-
1
-
-
0016850069
-
Kinky helix
-
Crick, F. H., and A. Klug. 1975. Kinky helix. Nature. 255:530-533.
-
(1975)
Nature
, vol.255
, pp. 530-533
-
-
Crick, F.H.1
Klug, A.2
-
2
-
-
0029041940
-
Stereochemical basis of DNA bending by transcription factors
-
Suzuki, M., and N. Yagi. 1995. Stereochemical basis of DNA bending by transcription factors. Nucleic Acids Res. 23:2083-2091.
-
(1995)
Nucleic Acids Res.
, vol.23
, pp. 2083-2091
-
-
Suzuki, M.1
Yagi, N.2
-
3
-
-
0030046809
-
Intercalation, DNA kinking, and the control of transcription
-
Werner, M. H., A. M. Gronenborn, and G. M. Clore. 1996. Intercalation, DNA kinking, and the control of transcription. Science. 271:778-784.
-
(1996)
Science
, vol.271
, pp. 778-784
-
-
Werner, M.H.1
Gronenborn, A.M.2
Clore, G.M.3
-
4
-
-
0032522139
-
DNA bending: The prevalence of kinkiness and the virtues of normality
-
Dickerson, R. E. 1998. DNA bending: the prevalence of kinkiness and the virtues of normality. Nucleic Acids Res. 26:1906-1926.
-
(1998)
Nucleic Acids Res.
, vol.26
, pp. 1906-1926
-
-
Dickerson, R.E.1
-
5
-
-
33749259954
-
Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles
-
DOI 10.1016/j.str.2006.08.004, PII S0969212606003522
-
Lankas, F., R. Lavery, and J. H. Maddocks. 2006. Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure. 14:1527-1534. (Pubitemid 44486810)
-
(2006)
Structure
, vol.14
, Issue.10
, pp. 1527-1534
-
-
Lankas, F.1
Lavery, R.2
Maddocks, J.H.3
-
6
-
-
19544379865
-
Localized single-stranded bubble mechanism for cyclization of short double helix DNA
-
Yan, J., and J. F. Marko. 2004. Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Phys. Rev. Lett. 93:108108.
-
(2004)
Phys. Rev. Lett.
, vol.93
, pp. 108108
-
-
Yan, J.1
Marko, J.F.2
-
7
-
-
32644444430
-
Sequence-dependent base pair opening in DNA double helix
-
Krueger, A., E. Protozanova, and M. D. Frank-Kamenetskii. 2006. Sequence-dependent base pair opening in DNA double helix. Biophys. J. 90:3091-3099.
-
(2006)
Biophys. J.
, vol.90
, pp. 3091-3099
-
-
Krueger, A.1
Protozanova, E.2
Frank-Kamenetskii, M.D.3
-
8
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
DOI 10.1073/pnas.95.19.11163
-
Olson, W. K., A. A. Gorin, X. J. Lu, L. M. Hock, and V. B. Zhurkin. 1998. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proc. Natl. Acad. Sci. USA. 95:11163-11168. (Pubitemid 28450099)
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, Issue.19
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.-J.3
Hock, L.M.4
Zhurkin, V.B.5
-
10
-
-
4444260310
-
Stacked-unstacked equilibrium at the nick site of DNA
-
DOI 10.1016/j.jmb.2004.07.075, PII S0022283604009167
-
Protozanova, E., P. Yakovchuk, and M. D. Frank-Kamenetskii. 2004. Stacked-unstacked equilibrium at the nick site of DNA. J. Mol. Biol. 342:775-785. (Pubitemid 39165649)
-
(2004)
Journal of Molecular Biology
, vol.342
, Issue.3
, pp. 775-785
-
-
Protozanova, E.1
Yakovchuk, P.2
Frank-Kamenetskii, M.D.3
-
11
-
-
0023256126
-
A single mode of DNA base-pair opening drives imino proton exchange
-
DOI 10.1038/328089a0
-
Gueron, M., M. Kochoyan, and J. L. Leroy. 1987. A single mode of DNA base-pair opening drives imino proton exchange. Nature. 328:89-92. (Pubitemid 17103590)
-
(1987)
Nature
, vol.328
, Issue.6125
, pp. 89-92
-
-
Gueron, M.1
Kochoyan, M.2
Leroy, J.-L.3
-
12
-
-
27744578574
-
A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA
-
DOI 10.1529/biophysj.105.065763
-
Coman, D., and I. M. Russu. 2005. A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA. Biophys. J. 89:3285-3292. (Pubitemid 41636083)
