-
1
-
-
34547642985
-
Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli
-
Becker, N. A., J. D. Kahn, and L. J. Maher, 3rd. 2007. Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli. Nucleic Acids Res. 35:3988-4000.
-
(2007)
Nucleic Acids Res
, vol.35
, pp. 3988-4000
-
-
Becker, N.A.1
Kahn, J.D.2
Maher III, L.J.3
-
2
-
-
33745135817
-
Structural analysis of hyperperiodic DNA from Caenorhabditis elegans
-
Moreno-Herrero, F., R. Seidel,., N. H. Dekker. 2006. Structural analysis of hyperperiodic DNA from Caenorhabditis elegans. Nucleic Acids Res. 34:3057-3066.
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3057-3066
-
-
Moreno-Herrero, F.1
Seidel, R.2
Dekker, N.H.3
-
3
-
-
38649114349
-
Threedimensional architecture of the bacteriophage 429 packaged genome and elucidation of its packaging process
-
Comolli, L. R., A. J. Spakowitz, ., K. H. Downing. 2008. Threedimensional architecture of the bacteriophage 429 packaged genome and elucidation of its packaging process. Virology. 371:267-277.
-
(2008)
Virology
, vol.371
, pp. 267-277
-
-
Comolli, L.R.1
Spakowitz, A.J.2
Downing, K.H.3
-
4
-
-
77449116980
-
The bacteriophage genome undergoes a succession of intracapsid phase transitions upon DNA ejection
-
Leforestier, A., and F. Livolant. 2010. The bacteriophage genome undergoes a succession of intracapsid phase transitions upon DNA ejection. J. Mol. Biol. 396:384-395.
-
(2010)
J. Mol. Biol.
, vol.396
, pp. 384-395
-
-
Leforestier, A.1
Livolant, F.2
-
5
-
-
34547852967
-
Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
-
Zhang, Y., A. E. McEwen, ., S. D. Levene. 2006. Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping. PLoS ONE. 1:e136.
-
(2006)
PLoS ONE
, vol.1
-
-
Zhang, Y.1
McEwen, A.E.2
Levene, S.D.3
-
6
-
-
66249118030
-
Concentration and length dependence of DNA looping in transcriptional regulation
-
Han, L., H. G. Garcia, ., R. Phillips. 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
Phillips, R.3
-
7
-
-
0001191247
-
DNA flexibility studied by covalent closure of short fragments into circles
-
Shore, D., J. Langowski, and R. L. Baldwin. 1981. DNA flexibility studied by covalent closure of short fragments into circles. Proc. Natl. Acad. Sci. USA. 78:4833-4837.
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 4833-4837
-
-
Shore, D.1
Langowski, J.2
Baldwin, R.L.3
-
9
-
-
33845810345
-
High flexibility of DNA on short length scales probed by atomic force microscopy
-
Wiggins, P. A., T. van der Heijden, ., P. C. Nelson. 2006. High flexibility of DNA on short length scales probed by atomic force microscopy. Nat. Nanotechnol. 1:137-141.
-
(2006)
Nat. Nanotechnol.
, vol.1
, pp. 137-141
-
-
Wiggins, P.A.1
Heijden Der T.Van2
Nelson, P.C.3
-
10
-
-
2342518189
-
Spontaneous sharp bending of double-stranded DNA
-
Cloutier, T. E., and J. Widom. 2004. Spontaneous sharp bending of double-stranded DNA. Mol. Cell. 14:355-362.
-
(2004)
Mol. Cell.
, vol.14
, pp. 355-362
-
-
Cloutier, T.E.1
Widom, J.2
-
11
-
-
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
-
13
-
-
40749090377
-
DNA bending stiffness on small length scales
-
Yuan, C., H. Chen, ., L. A. Archer. 2008. DNA bending stiffness on small length scales. Phys. Rev. Lett. 100:018102.
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 018102
-
-
Yuan, C.1
Chen, H.2
Archer, L.A.3
-
14
-
-
68949092305
-
Microscopic mechanism for experimentally observed anomalous elasticity of DNA in two dimensions
-
Destainville, N., M. Manghi, and J. Palmeri. 2009. Microscopic mechanism for experimentally observed anomalous elasticity of DNA in two dimensions. Biophys. J. 96:4464-4469.
