-
2
-
-
2342640588
-
Enzyme-mediated DNA-looping
-
Halford,S.E., Welsh,A.J. and Szczelkun,M.D. (2004) Enzyme-mediated DNA-looping. Annu. Rev. Biophys. Biomol. Struct., 33, 1-24.
-
(2004)
Annu. Rev. Biophys. Biomol. Struct
, vol.33
, pp. 1-24
-
-
Halford, S.E.1
Welsh, A.J.2
Szczelkun, M.D.3
-
3
-
-
33644626371
-
DNA mismatch repair: Functions and mechanisms
-
Iyer,R.R., Pluciennik,A., Burdett,V. and Modrich,P.L. (2006) DNA mismatch repair: Functions and mechanisms. Chem. Rev., 106, 302-323.
-
(2006)
Chem. Rev
, vol.106
, pp. 302-323
-
-
Iyer, R.R.1
Pluciennik, A.2
Burdett, V.3
Modrich, P.L.4
-
4
-
-
33746382212
-
Mechanisms of site-specific recombination
-
Grindley,N.D.F., Whiteson,K.L. and Rice,P.A. (2006) Mechanisms of site-specific recombination. Annu. Rev. Biochem., 75, 567-605.
-
(2006)
Annu. Rev. Biochem
, vol.75
, pp. 567-605
-
-
Grindley, N.D.F.1
Whiteson, K.L.2
Rice, P.A.3
-
5
-
-
33746824311
-
Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched of" at low force
-
Gemmen,G.J., Millin,R. and Smith,D.E. (2006) Tension-dependent DNA cleavage by restriction endonucleases: Two-site enzymes are "switched of" at low force. Proc. Natl Acad. Sci. USA, 103, 11555-11560.
-
(2006)
Proc. Natl Acad. Sci. USA
, vol.103
, pp. 11555-11560
-
-
Gemmen, G.J.1
Millin, R.2
Smith, D.E.3
-
6
-
-
20444382737
-
Regulation of transcription: From lambda to eukaryotes
-
Ptashne,M. (2005) Regulation of transcription: From lambda to eukaryotes. Trends Biochem. Sci., 30, 275-279.
-
(2005)
Trends Biochem. Sci
, vol.30
, pp. 275-279
-
-
Ptashne, M.1
-
7
-
-
0025622722
-
Stable DNA loops in vivo and in vitro: Roles in gene regulation at a distance and in biophysical characterization of DNA
-
Bellomy,G.R. and Record,M.T. Jr. (1990) Stable DNA loops in vivo and in vitro: Roles in gene regulation at a distance and in biophysical characterization of DNA. Prog. Nucleic Acid Res. Mol. Biol., 39 81-128.
-
(1990)
Prog. Nucleic Acid Res. Mol. Biol
, vol.39
, pp. 81-128
-
-
Bellomy, G.R.1
Record Jr., M.T.2
-
8
-
-
33645991551
-
Statistical-mechanical theory of DNA looping
-
Zhang,Y., McEwen,A.E., Crothers,D.M. and Levene,S.D. (2006) Statistical-mechanical theory of DNA looping. Biophys. J., 90 1903-1912.
-
(2006)
Biophys. J
, vol.90
, pp. 1903-1912
-
-
Zhang, Y.1
McEwen, A.E.2
Crothers, D.M.3
Levene, S.D.4
-
9
-
-
33645275997
-
Loops in DNA: An overview of experimental and theoretical approaches
-
Allemand,J.F., Cocco,S., Douarche,N. and Lia,G. (2006) Loops in DNA: An overview of experimental and theoretical approaches. Eur. Phys. J. E, Soft Matter, 19, 293-302.
-
(2006)
Eur. Phys. J. E, Soft Matter
, vol.19
, pp. 293-302
-
-
Allemand, J.F.1
Cocco, S.2
Douarche, N.3
Lia, G.4
-
10
-
-
0242350920
-
Diffusion-limited loop formation of semiflexible polymers: Kramer's theory and the intertwined time scales of chain relaxation and closing
-
Jun,S., Bechhoefer,J. and Ha,B-Y. (2003) Diffusion-limited loop formation of semiflexible polymers: Kramer's theory and the intertwined time scales of chain relaxation and closing. Europhys. Lett., 64, 420-426.
