-
1
-
-
33744807717
-
DNA looping: The consequences and its control
-
DOI 10.1016/j.sbi.2006.05.008, PII S0959440X06000790
-
Saiz, L. and Vilar, J.M. (2006) DNA looping: the consequences and its control. Curr. Opin. Struct. Biol., 16, 344-350. (Pubitemid 43831652)
-
(2006)
Current Opinion in Structural Biology
, vol.16
, Issue.3
, pp. 344-350
-
-
Saiz, L.1
Vilar, J.M.2
-
2
-
-
0037040271
-
Many type IIs restriction endonucleases interact with two recognition sites before cleaving DNA
-
DOI 10.1074/jbc.M108441200
-
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. (Pubitemid 34968658)
-
(2002)
Journal of Biological Chemistry
, vol.277
, Issue.6
, pp. 4024-4033
-
-
Bath, A.J.1
Milsom, S.E.2
Gormley, N.A.3
Halford, S.E.4
-
3
-
-
2342640588
-
Enzyme-mediated DNA looping
-
DOI 10.1146/annurev.biophys.33.110502.132711
-
Halford, S.E., Welsh, A.J. and Szczelkun, M.D. (2004) Enzyme-mediated DNA looping. Annu. Rev. Biophys. Biomol. Struct., 33, 1-24. (Pubitemid 38829949)
-
(2004)
Annual Review of Biophysics and Biomolecular Structure
, vol.33
, pp. 1-24
-
-
Halford, S.E.1
Welsh, A.J.2
Szczelkun, M.D.3
-
5
-
-
0025801446
-
NaeI endonuclease binding to pBR322 DNA induces looping
-
Topal, M.D., Thresher, R.J., Conrad, M. and Griffith, J. (1991) NaeI endonuclease binding to pBR322 DNA induces looping. Biochemistry, 30, 2006-2010.
-
(1991)
Biochemistry
, vol.30
, pp. 2006-2010
-
-
Topal, M.D.1
Thresher, R.J.2
Conrad, M.3
Griffith, J.4
-
6
-
-
0035902832
-
DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites
-
DOI 10.1006/jmbi.2001.4892
-
Embleton, M.L., Siksnys, V. and Halford, S.E. (2001) DNA cleavage reactions by type II restriction enzymes that require two copies of their recognition sites. J. Mol. Biol., 311, 503-514. (Pubitemid 32816585)
-
(2001)
Journal of Molecular Biology
, vol.311
, Issue.3
, pp. 503-514
-
-
Embleton, M.L.1
Siksnys, V.2
Halford, S.E.3
-
8
-
-
77953512028
-
Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription
-
Finzi, L. and Dunlap, D.D. (2010) Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription. J. Biol. Chem., 285, 18973-18978.
-
(2010)
J. Biol. Chem.
, vol.285
, pp. 18973-18978
-
-
Finzi, L.1
Dunlap, D.D.2
-
9
-
-
37049024837
-
Near-field-magnetic-tweezer manipulation of single DNA molecules
-
Yan, J., Skoko, D. and Marko, J.F. (2004) Near-field-magnetic-tweezer manipulation of single DNA molecules. Phys. Rev. E Stat. Nonlin. Soft Matter Phys., 70, 011905.
-
(2004)
Phys. Rev. e Stat. Nonlin. Soft Matter Phys.
, vol.70
, pp. 011905
-
-
Yan, J.1
Skoko, D.2
Marko, J.F.3
-
10
-
-
44449136151
-
Recent advances in optical tweezers
-
Moffitt, J.R., Chemla, Y.R., Smith, S.B. and Bustamante, C. (2008) Recent advances in optical tweezers. Annu. Rev. Biochem., 77, 205-228.
-
(2008)
Annu. Rev. Biochem.