-
(2009)
Biophys. J.
, vol.96
, pp. 4464-4469
-
-
Destainville, N.1
Manghi, M.2
Palmeri, J.3
-
15
-
-
17244362931
-
Cyclization of short DNA fragments and bending fluctuations of the double helix
-
Du, Q., C. Smith, ., A. Vologodskii. 2005. Cyclization of short DNA fragments and bending fluctuations of the double helix. Proc. Natl. Acad. Sci. USA. 102:5397-5402.
-
(2005)
Proc. Natl. Acad. Sci. USA
, vol.102
, pp. 5397-5402
-
-
Du, Q.1
Smith, C.2
Vologodskii, A.3
-
16
-
-
34547349079
-
Wormlike chain theory and bending of short DNA
-
Mazur, A. K. 2007. Wormlike chain theory and bending of short DNA. Phys. Rev. Lett. 98:218102.
-
(2007)
Phys. Rev. Lett.
, vol.98
, pp. 218102
-
-
Mazur, A.K.1
-
17
-
-
70349602563
-
Probing the conformational distributions of subpersistence length DNA
-
Mastroianni, A. J., D. A. Sivak, ., A. P. Alivisatos. 2009. Probing the conformational distributions of subpersistence length DNA. Biophys. J. 97:1408-1417.
-
(2009)
Biophys. J.
, vol.97
, pp. 1408-1417
-
-
Mastroianni, A.J.1
Sivak, D.A.2
Alivisatos, A.P.3
-
18
-
-
59149096327
-
Torsional stiffness of single superparamagnetic microspheres in an external magnetic field
-
Klaue, D., and R. Seidel. 2009. Torsional stiffness of single superparamagnetic microspheres in an external magnetic field. Phys. Rev. Lett. 102:028302.
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 028302
-
-
Klaue, D.1
Seidel, R.2
-
19
-
-
61349129512
-
Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers
-
Mosconi, F., J. F. Allemand, ., V. Croquette. 2009. Measurement of the torque on a single stretched and twisted DNA using magnetic tweezers. Phys. Rev. Lett. 102:078301.
-
(2009)
Phys. Rev. Lett.
, vol.102
, pp. 078301
-
-
Mosconi, F.1
Allemand, J.F.2
Croquette, V.3
-
20
-
-
77950659882
-
Energetics at the DNA supercoiling transition
-
Brutzer, H., N. Luzzietti, ., R. Seidel. 2010. Energetics at the DNA supercoiling transition. Biophys. J. 98:1267-1276.
-
(2010)
Biophys. J.
, vol.98
, pp. 1267-1276
-
-
Brutzer, H.1
Luzzietti, N.2
Seidel, R.3
-
21
-
-
41949110996
-
Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules
-
Forth, S., C. Deufel,., M. D. Wang. 2008. Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules. Phys. Rev. Lett. 100:148301.
-
(2008)
Phys. Rev. Lett.
, vol.100
, pp. 148301
-
-
Forth, S.1
Deufel, C.2
Wang, M.D.3
-
22
-
-
77957562056
-
DNA-DNA interactions in tight supercoils are described by a small effective charge density
-
Maffeo, C., R. Schöpflin, ., R. Seidel. 2010. DNA-DNA interactions in tight supercoils are described by a small effective charge density. Phys. Rev. Lett. 105:158101.
-
(2010)
Phys. Rev. Lett.
, vol.105
, pp. 158101
-
-
Maffeo, C.1
-
23
-
-
79954537249
-
Torque-induced deformations of charged elastic DNA rods: Thin helices, loops, and precursors of DNA supercoiling
-
Cherstvy, A. G. 2011. Torque-induced deformations of charged elastic DNA rods: thin helices, loops, and precursors of DNA supercoiling. J. Biol. Phys. 37:227-238.
-
(2011)
J. Biol. Phys.
, vol.37
, pp. 227-238
-
-
Cherstvy, A.G.1
-
24
-
-
84856529153
-
Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA
-
Marko, J. F., and S. Neukirch. 2012. Competition between curls and plectonemes near the buckling transition of stretched supercoiled DNA. Phys. Rev. E. 85:011908.
