-
1
-
-
0002291771
-
Torsion dynamics and depolarization of fluorescence of linear macro-molecules. I. Theory and application to DNA
-
Allison, S. A. & Schurr, J. M. (1979). Torsion dynamics and depolarization of fluorescence of linear macro-molecules. I. Theory and application to DNA. Chem. Phys. 41, 35-59.
-
(1979)
Chem. Phys.
, vol.41
, pp. 35-59
-
-
Allison, S.A.1
Schurr, J.M.2
-
2
-
-
0023202898
-
Structure of the repressor-operator complex of bacteriophage 434
-
Anderson, J. E., Ptashne, M. & Harrison, S. C. (1987). Structure of the repressor-operator complex of bacteriophage 434. Nature, 326, 846-852.
-
(1987)
Nature
, vol.326
, pp. 846-852
-
-
Anderson, J.E.1
Ptashne, M.2
Harrison, S.C.3
-
3
-
-
0017795493
-
Structure and reactions of closed duplex DNA
-
Bauer, W. R. (1978). Structure and reactions of closed duplex DNA. Annu. Rev. Biophys. Bioeng. 7, 287-313.
-
(1978)
Annu. Rev. Biophys. Bioeng.
, vol.7
, pp. 287-313
-
-
Bauer, W.R.1
-
4
-
-
0028184699
-
Kinetics of DNA supercoiling studied by Brownian dynamics simulation
-
Chirico, G. & Langowski, J. (1994). Kinetics of DNA supercoiling studied by Brownian dynamics simulation. Biopolymers, 34, 415-433.
-
(1994)
Biopolymers
, vol.34
, pp. 415-433
-
-
Chirico, G.1
Langowski, J.2
-
5
-
-
0028166869
-
Circularization of small DNAs in the presence of ethidium: A theoretical analysis
-
Clendenning, J. B. & Schurr, J. M. (1994). Circularization of small DNAs in the presence of ethidium: a theoretical analysis. Biopolymers, 34, 849-868.
-
(1994)
Biopolymers
, vol.34
, pp. 849-868
-
-
Clendenning, J.B.1
Schurr, J.M.2
-
6
-
-
0027985577
-
Effect of ethidium binding and superhelix density on the supercoiling free energy and torsion and bending constants of p30δ DNA
-
Clendenning, J. B., Naimushin, A. N., Fujimoto, B. S., Stewart, D. W. & Schurr, J. M. (1994). Effect of ethidium binding and superhelix density on the supercoiling free energy and torsion and bending constants of p30δ DNA. Biophys. Chem. 52, 191-218.
-
(1994)
Biophys. Chem.
, vol.52
, pp. 191-218
-
-
Clendenning, J.B.1
Naimushin, A.N.2
Fujimoto, B.S.3
Stewart, D.W.4
Schurr, J.M.5
-
7
-
-
0022230224
-
Bending and its relation to nucleosome positioning
-
Drew, H. R. & Travers, A. A. (1985). Bending and its relation to nucleosome positioning. J. Mol. Biol. 186, 773-790.
-
(1985)
J. Mol. Biol.
, vol.186
, pp. 773-790
-
-
Drew, H.R.1
Travers, A.A.2
-
8
-
-
0027238534
-
The helical repeat of DNA at high temperature
-
Duguet, M. (1993). The helical repeat of DNA at high temperature. Nucl. Acids Res. 21, 463-468.
-
(1993)
Nucl. Acids Res.
, vol.21
, pp. 463-468
-
-
Duguet, M.1
-
10
-
-
0000145810
-
Transient electric birefringence study of the persistence length and electrical polarizability of restriction fragments of DNA
-
Elias, J. G. & Eden, D. (1981). Transient electric birefringence study of the persistence length and electrical polarizability of restriction fragments of DNA. Macromolecules, 14, 410-419.