, vol.77
, pp. 205-228
-
-
Moffitt, J.R.1
Chemla, Y.R.2
Smith, S.B.3
Bustamante, C.4
-
11
-
-
48349090299
-
See me, feel me: Methods to concurrently visualize and manipulate single DNA molecules and associated proteins
-
Van Mameren, J., Peterman, E.J. and Wuite, G.J.L. (2008) See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins. Nucleic Acids Res., 36, 4381-4389.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 4381-4389
-
-
Van Mameren, J.1
Peterman, E.J.2
Wuite, G.J.L.3
-
12
-
-
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
-
13
-
-
31544452261
-
Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
-
DOI 10.1093/nar/gkj432
-
Van den Broek, B., Vanzi, F., Normanno, D., Pavone, F.S. and Wuite, G.J.L. (2006) Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res., 34, 167-174. (Pubitemid 43160041)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.1
, pp. 167-174
-
-
Van Den Broek, B.1
Vanzi, F.2
Normanno, D.3
Pavone, F.S.4
Wuite, G.J.L.5
-
14
-
-
70449704619
-
Dissecting protein-induced DNA looping dynamics in real time
-
Laurens, N., Bellamy, S.R., Harms, A.F., Kovacheva, Y.S., Halford, S.E. and Wuite, G.J. (2009) Dissecting protein-induced DNA looping dynamics in real time. Nucleic Acids Res., 37, 5454-5464.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 5454-5464
-
-
Laurens, N.1
Bellamy, S.R.2
Harms, A.F.3
Kovacheva, Y.S.4
Halford, S.E.5
Wuite, G.J.6
-
15
-
-
68349150612
-
First-principles calculation of DNA looping in tethered particle experiments
-
Towles, K.B., Beausang, J.F., Garcia, H.G., Phillips, R. and Nelson, P.C. (2009) First-principles calculation of DNA looping in tethered particle experiments. Phys. Biol., 6, 025001.
-
(2009)
Phys. Biol.
, vol.6
, pp. 025001
-
-
Towles, K.B.1
Beausang, J.F.2
Garcia, H.G.3
Phillips, R.4
Nelson, P.C.5
-
16
-
-
78651299353
-
DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme
-
Zaremba, M., Owsicka, A., Tamulaitis, G., Sasnauskas, G., Shlyakhtenko, L.S., Lushnikov, A.Y., Lyubchenko, Y.L., Laurens, N., Van den Broek, B. and Wuite, G.J. (2010) DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. Nucleic Acids Res., 38, 7142-7154.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 7142-7154
-
-
Zaremba, M.1
Owsicka, A.2
Tamulaitis, G.3
Sasnauskas, G.4
Shlyakhtenko, L.S.5
Lushnikov, A.Y.6
Lyubchenko, Y.L.7
Laurens, N.8
Van Den Broek, B.9
Wuite, G.J.10
-
17
-
-
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
-
18
-
-
0038652096
-
How the BfiI restriction enzyme uses one active site to cut two DNA strands
-
DOI 10.1073/pnas.1131003100
-
Sasnauskas, G., Halford, S.E. and Siksnys, V. (2003) How the BfiI restriction enzyme uses one active site to cut two DNA strands. Proc. Natl Acad. Sci. USA, 100, 6410-6415. (Pubitemid 36666595)
-
(2003)
Proceedings of the National Academy of Sciences of the United States of America
, vol.100
, Issue.11
, pp. 6410-6415
-
-
Sasnauskas, G.1
Halford, S.E.2
Siksnys, V.3
-
19
-
-
84862178378
-
DNA looping by FokI: The impact of synapse geometry on loop topology at varied site orientations
-
Rusling, D.A., Laurens, N., Pernstich, C., Wuite, G.J.L. and Halford, S.E. (2012) DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations. Nucleic Acids Res., 40, 4977-4987.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 4977-4987
-
-
Rusling, D.A.1
Laurens, N.2
Pernstich, C.3
Wuite, G.J.L.4
Halford, S.E.5
-
20
-
-
0032167717
-
Foki dimerization is required for dna cleavage
-
DOI 10.1073/pnas.95.18.10570
-
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. (Pubitemid 28413108)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.18
, pp. 10570-10575
-
-
Bitinaite, J.1
Wah, D.A.2
Aggarwal, A.K.3
Schildkraut, I.4
-
21
-
-
0032169674
-
Structure of FokI has implications for DNA cleavage
-
DOI 10.1073/pnas.95.18.10564
-
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. (Pubitemid 28413107)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.18
, pp. 10564-10569
-
-
Wah, D.A.1
Bitinaite, J.2
Schildkraut, I.3
Aggarwal, A.K.4
-
22
-
-
65549139378
-
Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands
-
Sanders, K.L., Catto, L.E., Bellamy, S.R. and Halford, S.E. (2009) Targeting individual subunits of the FokI restriction endonuclease to specific DNA strands. Nucleic Acids Res., 37, 2105-2115.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2105-2115
-
-
Sanders, K.L.1
Catto, L.E.2
Bellamy, S.R.3
Halford, S.E.4
-
23
-
-
84856895490
-
Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer
-
Pernstich, C. and Halford, S.E. (2012) Illuminating the reaction pathway of the FokI restriction endonuclease by fluorescence resonance energy transfer. Nucleic Acids Res., 40, 1203-1213.