-
(2005)
Biophysical Journal
, vol.89
, Issue.5
, pp. 3285-3292
-
-
Coman, D.1
Russu, I.M.2
-
13
-
-
2342518189
-
Spontaneous sharp bending of double-stranded DNA
-
DOI 10.1016/S1097-2765(04)00210-2, PII S1097276504002102
-
Cloutier, T. E., and J. Widom. 2004. Spontaneous sharp bending of double-stranded DNA. Mol. Cell. 14:355-362. (Pubitemid 38591406)
-
(2004)
Molecular Cell
, vol.14
, Issue.3
, pp. 355-362
-
-
Cloutier, T.E.1
Widom, J.2
-
15
-
-
17244362931
-
Cyclization of short DNA fragments and bending fluctuations of the double helix
-
DOI 10.1073/pnas.0500983102
-
Du, Q., C. Smith, N. Shiffeldrim, M. Vologodskaia, and A. Vologodskii. 2005. Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc. Natl. Acad. Sci. USA. 102:5397-5402. (Pubitemid 40530269)
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, Issue.15
, pp. 5397-5402
-
-
Du, Q.1
Smith, C.2
Shiffeldrim, N.3
Vologodskaia, M.4
Vologodskii, A.5
-
17
-
-
40249090005
-
Kinking the double helix by bending deformation
-
Du, Q., A. Kotlyar, and A. Vologodskii. 2008. Kinking the double helix by bending deformation. Nucleic Acids Res. 36:1120-1128.
-
(2008)
Nucleic Acids Res.
, vol.36
, pp. 1120-1128
-
-
Du, Q.1
Kotlyar, A.2
Vologodskii, A.3
-
18
-
-
0015738909
-
Cleavage of circular, superhelical simian virus 40 DNA to a linear duplex by S1 nuclease
-
Beard, P., J. F. Morrow, and P. Berg. 1973. Cleavage of circular, superhelical simian virus 40 DNA to a linear duplex by S1 nuclease. J. Virol. 12:1303-1313.
-
(1973)
J. Virol.
, vol.12
, pp. 1303-1313
-
-
Beard, P.1
Morrow, J.F.2
Berg, P.3
-
19
-
-
0016295651
-
Interactions between twisted DNAs and enzymes: The effects of superhelical turns
-
Wang, J. C. 1974. Interactions between twisted DNAs and enzymes: the effects of superhelical turns. J. Mol. Biol. 87:797-816.
-
(1974)
J. Mol. Biol.
, vol.87
, pp. 797-816
-
-
Wang, J.C.1
-
20
-
-
0016766372
-
Extracellular nucleases of Pseudomonas BAL 31. I. Characterization of single strand-specific deoxyriboendo-nuclease and double-strand deoxyriboexonuclease activities
-
Gray, H. B., Jr., D. A. Ostrander, J. L. Hodnett, R. J. Legerski, and D. L. Robberson. 1975. Extracellular nucleases of Pseudomonas BAL 31. I. Characterization of single strand-specific deoxyriboendo-nuclease and double-strand deoxyriboexonuclease activities. Nucleic Acids Res. 2:1459-1492.
-
(1975)
Nucleic Acids Res.
, vol.2
, pp. 1459-1492
-
-
Gray Jr., H.B.1
Ostrander, D.A.2
Hodnett, J.L.3
Legerski, R.J.4
Robberson, D.L.5
-
21
-
-
0019087696
-
The inverted repeat as a recognizable structural feature in supercoiled DNA molecules
-
Lilley, D. M. 1980. The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. Proc. Natl. Acad. Sci. USA. 77:6468-6472.
-
(1980)
Proc. Natl. Acad. Sci. USA
, vol.77
, pp. 6468-6472
-
-
Lilley, D.M.1
-
22
-
-
0019932819
-
Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions
-
DOI 10.1038/299312a0
-
Singleton, C. K., J. Klysik, S. M. Stirdivant, and R. D. Wells. 1982. Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions. Nature. 299:312-316. (Pubitemid 12012856)
-
(1982)
Nature
, vol.299
, Issue.5881
, pp. 312-316
-
-
Singleton, C.K.1
Klysik, J.2
Stirdivant, S.M.3
Wells, R.D.4
-
24
-
-
0014413542
-
Early and late helixcoil transitions in closed circular DNA. The number of superhelical turns in polyoma DNA
-
Vinograd, J., J. Lebowitz, and R. Watson. 1968. Early and late helixcoil transitions in closed circular DNA. The number of superhelical turns in polyoma DNA. J. Mol. Biol. 33:173-197.