-
(1981)
Macromolecules
, vol.14
, pp. 410-419
-
-
Elias, J.G.1
Eden, D.2
-
11
-
-
0021806558
-
Torsional and bending rigidity of the double helix from data on small DNA rings
-
Frank-Kamenetskii, M. D., Lukashin, A. V., Anshelevich, V. V. & Vologodskii, A. V. (1985). Torsional and bending rigidity of the double helix from data on small DNA rings. J. Biomol. Struct. Dynam. 2, 1005-1012.
-
(1985)
J. Biomol. Struct. Dynam.
, vol.2
, pp. 1005-1012
-
-
Frank-Kamenetskii, M.D.1
Lukashin, A.V.2
Anshelevich, V.V.3
Vologodskii, A.V.4
-
12
-
-
0025366778
-
Dependence of the torsional rigidity of DNA on base-composition
-
Fujimoto, B. S. & Schurr, J. M. (1990). Dependence of the torsional rigidity of DNA on base-composition. Nature, 344, 175-178.
-
(1990)
Nature
, vol.344
, pp. 175-178
-
-
Fujimoto, B.S.1
Schurr, J.M.2
-
13
-
-
0002302645
-
An attempt to measure the dynamic persistence length of DNA
-
Fujimoto, B. S. & Schurr, J. M. (1995). An attempt to measure the dynamic persistence length of DNA. Biophys. J. 68, A101.
-
(1995)
Biophys. J.
, vol.68
-
-
Fujimoto, B.S.1
Schurr, J.M.2
-
14
-
-
0028869662
-
Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs
-
Gebe, J. A., Allison, S. A., Clendenning, J. B. & Schurr, J. M. (1995a). Monte Carlo simulations of supercoiling free energies for unknotted and trefoil knotted DNAs. Biophys. J. 68, 619-633.
-
(1995)
Biophys. J.
, vol.68
, pp. 619-633
-
-
Gebe, J.A.1
Allison, S.A.2
Clendenning, J.B.3
Schurr, J.M.4
-
15
-
-
0011724557
-
2+ and superhelix density on the conformations of circular DNAs. Experiments and Monte Carlo simulations
-
2+ and superhelix density on the conformations of circular DNAs. Experiments and Monte Carlo simulations. Biophys. J. 68, A106.
-
(1995)
Biophys. J.
, vol.68
-
-
Gebe, J.A.1
Heath, P.J.2
Delrow, J.J.3
Schurr, J.M.4
-
18
-
-
84985720098
-
Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains
-
Hagerman, P. J. & Zimm, B. H. (1981). Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains. Biopolymers, 20, 1481-1502.
-
(1981)
Biopolymers
, vol.20
, pp. 1481-1502
-
-
Hagerman, P.J.1
Zimm, B.H.2
-
20
-
-
0030572145
-
Comparison of analytical theory with Brownian dynamics simulations for small linear and circular DNAs
-
Heath, P. J., Allison, S. A. & Schurr, J. M. (1996). Comparison of analytical theory with Brownian dynamics simulations for small linear and circular DNAs. Macromolecules, 29, 3583-3596.
-
(1996)
Macromolecules
, vol.29
, pp. 3583-3596
-
-
Heath, P.J.1
Allison, S.A.2
Schurr, J.M.3
-
21
-
-
0024962406
-
DNA ring closure mediated by protein HU
-
Hodges-Garcia, Y., Hagerman, P. J. & Pettijohn, D. E. (1989). DNA ring closure mediated by protein HU. J. Biol. Chem. 164, 14621-14623.
-
(1989)
J. Biol. Chem.
, vol.164
, pp. 14621-14623
-
-
Hodges-Garcia, Y.1
Hagerman, P.J.2
Pettijohn, D.E.3
-
22
-
-
0021320555
-
Torsional rigidity of DNA and length dependence of the free energy of supercoiling
-
Horowitz, D. A. & Wang, J. C. (1984). Torsional rigidity of DNA and length dependence of the free energy of supercoiling. J. Mol. Biol. 173, 75-91.