-
(2003)
Europhys. Lett
, vol.64
, pp. 420-426
-
-
Jun, S.1
Bechhoefer, J.2
Ha, B.-Y.3
-
11
-
-
0032573605
-
Internal motion of supercoiled DNA: Brownian dynamic simulations of site juxtaposition
-
Jian,H., Schlick,T. and Vologodskii,A. (1998) Internal motion of supercoiled DNA: Brownian dynamic simulations of site juxtaposition. J. Mol. Biol., 284, 287-296.
-
(1998)
J. Mol. Biol
, vol.284
, pp. 287-296
-
-
Jian, H.1
Schlick, T.2
Vologodskii, A.3
-
12
-
-
0035970101
-
Dynamics of site juxtaposition in supercoiled DNA
-
Huang,J., Schlick,T. and Vologodskii,A. (2001) Dynamics of site juxtaposition in supercoiled DNA. Proc. Natl Acad. Sci. USA, 98 968-973.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 968-973
-
-
Huang, J.1
Schlick, T.2
Vologodskii, A.3
-
13
-
-
0034815621
-
Intrachain reactions of supercoiled DNA simulated by Brownian dynamics
-
Klenin,K.V. and Langowski,J. (2001) Intrachain reactions of supercoiled DNA simulated by Brownian dynamics. Biophys. J., 81, 1924-1929.
-
(2001)
Biophys. J
, vol.81
, pp. 1924-1929
-
-
Klenin, K.V.1
Langowski, J.2
-
14
-
-
2342538957
-
Dynamics of DNA loop capture by the Sfil restriction endonuclease on supercoiled and relaxed DNA
-
Embleton,M.L., Vologodskii,A.V. and Halford,S.E. (2004) Dynamics of DNA loop capture by the Sfil restriction endonuclease on supercoiled and relaxed DNA. J. Mol. Biol., 339, 53-66.
-
(2004)
J. Mol. Biol
, vol.339
, pp. 53-66
-
-
Embleton, M.L.1
Vologodskii, A.V.2
Halford, S.E.3
-
15
-
-
0028956979
-
Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules
-
Finzi,L. and Gelles,J. (1995) Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science, 267, 378-380.
-
(1995)
Science
, vol.267
, pp. 378-380
-
-
Finzi, L.1
Gelles, J.2
-
16
-
-
0141482089
-
Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping
-
Lia,G., Bensimon,D., Croquette,V., Allemand,J.F., Dunlap,D., Lewis,D.E., Adhya,S. and Finzi,L. (2003) Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc. Natl Acad. Sci. USA, 100, 11373-11377.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 11373-11377
-
-
Lia, G.1
Bensimon, D.2
Croquette, V.3
Allemand, J.F.4
Dunlap, D.5
Lewis, D.E.6
Adhya, S.7
Finzi, L.8
-
17
-
-
31544452261
-
Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
-
van den Broek,B., Vanzi,F., Normanno,D., Pavone,F.S. and Wuite,G.J. (2006) Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res., 34, 167-174.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 167-174
-
-
van den Broek, B.1
Vanzi, F.2
Normanno, D.3
Pavone, F.S.4
Wuite, G.J.5
-
18
-
-
33845353937
-
Dynamics of single DNA looping and cleavage by Sau3AI and e.ect of tension applied to the DNA
-
Gemmen,G.J., Millin,R. and Smith,D.E. (2006) Dynamics of single DNA looping and cleavage by Sau3AI and e.ect of tension applied to the DNA. Biophys. J., 91, 4154-4165.
-
(2006)
Biophys. J
, vol.91
, pp. 4154-4165
-
-
Gemmen, G.J.1
Millin, R.2
Smith, D.E.3
-
19
-
-
0036392202
-
Kinetics of site-site interactions in supercoiled DNA with bent sequences
-
Bussiek,M., Klenin,K. and Langowski,J. (2002) Kinetics of site-site interactions in supercoiled DNA with bent sequences. J. Mol. Biol. 322, 707-718.