-
(1968)
J. Mol. Biol.
, vol.33
, pp. 173-197
-
-
Vinograd, J.1
Lebowitz, J.2
Watson, R.3
-
25
-
-
0027740297
-
The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA
-
Bauer, W. R., and C. J. Benham. 1993. The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA. J. Mol. Biol. 234:1184-1196.
-
(1993)
J. Mol. Biol.
, vol.234
, pp. 1184-1196
-
-
Bauer, W.R.1
Benham, C.J.2
-
26
-
-
0019870039
-
Sequence dependence of the helical repeat of DNA in solution
-
DOI 10.1038/292375a0
-
Peck, L. J., and J. C. Wang. 1981. Sequence dependence of the helical repeat of DNA in solution. Nature. 292:375-378. (Pubitemid 11050350)
-
(1981)
Nature
, vol.292
, Issue.5821
, pp. 375-378
-
-
Peck, L.J.1
Wang, J.C.2
-
27
-
-
0021133086
-
Twist and writing of short circular DNAs according to the first-order elasticity
-
Le Bret, M. 1984. Twist and writing of short circular DNAs according to the first-order elasticity. Biopolymers. 23:1835-1867.
-
(1984)
Biopolymers
, vol.23
, pp. 1835-1867
-
-
Le Bret, M.1
-
29
-
-
5744249209
-
Equation of state calculations by fast computing machines
-
Metropolis, N., A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller. 1953. Equation of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1092.
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1092
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Rosenbluth, M.N.3
Teller, A.H.4
Teller, E.5
-
31
-
-
0021022977
-
Energetics of DNA twisting. I. Relation between twist and cyclization probability
-
Shore, D., and R. L. Baldwin. 1983. Energetics of DNA twisting. I. Relation between twist and cyclization probability. J. Mol. Biol. 170:957-981.
-
(1983)
J. Mol. Biol.
, vol.170
, pp. 957-981
-
-
Shore, D.1
Baldwin, R.L.2
-
32
-
-
0000545475
-
Ring-closure probabilities for twisted wormlike chains. Application to DNA
-
Shimada, J., and H. Yamakawa. 1984. Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules. 17:689-698.
-
(1984)
Macromolecules
, vol.17
, pp. 689-698
-
-
Shimada, J.1
Yamakawa, H.2
-
33
-
-
0037215722
-
Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization
-
Zhang, Y., and D. M. Crothers. 2003. Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophys. J. 84:136-153. (Pubitemid 36026386)
-
(2003)
Biophysical Journal
, vol.84
, Issue.1
, pp. 136-153
-
-
Zhang, Y.1
Crothers, D.M.2
-
34
-
-
0017035197
-
Fluctuational opening of the double helix as revealed by theoretical and experimental study of DNA interaction with formaldehyde
-
DOI 10.1016/S0022-2836(76)80111-8
-
Lukashin, A. V., A. V. Vologodskii, M. D. Frank-Kamenetskii, and Y. L. Lyubchenko. 1976. Fluctuational opening of the double helix as revealed by theoretical and experimental study of DNA interaction with formaldehyde. J. Mol. Biol. 108:665-682. (Pubitemid 8014661)
-
(1976)
Journal of Molecular Biology
, vol.108
, Issue.4
, pp. 665-682
-
-
Lukashin, A.V.1
Vologodskii, A.V.2
Frank Kamenetskii, M.D.3
Lyubchenko Yu, L.4
-
35
-
-
0035883736
-
AdoMet-dependent methylation, DNA methyltransferases and base flipping
-
Cheng, X., and R. J. Roberts. 2001. AdoMet-dependent methylation, DNA methyltransferases and base flipping. Nucleic Acids Res. 29:3784-3795.
-
(2001)
Nucleic Acids Res.
, vol.29
, pp. 3784-3795
-
-
Cheng, X.1
Roberts, R.J.2
-
36
-
-
0037335588
-
Base pair opening within B-DNA: Free energy pathways for GC and at pairs from umbrella sampling simulations
-
Giudice, E., P. Varnai, and R. Lavery. 2003. Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Res. 31:1434-1443.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 1434-1443
-
-
Giudice, E.1
Varnai, P.2
Lavery, R.3
|