-
(1984)
J. Mol. Biol.
, vol.173
, pp. 75-91
-
-
Horowitz, D.A.1
Wang, J.C.2
-
23
-
-
0027406834
-
Motions of short DNA duplexes: An analysis of DNA dynamics using an epr-active probe
-
Hustedt, E. J., Spaltenstein, A., Kirchner, J. E., Mailer, C., Hopkins, P. B. & Robinson, B. H. (1993). Motions of short DNA duplexes: an analysis of DNA dynamics using an epr-active probe. Biochemistry, 32, 1774-1787.
-
(1993)
Biochemistry
, vol.32
, pp. 1774-1787
-
-
Hustedt, E.J.1
Spaltenstein, A.2
Kirchner, J.E.3
Mailer, C.4
Hopkins, P.B.5
Robinson, B.H.6
-
24
-
-
0026702293
-
Torsion stress generated by RecA protein during DNA strand exchange separates strands of a heterologous insert
-
Jwang, B. & Radding, C. M. (1991). Torsion stress generated by RecA protein during DNA strand exchange separates strands of a heterologous insert. Proc. Natl. Acad. Sci. USA, 89, 7596-7600.
-
(1991)
Proc. Natl. Acad. Sci. USA
, vol.89
, pp. 7596-7600
-
-
Jwang, B.1
Radding, C.M.2
-
25
-
-
0027133746
-
8 sequence on secondary structure
-
8 sequence on secondary structure. Biopolymers, 33, 1725-1745.
-
(1993)
Biopolymers
, vol.33
, pp. 1725-1745
-
-
Kim, U.S.1
Fujimoto, B.S.2
Furlong, C.E.3
Sundstrom, J.A.4
Humbert, R.5
Teller, D.C.6
Schurr, J.M.7
-
26
-
-
0022074904
-
Deformational dynamics and nmr relaxation of supercoiled DNAs
-
Langowski, J., Fujimoto, B. S., Wemmer, D. E., Benight, A. S., Drobny, G., Shibata, J. H. & Schurr, J. M. (1985a). Deformational dynamics and nmr relaxation of supercoiled DNAs. Biopolymers, 24, 1023-1056.
-
(1985)
Biopolymers
, vol.24
, pp. 1023-1056
-
-
Langowski, J.1
Fujimoto, B.S.2
Wemmer, D.E.3
Benight, A.S.4
Drobny, G.5
Shibata, J.H.6
Schurr, J.M.7
-
27
-
-
0022367194
-
Change of conformation and internal dynamics of supercoiled DNA upon binding of E. coli single-strand binding protein
-
Langowski, J., Benight, A. S., Fujimoto, B. S. & Schurr, J. M. (1985b). Change of conformation and internal dynamics of supercoiled DNA upon binding of E. coli single-strand binding protein. Biochemistry, 24, 4022-4028.
-
(1985)
Biochemistry
, vol.24
, pp. 4022-4028
-
-
Langowski, J.1
Benight, A.S.2
Fujimoto, B.S.3
Schurr, J.M.4
-
28
-
-
0028066752
-
Solution structure and dynamics of DNA topoisomers: Dynamic light scattering studies and Monte Carlo simulations
-
Langowski, J., Kapp, U., Klenin, K. & Vologodskii, A. V. (1994). Solution structure and dynamics of DNA topoisomers: dynamic light scattering studies and Monte Carlo simulations. Biopolymers, 34, 639-646.
-
(1994)
Biopolymers
, vol.34
, pp. 639-646
-
-
Langowski, J.1
Kapp, U.2
Klenin, K.3
Vologodskii, A.V.4
-
29
-
-
0028143614
-
CRP fixes the rotational orientation of covalently closed DNA molecules
-
Lavigne, M., Kolb, A., Yeramanian, E. & Buc, H. (1994). CRP fixes the rotational orientation of covalently closed DNA molecules. EMBO J. 13, 4983-4990.