-
(2012)
Phys. Rev. e
, vol.85
, pp. 011908
-
-
Marko, J.F.1
Neukirch, S.2
-
25
-
-
84860012641
-
Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA
-
Oberstrass, F. C., L. E. Fernandes, and Z. Bryant. 2012. Torque measurements reveal sequence-specific cooperative transitions in supercoiled DNA. Proc. Natl. Acad. Sci. USA. 109:6106-6111.
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 6106-6111
-
-
Oberstrass, F.C.1
Fernandes, L.E.2
Bryant, Z.3
-
26
-
-
70350534421
-
Discontinuities at the DNA supercoiling transition
-
Daniels, B. C., S. Forth, ., J. P. Sethna. 2009. Discontinuities at the DNA supercoiling transition. Phys. Rev. E. 80:040901.
-
(2009)
Phys. Rev. e
, vol.80
, pp. 040901
-
-
Daniels, B.C.1
Forth, S.2
Sethna, J.P.3
-
27
-
-
0032160958
-
Kinetics of structural changes in superhelical DNA
-
Wedemann, G., C. Münkel, ., J. Langowski. 1998. Kinetics of structural changes in superhelical DNA. Phys. Rev. E. 58:3537-3546.
-
(1998)
Phys. Rev. e
, vol.58
, pp. 3537-3546
-
-
Wedemann, G.1
-
28
-
-
84860541753
-
The dependence of DNA supercoiling on solution electrostatics
-
Argudo, D., and P. K. Purohit. 2012. The dependence of DNA supercoiling on solution electrostatics. Acta Biomater. 8:2133-2143.
-
(2012)
Acta Biomater.
, vol.8
, pp. 2133-2143
-
-
Argudo, D.1
Purohit, P.K.2
-
29
-
-
84864769629
-
Multi-plectoneme phase of double-stranded DNA under torsion
-
arXiv:1204.1324v2
-
Emanuel, M., G. Lanzani, and H. Schiessel. 2012. Multi-plectoneme phase of double-stranded DNA under torsion. Biomolecules. arXiv:1204.1324v2.
-
(2012)
Biomolecules
-
-
Emanuel, M.1
Lanzani, G.2
Schiessel, H.3
-
30
-
-
80052404576
-
Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids
-
Lipfert, J., M. Wiggin, ., N. H. Dekker. 2011. Freely orbiting magnetic tweezers to directly monitor changes in the twist of nucleic acids. Nat. Commun. 2:439.
-
(2011)
Nat. Commun.
, vol.2
, pp. 439
-
-
Lipfert, J.1
Wiggin, M.2
Dekker, N.H.3
-
31
-
-
83655192457
-
Direct mechanical measurements reveal the material properties of three-dimensional DNA origami
-
Kauert, D. J., T. Kurth, ., R. Seidel. 2011. Direct mechanical measurements reveal the material properties of three-dimensional DNA origami. Nano Lett. 11:5558-5563.
-
(2011)
Nano Lett.
, vol.11
, pp. 5558-5563
-
-
Kauert, D.J.1
Kurth, T.2
Seidel, R.3
-
32
-
-
0036307707
-
Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 A° resolution
-
Davey, C. A., D. F. Sargent, ., T. J. Richmond. 2002. Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 A° resolution. J. Mol. Biol. 319:1097-1113.
-
(2002)
J. Mol. Biol.
, vol.319
, pp. 1097-1113
-
-
Davey, C.A.1
Sargent, D.F.2
Richmond, T.J.3
-
33
-
-
0035812627
-
Crystallographic analysis of Lac repressor bound to natural operator O1
-
Bell, C. E., and M. Lewis. 2001. Crystallographic analysis of Lac repressor bound to natural operator O1. J. Mol. Biol. 312:921-926.
-
(2001)
J. Mol. Biol.
, vol.312
, pp. 921-926
-
-
Bell, C.E.1
Lewis, M.2
-
34
-
-
0029938053
-
Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
-
Lewis, M., G. Chang, ., P. Lu. 1996. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science. 271:1247-1254.