-
(2002)
J. Mol. Biol
, vol.322
, pp. 707-718
-
-
Bussiek, M.1
Klenin, K.2
Langowski, J.3
-
20
-
-
0025817867
-
Dynamics of long-range interactions on DNA: The speed of synapsis during site-specific recombination by resolvase
-
Parker,C.N. and Halford,S.E. (1991) Dynamics of long-range interactions on DNA: The speed of synapsis during site-specific recombination by resolvase. Cell, 66, 781-791.
-
(1991)
Cell
, vol.66
, pp. 781-791
-
-
Parker, C.N.1
Halford, S.E.2
-
21
-
-
0031577319
-
Communications between distant sites on supercoiled DNA from the non-exponential kinetics of DNA synapsis by resolvase
-
Oram,M., Marko,J.F. and Halford,S.E. (1997) Communications between distant sites on supercoiled DNA from the non-exponential kinetics of DNA synapsis by resolvase. J. Mol. Biol., 270, 396-412.
-
(1997)
J. Mol. Biol
, vol.270
, pp. 396-412
-
-
Oram, M.1
Marko, J.F.2
Halford, S.E.3
-
22
-
-
33846078626
-
REBASE - enzymes and genes for DNA restriction and modification
-
Roberts,R.J., Vincze,T., Posfai,J. and Macelis,D. (2007) REBASE - enzymes and genes for DNA restriction and modification. Nucleic Acids Res., 35, D269-D270.
-
(2007)
Nucleic Acids Res
, vol.35
-
-
Roberts, R.J.1
Vincze, T.2
Posfai, J.3
Macelis, D.4
-
23
-
-
0032555294
-
DNA excision by the SfiI restriction endonuclease
-
Nobbs,T.J., Szczelkun,M.D., Wentzell,L.M. and Halford,S.E. (1998) DNA excision by the SfiI restriction endonuclease. J. Mol. Biol., 281, 419-432.
-
(1998)
J. Mol. Biol
, vol.281
, pp. 419-432
-
-
Nobbs, T.J.1
Szczelkun, M.D.2
Wentzell, L.M.3
Halford, S.E.4
-
24
-
-
0037040271
-
Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA
-
Bath,A.J., Milsom,S.E., Gormley,N.A. and Halford,S.E. (2002) Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA. J. Biol. Chem., 277, 4024-4033.
-
(2002)
J. Biol. Chem
, vol.277
, pp. 4024-4033
-
-
Bath, A.J.1
Milsom, S.E.2
Gormley, N.A.3
Halford, S.E.4
-
25
-
-
3042785825
-
One recognition sequence, seven restriction enzymes, five reaction mechanisms
-
Gowers,D.M., Bellamy,S.R.W. and Halford,S.E. (2004) One recognition sequence, seven restriction enzymes, five reaction mechanisms. Nucleic Acids Res., 32, 3469-3479.
-
(2004)
Nucleic Acids Res
, vol.32
, pp. 3469-3479
-
-
Gowers, D.M.1
Bellamy, S.R.W.2
Halford, S.E.3
-
26
-
-
33847162746
-
Restriction endonucleases that bridge and excise two recognition sites from DNA
-
Marshall,J.M., Gowers,D.M. and Halford,S.E. (2007) Restriction endonucleases that bridge and excise two recognition sites from DNA. J. Mol. Biol., 387, 419-431.
-
(2007)
J. Mol. Biol
, vol.387
, pp. 419-431
-
-
Marshall, J.M.1
Gowers, D.M.2
Halford, S.E.3
-
27
-
-
33645522837
-
Protein assembly and DNA looping by the FokI restriction endonuclease
-
Catto,L.E., Ganguly,S., Milsom,S.E., Welsh,A.J. and Halford,S.E. (2006) Protein assembly and DNA looping by the FokI restriction endonuclease. Nucleic Acids Res., 34, 1711-1720.