-
(1994)
Embo J.
, vol.13
, pp. 4983-4990
-
-
Lavigne, M.1
Kolb, A.2
Yeramanian, E.3
Buc, H.4
-
30
-
-
0028104309
-
Effect of ethidium binding and superhelix density on the apparent supercoiling free energy and torsion constants of pBR322 DNA
-
Naimushin, A. N., Clendenning, J. B., Kim, U. S., Song. L., Fujimoto, B. S., Stewart, D. W. & Schurr, J. M. (1994). Effect of ethidium binding and superhelix density on the apparent supercoiling free energy and torsion constants of pBR322 DNA. Biophys. Chem. 52, 219-226.
-
(1994)
Biophys. Chem.
, vol.52
, pp. 219-226
-
-
Naimushin, A.N.1
Clendenning, J.B.2
Kim, U.S.3
Song, L.4
Fujimoto, B.S.5
Stewart, D.W.6
Schurr, J.M.7
-
31
-
-
0025773296
-
Zinc-finger-DNA recognition: Crystal structure of a Zif268-DNA complex at 2.1 Å
-
Pavlevitch, N. P. & Pabo, C. O. (1991). Zinc-finger-DNA recognition: crystal structure of a Zif268-DNA complex at 2.1 Å. Science, 252, 809-817.
-
(1991)
Science
, vol.252
, pp. 809-817
-
-
Pavlevitch, N.P.1
Pabo, C.O.2
-
32
-
-
0016423686
-
The sense of naturally occurring superhelices and the unwinding angle of ethidium
-
Pulleyblank, D. E. & Morgan, A. R. (1975). The sense of naturally occurring superhelices and the unwinding angle of ethidium. J. Mol. Biol. 91, 1-13.
-
(1975)
J. Mol. Biol.
, vol.91
, pp. 1-13
-
-
Pulleyblank, D.E.1
Morgan, A.R.2
-
33
-
-
0026502006
-
Direct evidence for the effect of transcription on local DNA supercoiling in vivo
-
Rahmouni, A. R. & Wells, R. D. (1992). Direct evidence for the effect of transcription on local DNA supercoiling in vivo. J. Mol. Biol. 223, 131-144.
-
(1992)
J. Mol. Biol.
, vol.223
, pp. 131-144
-
-
Rahmouni, A.R.1
Wells, R.D.2
-
35
-
-
0002851534
-
Rotational diffusion of deformable macromolecules with mean local cylindrical symmetry
-
Schurr, J. M. (1984). Rotational diffusion of deformable macromolecules with mean local cylindrical symmetry. Chem. Phys. 84, 71-96.
-
(1984)
Chem. Phys.
, vol.84
, pp. 71-96
-
-
Schurr, J.M.1
-
36
-
-
0022385297
-
DNA motions in the DNA core particle. A reanalysis
-
Schurr, J. M. & Schurr, R. L. (1985). DNA motions in the DNA core particle. A reanalysis. Biopolymers. 24, 1931-1940.
-
(1985)
Biopolymers
, vol.24
, pp. 1931-1940
-
-
Schurr, J.M.1
Schurr, R.L.2
-
37
-
-
0000166387
-
Fluorescence studies of nucleic acids: Dynamics, rigidities and structures
-
(Lakowicz, J. R., ed.), Plenum Press, New York
-
Schurr, J. M., Fujimoto, B. S., Wu, P. & Song, L. (1992). Fluorescence studies of nucleic acids: dynamics, rigidities and structures. In Topics in Fluorescence Spectroscopy (Lakowicz, J. R., ed.), vol. 3, pp. 137-229, Plenum Press, New York.
-
(1992)
Topics in Fluorescence Spectroscopy
, vol.3
, pp. 137-229
-
-
Schurr, J.M.1
Fujimoto, B.S.2
Wu, P.3
Song, L.4
-
38
-
-
0028844668
-
Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs
-
Schurr, J. M., Babcock, H. P. & Gebe, J. A. (1995). Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs. Biopolymers, 36, 633-641.