-
(1996)
Science
, vol.271
, pp. 1247-1254
-
-
Lewis, M.1
Chang, G.2
Lu, P.3
-
35
-
-
77957240284
-
DNA curvature and flexibility in vitro and in vivo
-
Peters, 3rd, J. P., and L. J. Maher. 2010. DNA curvature and flexibility in vitro and in vivo. Q. Rev. Biophys. 43:23-63.
-
(2010)
Q. Rev. Biophys.
, vol.43
, pp. 23-63
-
-
Peters Iii, J.P.1
Maher, L.J.2
-
36
-
-
53549090982
-
Conformation of circular DNA in two dimensions
-
Witz, G., K. Rechendorff, ., G. Dietler. 2008. Conformation of circular DNA in two dimensions. Phys. Rev. Lett. 101:148103.
-
(2008)
Phys. Rev. Lett.
, vol.101
, pp. 148103
-
-
Witz, G.1
Rechendorff, K.2
Dietler, G.3
-
38
-
-
68149152978
-
Comment on "remeasuring the double helix"
-
Becker, N. B., and R. Everaers. 2009. Comment on Remeasuring the double helix. Science. 325:538.
-
(2009)
Science
, vol.325
, pp. 538
-
-
Becker, N.B.1
Everaers, R.2
-
39
-
-
66249118371
-
Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
-
Demurtas, D., A. Amzallag, ., A. Stasiak. 2009. Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles. Nucleic Acids Res. 37:2882-2893.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2882-2893
-
-
Demurtas, D.1
Amzallag, A.2
Stasiak, A.3
-
40
-
-
77957255973
-
Sequence dependence of DNA bending rigidity
-
Geggier, S., and A. Vologodskii. 2010. Sequence dependence of DNA bending rigidity. Proc. Natl. Acad. Sci. USA. 107:15421-15426.
-
(2010)
Proc. Natl. Acad. Sci. USA
, vol.107
, pp. 15421-15426
-
-
Geggier, S.1
Vologodskii, A.2
-
41
-
-
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
-
42
-
-
79960647806
-
Analytical description of extension, torque, and supercoiling radius of a stretched twisted DNA
-
Neukirch, S., and J. F. Marko. 2011. Analytical description of extension, torque, and supercoiling radius of a stretched twisted DNA. Phys. Rev. Lett. 106:138104.
-
(2011)
Phys. Rev. Lett.
, vol.106
, pp. 138104
-
-
Neukirch, S.1
Marko, J.F.2
-
43
-
-
0032497194
-
Entropic elasticity of twist-storing polymers
-
Moroz, J. D., and P. Nelson. 1998. Entropic elasticity of twist-storing polymers. Macromolecules. 31:6333-6347.
-
(1998)
Macromolecules
, vol.31
, pp. 6333-6347
-
-
Moroz, J.D.1
Nelson, P.2
-
44
-
-
0031880233
-
A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes
-
Klenin, K., H. Merlitz, and J. Langowski. 1998. A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. Biophys. J. 74:780-788.
-
(1998)
Biophys. J.
, vol.74
, pp. 780-788
-
-
Klenin, K.1
Merlitz, H.2
Langowski, J.3
-
45
-
-
0036099317
-
Computer simulation of the 30-nanometer chromatin fiber
-
Wedemann, G., and J. Langowski. 2002. Computer simulation of the 30-nanometer chromatin fiber. Biophys. J. 82:2847-2859.
-
(2002)
Biophys. J.
, vol.82
, pp. 2847-2859
-
-
Wedemann, G.1
Langowski, J.2
-
46
-
-
0017389770
-
Interactions of highly charged colloidal cylinders with applications to double-stranded
-
Stigter, D. 1977. Interactions of highly charged colloidal cylinders with applications to double-stranded. Biopolymers. 16:1435-1448.
-
(1977)
Biopolymers
, vol.16
, pp. 1435-1448
-
-
Stigter, D.1
-
47
-
-
0031047888
-
Stretching DNA with optical tweezers
-
Wang, M. D., H. Yin, ., S. M. Block. 1997. Stretching DNA with optical tweezers. Biophys. J. 72:1335-1346.
-
(1997)
Biophys. J.
