
, pp. 96-101
-
-
Flick, K.E.1
Jurica, M.S.2
Monnat Jr, R.J.3
Stoddard, B.L.4
-
22
-
-
0032708112
-
A novel endonuclease mechanism directly visualized for I-PpoI
-
Galburt,E.A., Chevalier,B., Tang,W., Jurica,M.S., Flick,K.E., Monnat,R.J., Jr and Stoddard,B.L. (1999) A novel endonuclease mechanism directly visualized for I-PpoI. Nat. Struct. Biol., 6, 1096-1099.
-
(1999)
Nat. Struct. Biol
, vol.6
, pp. 1096-1099
-
-
Galburt, E.A.1
Chevalier, B.2
Tang, W.3
Jurica, M.S.4
Flick, K.E.5
Monnat Jr, R.J.6
Stoddard, B.L.7
-
23
-
-
0031456272
-
Crystallization and preliminary X-ray studies of I-PpoI: A nuclear, intron-encoded homing endonuclease, from Physarum polycephalum
-
Flick,K.E., McHugh,D., Heath,J.D., Stephens,K.M., Monnat,R.J., Jr and Stoddard,B.L. (1997) Crystallization and preliminary X-ray studies of I-PpoI: A nuclear, intron-encoded homing endonuclease, from Physarum polycephalum. Protein Sci., 6, 1-4.
-
(1997)
Protein Sci
, vol.6
, pp. 1-4
-
-
Flick, K.E.1
McHugh, D.2
Heath, J.D.3
Stephens, K.M.4
Monnat Jr, R.J.5
Stoddard, B.L.6
-
24
-
-
0032540751
-
-
Argast,G.M., Stephens,K.M., Emond,M.J. and Monnat.R.J. (1998) I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential vitro enrichment. J. Mol. Biol., 280, 345-353.
-
Argast,G.M., Stephens,K.M., Emond,M.J. and Monnat.R.J. (1998) I-PpoI and I-CreI homing site sequence degeneracy determined by random mutagenesis and sequential vitro enrichment. J. Mol. Biol., 280, 345-353.
-
-
-
-
25
-
-
0032484598
-
Degenerate, DNA recognition by I-PpoI endonuclease
-
Wittmayer,P.K., McKenzie,J.L. and Raines,R.T. (1998), Degenerate, DNA recognition by I-PpoI endonuclease. Gene, 206, 11-21.
-
(1998)
Gene
, vol.206
, pp. 11-21
-
-
Wittmayer, P.K.1
McKenzie, J.L.2
Raines, R.T.3
-
26
-
-
0034697977
-
Conformational changes and cleavage by the homing endonuclease I-PpoI: A critical role for a leucine residue in the active site
-
Galburt,E.A., Chadsey,M.S., Jurica,M.S., Chevalier,B.S., Ehro,D., Tang,W., Monnat,R.J, Jr and Stoddard,B.L. (2000) Conformational changes and cleavage by the homing endonuclease I-PpoI: A critical role for a leucine residue in the active site. J. Mol. Biol., 300, 877-887.
-
(2000)
J. Mol. Biol
, vol.300
, pp. 877-887
-
-
Galburt, E.A.1
Chadsey, M.S.2
Jurica, M.S.3
Chevalier, B.S.4
Ehro, D.5
Tang, W.6
Monnat Jr, R.J.7
Stoddard, B.L.8
-
27
-
-
0018608548
-
Sterile host yeasts (SHY): A eukaryotic system of biological containment for recombinant DNA experiments
-
Botstein,D., Falco,S.C., Stewart,S.E., Brennan,M., Scherer,S., Stinchcomb,D.T., Struhl,K. and Davis,R.W. (1979) Sterile host yeasts (SHY): A eukaryotic system of biological containment for recombinant DNA experiments. Gene, 8, 17-24.