-
(1995)
Biopolymers
, vol.36
, pp. 633-641
-
-
Schurr, J.M.1
Babcock, H.P.2
Gebe, J.A.3
-
39
-
-
0026580159
-
Torsional rigidity of positively and negatively supercoiled DNA
-
Selvin, P. R., Cook, D. N., Pon, N. G., Bauer, W. R., Klein, M. P. & Hearst, J. E. (1991). Torsional rigidity of positively and negatively supercoiled DNA. Science, 255, 82-31.
-
(1991)
Science
, vol.255
, pp. 82-131
-
-
Selvin, P.R.1
Cook, D.N.2
Pon, N.G.3
Bauer, W.R.4
Klein, M.P.5
Hearst, J.E.6
-
40
-
-
0021761497
-
Structures and dynamics of a supercoiled DNA
-
Shibata, J. H., Wilcoxon, J., Schurr, J. M. & Knauf, V. (1984). Structures and dynamics of a supercoiled DNA. Biochemistry, 23, 1188-1194.
-
(1984)
Biochemistry
, vol.23
, pp. 1188-1194
-
-
Shibata, J.H.1
Wilcoxon, J.2
Schurr, J.M.3
Knauf, V.4
-
41
-
-
0000545475
-
Ring closure probabilities for twisted wormlike chains. Application to DNA
-
Shimada, J. & Yamakawa, H. (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
-
42
-
-
0021847771
-
Statistical mechanics of DNA topoisomers. The helical wormlike chain
-
Shimada, J. & Yamakawa, H. (1985). Statistical mechanics of DNA topoisomers. The helical wormlike chain. J. Mol. Biol. 184, 319-329.
-
(1985)
J. Mol. Biol.
, vol.184
, pp. 319-329
-
-
Shimada, J.1
Yamakawa, H.2
-
43
-
-
0021089697
-
Energetics of DNA twisting II. Topoisomer analysis
-
Shore, D. & Baldwin, R. L. (1983a). Energetics of DNA twisting II. Topoisomer analysis. J. Mol. Biol. 170, 983-1007.
-
(1983)
J. Mol. Biol.
, vol.170
, pp. 983-1007
-
-
Shore, D.1
Baldwin, R.L.2
-
44
-
-
0021022977
-
Energetics of DNA twisting I. Relation between twist and cyclization probability
-
Shore D. & Baldwin, R. L. (1983b). 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
-
45
-
-
0026495432
-
Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads
-
Smith, S. B., Finzi, L. & Bustamante, C. (1992). Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. Science, 258, 1122-1126.
-
(1992)
Science
, vol.258
, pp. 1122-1126
-
-
Smith, S.B.1
Finzi, L.2
Bustamante, C.3
-
46
-
-
0025089220
-
Dynamic bending rigidity of DNA
-
Song, L. & Schurr, J. M. (1990). Dynamic bending rigidity of DNA. Biopolymers, 30, 229-237.
-
(1990)
Biopolymers
, vol.30
, pp. 229-237
-
-
Song, L.1
Schurr, J.M.2
-
47
-
-
0025370846
-
Normal mode theory for the Brownian dynamics of a weakly bending rod: Comparison with Brownian dynamics simulations
-
Song, L., Allison, S. A. & Schurr, J. M. (1990). Normal mode theory for the Brownian dynamics of a weakly bending rod: comparison with Brownian dynamics simulations. Biopolymers, 29, 1773-1791.
-
(1990)
Biopolymers
, vol.29
, pp. 1773-1791
-
-
Song, L.1
Allison, S.A.2
Schurr, J.M.3
-
48
-
-
0025298856
-
Evidence for allosteric transitions in secondary structure induced by superhelical stress
-
Song, L., Fujimoto, B. S., Wu, P., Thomas, J. C., Shibata, J. H. & Schurr, J. M. (1990). Evidence for allosteric transitions in secondary structure induced by superhelical stress. J. Mol. Biol. 214, 307-326.