-
(2006)
Nucleic Acids Res
, vol.34
, pp. 1711-1720
-
-
Catto, L.E.1
Ganguly, S.2
Milsom, S.E.3
Welsh, A.J.4
Halford, S.E.5
-
28
-
-
0035946911
-
FokI requires two specific DNA sites for cleavage
-
Vanamee,E.S., Santagata,S. and Aggarwal,A.K. (2001) FokI requires two specific DNA sites for cleavage. J. Mol. Biol., 309, 69-78.
-
(2001)
J. Mol. Biol
, vol.309
, pp. 69-78
-
-
Vanamee, E.S.1
Santagata, S.2
Aggarwal, A.K.3
-
29
-
-
0036440653
-
Type II restriction endonucleases
-
Perona,J.J. (2002) Type II restriction endonucleases. Methods, 28, 353-364.
-
(2002)
Methods
, vol.28
, pp. 353-364
-
-
Perona, J.J.1
-
30
-
-
0030985132
-
Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease
-
Erskine,S.G., Baldwin,G.S. and Halford,S.E. (1997) Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease. Biochemistry, 36, 7567-7576.
-
(1997)
Biochemistry
, vol.36
, pp. 7567-7576
-
-
Erskine, S.G.1
Baldwin, G.S.2
Halford, S.E.3
-
31
-
-
0033527546
-
The kinetic mechanism of EcoRI endonuclease
-
Wright,D.J., Jack,W.E. and Modrich,P. (1999) The kinetic mechanism of EcoRI endonuclease. J. Biol. Chem., 274, 31896-31902.
-
(1999)
J. Biol. Chem
, vol.274
, pp. 31896-31902
-
-
Wright, D.J.1
Jack, W.E.2
Modrich, P.3
-
32
-
-
17144383262
-
Cleavage of individual DNA strands by the different subunits of the heterodimeric restriction endonuclease BbvCI
-
Bellamy,S.R.W., Milsom,S.E., Scott,D.J., Daniels,L.E., Wilson,G.G. and Halford,S.E. (2005) Cleavage of individual DNA strands by the different subunits of the heterodimeric restriction endonuclease BbvCI. J. Mol. Biol., 348, 641-653.
-
(2005)
J. Mol. Biol
, vol.348
, pp. 641-653
-
-
Bellamy, S.R.W.1
Milsom, S.E.2
Scott, D.J.3
Daniels, L.E.4
Wilson, G.G.5
Halford, S.E.6
-
33
-
-
0027419084
-
Atypical DNA-binding properties of class-IIS restriction endonucleases: Evidence for recognition of the cognate sequence by a FokI monomer
-
Skowron,P., Kaczorowski,T., Tucholski,J. and Podhajska,A.J. (1993) Atypical DNA-binding properties of class-IIS restriction endonucleases: evidence for recognition of the cognate sequence by a FokI monomer. Gene, 125, 1-10.
-
(1993)
Gene
, vol.125
, pp. 1-10
-
-
Skowron, P.1
Kaczorowski, T.2
Tucholski, J.3
Podhajska, A.J.4
-
34
-
-
0030790696
-
Structure of the multimodular endonuclease FokI bound to DNA
-
Wah,D.A., Hirsch,J.A., Dorner,L.F., Schildkraut,I. and Aggarwal,A.K. (1997) Structure of the multimodular endonuclease FokI bound to DNA. Nature, 388, 97-100.
-
(1997)
Nature
, vol.388
, pp. 97-100
-
-
Wah, D.A.1
Hirsch, J.A.2
Dorner, L.F.3
Schildkraut, I.4
Aggarwal, A.K.5
-
35
-
-
0032169674
-
Structure of FokI has implications for DNA cleavage
-
Wah,D.A., Bitinaite,J., Schildkraut,I. and Aggarwal,A.K. (1998) Structure of FokI has implications for DNA cleavage. Proc. Natl Acad. Sci. USA, 95, 10564-10569.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 10564-10569
-
-
Wah, D.A.1
Bitinaite, J.2
Schildkraut, I.3
Aggarwal, A.K.4
-
36
-
-
0032167717
-
FokI dimerization is required for DNA cleavage
-
Bitinaite,J., Wah,D.A., Aggarwal,A.K. and Schildkraut,I. (1998) FokI dimerization is required for DNA cleavage. Proc. Natl Acad. Sci. USA 95, 10570-10575.