-
(1979)
Gene
, vol.8
, pp. 17-24
-
-
Botstein, D.1
Falco, S.C.2
Stewart, S.E.3
Brennan, M.4
Scherer, S.5
Stinchcomb, D.T.6
Struhl, K.7
Davis, R.W.8
-
28
-
-
0024669291
-
A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae
-
Sikorski,R.S. and Hieter,P. (1989) A system of shuttle vectors and yeast host strains designed for efficient manipulation of DNA in Saccharomyces cerevisiae. Genetics, 122, 19-27.
-
(1989)
Genetics
, vol.122
, pp. 19-27
-
-
Sikorski, R.S.1
Hieter, P.2
-
29
-
-
33644792045
-
Yeast transformation by the LiAc/SS carrier DNA/PEG method
-
Gietz,R.D. and Woods,R.A. (2006) Yeast transformation by the LiAc/SS carrier DNA/PEG method. Methods Mol. Biol., 313, 107-120.
-
(2006)
Methods Mol. Biol
, vol.313
, pp. 107-120
-
-
Gietz, R.D.1
Woods, R.A.2
-
30
-
-
0036275447
-
Getting started with yeast
-
Sherman,F. (2002) Getting started with yeast. Meth. Enzymol., 350, 3-41.
-
(2002)
Meth. Enzymol
, vol.350
, pp. 3-41
-
-
Sherman, F.1
-
31
-
-
0035879501
-
Cloning of random oligonucleotides to create single-insert plasmid libraries
-
Worthington,M.T., Pelo,J. and Lo,R.Q. (2001) Cloning of random oligonucleotides to create single-insert plasmid libraries. Anal. Biochem., 294, 169-175.
-
(2001)
Anal. Biochem
, vol.294
, pp. 169-175
-
-
Worthington, M.T.1
Pelo, J.2
Lo, R.Q.3
-
32
-
-
0004270170
-
-
John Wiley & Sons, Now York, USA
-
Ausubel,F.M., Brent,R., Kingston,R.E., Moore,D.D., Seidman,J.G., Smith,J.A. and Struhl,K. (1987) Current Protocols in Molecular Biology John Wiley & Sons, Now York, USA.
-
(1987)
Current Protocols in Molecular Biology
-
-
Ausubel, F.M.1
Brent, R.2
Kingston, R.E.3
Moore, D.D.4
Seidman, J.G.5
Smith, J.A.6
Struhl, K.7
-
34
-
-
7044239239
-
A simple physical model for the prediction and design of protein-DNA interactions
-
Havranek,J.J., Duarte,C.M. and Baker,D. (2004) A simple physical model for the prediction and design of protein-DNA interactions. J. Mol. Biol., 344, 59-70.
-
(2004)
J. Mol. Biol
, vol.344
, pp. 59-70
-
-
Havranek, J.J.1
Duarte, C.M.2
Baker, D.3
-
35
-
-
27244460904
-
Protein-DNA binding specificity predictions with structural models
-
Morozov,A.V., Havranek,J.J., Baker,D. and Siggia,E.D. (2005) Protein-DNA binding specificity predictions with structural models. Nucleic Acids Res., 33, 5781-5798.
-
(2005)
Nucleic Acids Res
, vol.33
, pp. 5781-5798
-
-
Morozov, A.V.1
Havranek, J.J.2
Baker, D.3
Siggia, E.D.4
-
36
-
-
0027395847
-
A mobile Group I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of Saccharomyces cerevisiae
-
Muscarella,D.E. and Vogt,V.M. (1993) A mobile Group I intron from Physarum polycephalum can insert itself and induce point mutations in the nuclear ribosomal DNA of Saccharomyces cerevisiae. Mol. Cell. Biol., 13, 1023-1033.