-
(2012)
Nucleic Acids Res.
, vol.40
, pp. 1203-1213
-
-
Pernstich, C.1
Halford, S.E.2
-
24
-
-
41849085964
-
Dynamics and consequences of DNA looping by the FokI restriction endonuclease
-
DOI 10.1093/nar/gkn051
-
Catto, L.E., Bellamy, S.R., Retter, S.E. and Halford, S.E. (2008) Dynamics and consequences of DNA looping by the Foki restriction endonuclease. Nucleic Acids Res., 36, 2073-2081. (Pubitemid 351494248)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.6
, pp. 2073-2081
-
-
Catto, L.E.1
Bellamy, S.R.W.2
Retter, S.E.3
Halford, S.E.4
-
25
-
-
20444387232
-
A gamut of loops: Meandering DNA
-
DOI 10.1016/j.tibs.2005.04.009, PII S0968000405001179, Celebrating 50 Years of the IUBMB
-
Semsey, S., Virnik, K. and Adhya, S. (2005) A gamut of loops: meandering DNA. Trends Biochem. Sci., 30, 334-341. (Pubitemid 40799052)
-
(2005)
Trends in Biochemical Sciences
, vol.30
, Issue.6
, pp. 334-341
-
-
Semsey, S.1
Virnik, K.2
Adhya, S.3
-
26
-
-
33745595880
-
Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation
-
DOI 10.1073/pnas.0603557103
-
Swigon, D., Coleman, B.D. and Olson, W.K. (2006) Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proc. Natl Acad. Sci. USA, 103, 9879-9884. (Pubitemid 43993591)
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, Issue.26
, pp. 9879-9884
-
-
Swigon, D.1
Coleman, B.D.2
Olson, W.K.3
-
27
-
-
66249118030
-
Concentration and length dependence of DNA looping in transcriptional regulation
-
Han, L., Garcia, H.G., Blumberg, S., Towles, K.B., Beausang, J.F., Nelson, P.C. and Phillips, R. (2009) Concentration and length dependence of DNA looping in transcriptional regulation. PLos One, 4, e5621.
-
(2009)
PLos One
, vol.4
-
-
Han, L.1
Garcia, H.G.2
Blumberg, S.3
Towles, K.B.4
Beausang, J.F.5
Nelson, P.C.6
Phillips, R.7
-
28
-
-
17144415297
-
Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI
-
DOI 10.1016/j.jmb.2005.02.034
-
Heiter, D.F., Lunnen, K.D. and Wilson, G.G. (2005) Site-specific DNA-nicking mutants of the heterodimeric restriction endonuclease R.BbvCI. J. Mol. Biol., 348, 631-640. (Pubitemid 40520491)
-
(2005)
Journal of Molecular Biology
, vol.348
, Issue.3
, pp. 631-640
-
-
Heiter, D.F.1
Lunnen, K.D.2
Wilson, G.G.3
-
29
-
-
0018370487
-
Helical repeat of DNA in solution
-
Wang, J.C. (1979) Helical repeat of DNA in solution. Proc. Natl Acad. Sci. USA, 76, 200-203.