, vol.72
, pp. 1335-1346
-
-
Wang, M.D.1
Yin, H.2
Block, S.M.3
-
48
-
-
0003803285
-
-
University Science Books, Sausalito, CA
-
Bloomfield, V. A., D. M. Crothers, and I. Tinoco. 2000. Nucleic Acids: Structures, Properties, and Functions. University Science Books, Sausalito, CA.
-
(2000)
Nucleic Acids: Structures, Properties, and Functions
-
-
Bloomfield, V.A.1
Crothers, D.M.2
Tinoco, I.3
-
49
-
-
5744249209
-
Equations of state calculations by fast computing machines
-
Metropolis, N., A.W. Rosenbluth,., E. Teller. 1953. Equations of state calculations by fast computing machines. J. Chem. Phys. 21:1087-1091.
-
(1953)
J. Chem. Phys.
, vol.21
, pp. 1087-1091
-
-
Metropolis, N.1
Rosenbluth, A.W.2
Teller, E.3
-
50
-
-
0001202352
-
Monte Carlo studies on the freely jointed polymer chain with excluded volume interaction
-
Baumgärtner, A., and K. Binder. 1979. Monte Carlo studies on the freely jointed polymer chain with excluded volume interaction. J. Chem. Phys. 71:2541-2545.
-
(1979)
J. Chem. Phys.
, vol.71
, pp. 2541-2545
-
-
Baumgärtner, A.1
-
51
-
-
0030973367
-
Extension of torsionally stressed DNA by external force
-
Vologodskii, A. V., and J. F. Marko. 1997. Extension of torsionally stressed DNA by external force. Biophys. J. 73:123-132.
-
(1997)
Biophys. J.
, vol.73
, pp. 123-132
-
-
Vologodskii, A.V.1
Marko, J.F.2
-
52
-
-
33847708732
-
Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo
-
Arya, G., and T. Schlick. 2007. Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo. J. Chem. Phys. 126:044107.
-
(2007)
J. Chem. Phys.
, vol.126
, pp. 044107
-
-
Arya, G.1
Schlick, T.2
-
54
-
-
33747883688
-
Rapid knot detection and application to protein structure prediction
-
Khatib, F., M. T.Weirauch, and C. A. Rohl. 2006. Rapid knot detection and application to protein structure prediction. Bioinformatics. 22:e252-e259.
-
(2006)
Bioinformatics
, vol.22
-
-
Khatib, F.1
Weirauch, M.T.2
Rohl, C.A.3
-
55
-
-
0034668195
-
Computation of writhe in modeling of supercoiled DNA
-
Klenin, K., and J. Langowski. 2000. Computation of writhe in modeling of supercoiled DNA. Biopolymers. 54:307-317.
-
(2000)
Biopolymers.
, vol.54
, pp. 307-317
-
-
Klenin, K.1
Langowski, J.2
-
56
-
-
0038658626
-
Monte Carlo methods in statistical mechanics: Foundations and new algorithms
-
C. DeWitt-Morette, P. Cartier, and A. Folacci, editors. Cargèse, France
-
Sokal, A. D. 1997. Monte Carlo methods in statistical mechanics: foundations and new algorithms. In Functional Integration: Basics and Applications. Proc. NATO ASI B-136. C. DeWitt-Morette, P. Cartier, and A. Folacci, editors. Cargèse, France. 131-192.
-
(1997)
Functional Integration: Basics and Applications. Proc. NATO ASI B-136
, pp. 131-192
-
-
Sokal, A.D.1
-
57
-
-
0016379943
-
A physical method for deriving the electrostatic interaction between rod-like polyions at all mutual angles
-
Brenner, S. L., and V. A. Parsegian. 1974. A physical method for deriving the electrostatic interaction between rod-like polyions at all mutual angles. Biophys. J. 14:327-334.
-
(1974)
Biophys. J.
, vol.14
, pp. 327-334
-
-
Brenner, S.L.1
Parsegian, V.A.2
-
58
-
-
0017380736
-
Electrical double layer, z-potential, and electrophoretic charge of double-stranded DNA
-
Schellman, J. A., and D. Stigter. 1977. Electrical double layer, z-potential, and electrophoretic charge of double-stranded DNA. Biopolymers. 16:1415-1434.
-
(1977)
Biopolymers.
, vol.16
, pp. 1415-1434
-
-
Schellman, J.A.1
Stigter, D.2
|