-
(1998)
Proc. Natl Acad. Sci. USA
, vol.95
, pp. 10570-10575
-
-
Bitinaite, J.1
Wah, D.A.2
Aggarwal, A.K.3
Schildkraut, I.4
-
37
-
-
0344875225
-
DNA supercoiling enables the Type IIS restriction enzyme BspMI to recognise the relative orientation of two DNA sequences
-
Kingston,I.J., Gormley,N.A. and Halford,S.E. (2003) DNA supercoiling enables the Type IIS restriction enzyme BspMI to recognise the relative orientation of two DNA sequences. Nucleic Acids Res., 31, 5221-5228.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 5221-5228
-
-
Kingston, I.J.1
Gormley, N.A.2
Halford, S.E.3
-
38
-
-
33751298733
-
The identification of chemical intermediates in enzyme catalysis by the rapid quench-flow technique
-
Barman,T.E., Bellamy,S.R.W., Gutfreund,H., Halford,S.E. and Lionne,C. (2006) The identification of chemical intermediates in enzyme catalysis by the rapid quench-flow technique. Cell Mol. Life Sci., 63, 2571-2583.
-
(2006)
Cell Mol. Life Sci
, vol.63
, pp. 2571-2583
-
-
Barman, T.E.1
Bellamy, S.R.W.2
Gutfreund, H.3
Halford, S.E.4
Lionne, C.5
-
40
-
-
35348935490
-
Probability of the site juxtaposition determines the rate of protein-mediated DNA looping
-
Polikanov,Y.S., Bondarenko,V.A., Tchernaenko,V., Jiang,Y.I., Lutter,L.C., Vologodskii,A. and Studitsky,V.M. (2007) Probability of the site juxtaposition determines the rate of protein-mediated DNA looping. Biophys. J., 93, 2726-3271.
-
(2007)
Biophys. J
, vol.93
, pp. 2726-3271
-
-
Polikanov, Y.S.1
Bondarenko, V.A.2
Tchernaenko, V.3
Jiang, Y.I.4
Lutter, L.C.5
Vologodskii, A.6
Studitsky, V.M.7
-
41
-
-
0000773557
-
Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy
-
Millar,D.P., Robbins,R.J. and Zewail,A.H. (1980) Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy. Proc. Natl Acad. Sci. USA, 77, 5593-5597.
-
(1980)
Proc. Natl Acad. Sci. USA
, vol.77
, pp. 5593-5597
-
-
Millar, D.P.1
Robbins, R.J.2
Zewail, A.H.3
-
42
-
-
16244422033
-
Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: Oligomeric structure-stability-function correlations
-
Zaremba,M., Sasnauskas,G., Urbanke,C. and Siksnys,V. (2005) Conversion of the tetrameric restriction endonuclease Bse634I into a dimer: oligomeric structure-stability-function correlations. J. Mol. Biol. 348, 459-478.
-
(2005)
J. Mol. Biol
, vol.348
, pp. 459-478
-
-
Zaremba, M.1
Sasnauskas, G.2
Urbanke, C.3
Siksnys, V.4
-
43
-
-
35148841533
-
A switch in the mechanism of oommunication between the two DNA-binding sites in the SfiI restriction endonuclease
-
Bellamy,S.R.W., Milsom,S.E., Kovacheva,Y.S. and Halford,S.E. (2007) A switch in the mechanism of oommunication between the two DNA-binding sites in the SfiI restriction endonuclease. J. Mol. Biol., 373 1169-1183.
-
(2007)
J. Mol. Biol
, vol.373
, pp. 1169-1183
-
-
Bellamy, S.R.W.1
Milsom, S.E.2
Kovacheva, Y.S.3
Halford, S.E.4
|