-
(1979)
Proc. Natl Acad. Sci. USA
, vol.76
, pp. 200-203
-
-
Wang, J.C.1
-
30
-
-
0030973367
-
Extension of torsionally stressed DNA by external force
-
Vologodskii, A.V and Marko, J.F. (1997) Extension of torsionally stressed DNA by external force. Biophys. J., 73, 123-132. (Pubitemid 27274110)
-
(1997)
Biophysical Journal
, vol.73
, Issue.1
, pp. 123-132
-
-
Vologodskii, A.V.1
Marko, J.F.2
-
31
-
-
0029975889
-
Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
-
Mü ller, J., Oehler, S. and Mü ller-Hill, B. (1996) Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator. J. Mol. Biol., 257, 21-29.
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 21-29
-
-
Müller, J.1
Oehler, S.2
Müller-Hill, B.3
-
32
-
-
19444384194
-
DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway
-
DOI 10.1093/nar/gki565
-
Van den Broek, B., Noom, M.C. and Wuite, G.J.L. (2005) DNA-tension dependence of restriction enzyme activity reveals mechanochemical properties of the reaction pathway. Nucleic Acids Res., 33, 2676-2684. (Pubitemid 41511285)
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.8
, pp. 2676-2684
-
-
Van Den Broek, B.1
Noom, M.C.2
Wuite, G.J.L.3
-
33
-
-
0041305824
-
Structural transitions and elasticity from torque measurements on DNA
-
DOI 10.1038/nature01810
-
Bryant, Z., Stone, M.D., Gore, J., Smith, S.B., Cozzarelli, N.R. and Bustamante, C. (2003) Structural transitions and elasticity from torque measurements on DNA. Nature, 424, 338-341. (Pubitemid 36899378)
-
(2003)
Nature
, vol.424
, Issue.6946
, pp. 338-341
-
-
Bryant, Z.1
Stone, M.D.2
Gore, J.3
Smith, S.B.4
Cozzarelli, N.R.5
Bustamante, C.6
-
34
-
-
33845793417
-
Effect of supercoiling on formation of protein-mediated DNA loops
-
Purohit, P.K. and Nelson, P.C. (2006) Effect of supercoiling on formation of protein-mediated DNA loops. Phys. Rev. E, 74, 061907.
-
(2006)
Phys. Rev. e
, vol.74
, pp. 061907
-
-
Purohit, P.K.1
Nelson, P.C.2
-
36
-
-
22244443662
-
Gapped DNA and cyclization of short DNA fragments
-
DOI 10.1529/biophysj.104.055657
-
Du, Q., Vologodskaia, M., Kuhn, H., Frank-Kamenetskii, M. and Vologodskii, A. (2005) Gapped DNA and cyclization of short DNA fragments. Biophys. J., 88, 4137-4145. (Pubitemid 40991125)
-
(2005)
Biophysical Journal
, vol.88
, Issue.6
, pp. 4137-4145
-
-
Du, Q.1
Vologodskaia, M.2
Kuhn, H.3
Frank-Kamenetskii, M.4
Vologodskii, A.5
-
37
-
-
67649227952
-
Theoretical aspects of the biological catch bond
-
Prezhdo, O.V. and Pereverzev, Y.V. (2009) Theoretical aspects of the biological catch bond. Acc. Chem. Res., 42, 693-703.
-
(2009)
Acc. Chem. Res.
, vol.42
, pp. 693-703
-
-
Prezhdo, O.V.1
Pereverzev, Y.V.2
-
38
-
-
33751156715
-
Stiff chains and filaments under tension
-
Odijk, T. (1995) Stiff chains and filaments under tension. Macromolecules, 28, 7016-7018.
-
(1995)
Macromolecules
, vol.28
, pp. 7016-7018
-
-
Odijk, T.1
|