-
(1990)
J. Mol. Biol.
, vol.214
, pp. 307-326
-
-
Song, L.1
Fujimoto, B.S.2
Wu, P.3
Thomas, J.C.4
Shibata, J.H.5
Schurr, J.M.6
-
49
-
-
0018462927
-
Conformation and circular dichroism of DNA
-
Sprecher, C. A., Baase, W. A. & Johnson, W. C., Jr (1979). Conformation and circular dichroism of DNA. Biopolymers, 18, 1009-1019.
-
(1979)
Biopolymers
, vol.18
, pp. 1009-1019
-
-
Sprecher, C.A.1
Baase, W.A.2
Johnson W.C., Jr.3
-
50
-
-
0021109048
-
Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels
-
Stellwagen, N. C. (1983). Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels. Biochemistry, 22, 6168-6193.
-
(1983)
Biochemistry
, vol.22
, pp. 6168-6193
-
-
Stellwagen, N.C.1
-
51
-
-
0025355712
-
Application of the method of T4 phage DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat
-
Taylor, W. H. & Hagerman, P. J. (1990). Application of the method of T4 phage DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. J. Mol. Biol. 212, 363-376.
-
(1990)
J. Mol. Biol.
, vol.212
, pp. 363-376
-
-
Taylor, W.H.1
Hagerman, P.J.2
-
52
-
-
0019077298
-
Torsion dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral φ29 DNA
-
(1980)
-
Thomas, J. C., Allison, S. A., Appellof, C. J. & Schurr, J. M. (1980). Torsion dynamics and depolarization of fluorescence of linear macromolecules. II. Fluorescence polarization anisotropy measurements on a clean viral φ29 DNA. Biophys. Chem. 12, 177-188. (1980).
-
(1980)
Biophys. Chem.
, vol.12
, pp. 177-188
-
-
Thomas, J.C.1
Allison, S.A.2
Appellof, C.J.3
Schurr, J.M.4
-
54
-
-
0016333701
-
The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients
-
Wang, J. C. (1974). The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. J. Mol. Biol. 89, 783-801.
-
(1974)
J. Mol. Biol.
, vol.89
, pp. 783-801
-
-
Wang, J.C.1
-
55
-
-
0023743235
-
Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter
-
Wu, P.-G., Song, L., Clendenning, J. B., Fujimoto, B. S., Benight, A. S. & Schurr, J. M. (1988). Interaction of chloroquine with linear and supercoiled DNAs. Effect on the torsional dynamics, rigidity, and twist energy parameter. Biochemistry, 27, 8128-8144.
-
(1988)
Biochemistry
, vol.27
, pp. 8128-8144
-
-
Wu, P.-G.1
Song, L.2
Clendenning, J.B.3
Fujimoto, B.S.4
Benight, A.S.5
Schurr, J.M.6
-
56
-
-
0025840598
-
Effect of ethidium on the torsion constants of linear and supercoiled DNAs
-
Wu, P.-G., Fujimoto, B. A., Song, L. & Schurr, J. M. (1991). Effect of ethidium on the torsion constants of linear and supercoiled DNAs. Biophys. Chem. 41, 217-236.
-
(1991)
Biophys. Chem.
, vol.41
, pp. 217-236
-
-
Wu, P.-G.1
Fujimoto, B.A.2
Song, L.3
Schurr, J.M.4
-
57
-
-
0001412394
-
Application of the Kirkwood theory of transport in polymer solutions to rigid assemblies of beads
-
Yamakawa, H. & Yamaki, J. (1973). Application of the Kirkwood theory of transport in polymer solutions to rigid assemblies of beads. J. Chem. Phys. 58, 2049-2055.
-
(1973)
J. Chem. Phys.
, vol.58
, pp. 2049-2055
-
-
Yamakawa, H.1
Yamaki, J.2
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