-
(1993)
Mol. Cell. Biol
, vol.13
, pp. 1023-1033
-
-
Muscarella, D.E.1
Vogt, V.M.2
-
37
-
-
0344441707
-
Assessing the plasticity of DNA target site recognition of the PI-SceI homing endonuclease using a bacterial two-hybrid selection system
-
Gimble,F.S., Moure,C.M. and Posey,K.L. (2003) Assessing the plasticity of DNA target site recognition of the PI-SceI homing endonuclease using a bacterial two-hybrid selection system. J. Mol. Biol., 334, 993-1008.
-
(2003)
J. Mol. Biol
, vol.334
, pp. 993-1008
-
-
Gimble, F.S.1
Moure, C.M.2
Posey, K.L.3
-
39
-
-
33750621840
-
Indirect readout of DNA sequences by proteins: The roles of DNA sequence-dependent intrinsic and extrinsic forces
-
Koudelka,G.B., Mauro,S.A. and Ciubotaru,M. (2006) Indirect readout of DNA sequences by proteins: The roles of DNA sequence-dependent intrinsic and extrinsic forces. Prog. Nucleic Acid Res. Mol. Biol., 81 143-177.
-
(2006)
Prog. Nucleic Acid Res. Mol. Biol
, vol.81
, pp. 143-177
-
-
Koudelka, G.B.1
Mauro, S.A.2
Ciubotaru, M.3
-
40
-
-
33745278855
-
-
Ashworth,J., Havranek,J.J., Duarte,C.M., Sussman,D., Monnat,R.J., Stoddard,B.L. and Baker.D. (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature, 441, 656-659.
-
Ashworth,J., Havranek,J.J., Duarte,C.M., Sussman,D., Monnat,R.J., Stoddard,B.L. and Baker.D. (2006) Computational redesign of endonuclease DNA binding and cleavage specificity. Nature, 441, 656-659.
-
-
-
-
41
-
-
33644507991
-
Directed evolution and substrate specificity profile of homing endonuclease I-SceI
-
Doyon,J.B., Pattanayak,V., Meyer,C.B. and Liu,D.R. (2006) Directed evolution and substrate specificity profile of homing endonuclease I-SceI. J. Am. Chem. Soc., 128, 2477-2484.
-
(2006)
J. Am. Chem. Soc
, vol.128
, pp. 2477-2484
-
-
Doyon, J.B.1
Pattanayak, V.2
Meyer, C.B.3
Liu, D.R.4
-
42
-
-
0027384567
-
Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease
-
Puchta,H., Dujon,B. and Hohn,B. (1993) Homologous recombination in plant cells is enhanced by in vivo induction of double strand breaks into DNA by a site-specific endonuclease. Nucleic Acids Res., 21, 5034-5040.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 5034-5040
-
-
Puchta, H.1
Dujon, B.2
Hohn, B.3
-
43
-
-
0028061666
-
Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease
-
Rouet,P., Smih,F. and Jasin,M. (1994) Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease. Mol. Cell. Biol., 14, 8096-8106.
-
(1994)
Mol. Cell. Biol
, vol.14
, pp. 8096-8106
-
-
Rouet, P.1
Smih, F.2
Jasin, M.3
-
44
-
-
0028575712
-
Repair of a specific double-strand break generated within a mammalian chromosome by yeast endonuclease I-SceI
-
Lukacsovich,T., Yang,D. and Waldman,A.S. (1994) Repair of a specific double-strand break generated within a mammalian chromosome by yeast endonuclease I-SceI. Nucleic Acids Res., 22, 5649-5657.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 5649-5657
-
-
Lukacsovich, T.1
Yang, D.2
Waldman, A.S.3
-
45
-
-
33847246298
-
Meganucleases and DNA double-strand break-induced recombination: Perspectives on gene therapy
-
Pâques,F. and Duchateau,P. (2007) Meganucleases and DNA double-strand break-induced recombination: Perspectives on gene therapy. Curr. Gene Ther., 7, 49-66.
-
(2007)
Curr. Gene Ther
, vol.7
, pp. 49-66
-
-
Pâques, F.1
Duchateau, P.2
|