-
1
-
-
0025148348
-
Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination
-
H. Echols Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination J. Biol. Chem. 265 1990 14697 14700
-
(1990)
J. Biol. Chem.
, vol.265
, pp. 14697-14700
-
-
Echols, H.1
-
2
-
-
20444387232
-
A gamut of loops: Meandering DNA
-
DOI 10.1016/j.tibs.2005.04.009, PII S0968000405001179, Celebrating 50 Years of the IUBMB
-
S. Semsey, K. Virnik, and S. Adhya A gamut of loops: meandering DNA Trends Biochem. Sci. 30 2005 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
-
3
-
-
0023333893
-
Lac repressor forms loops with linear DNA carrying two suitably spaced lac operators
-
H. Krämer, and M. Niemöller B. Müller-Hill Lac repressor forms loops with linear DNA carrying two suitably spaced lac operators EMBO J. 6 1987 1481 1491
-
(1987)
EMBO J.
, vol.6
, pp. 1481-1491
-
-
Krämer, H.1
Niemöller, M.2
Müller-Hill, B.3
-
4
-
-
0024300816
-
Physical properties of DNA in vivo as probed by the length dependence of the lac operator looping process
-
G.R. Bellomy, M.C. Mossing, and M.T. Record Jr. Physical properties of DNA in vivo as probed by the length dependence of the lac operator looping process Biochemistry 27 1988 3900 3906
-
(1988)
Biochemistry
, vol.27
, pp. 3900-3906
-
-
Bellomy, G.R.1
Mossing, M.C.2
Record Jr., M.T.3
-
5
-
-
0029975889
-
Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
-
J. Müller, S. Oehler, and B. Müller-Hill Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator J. Mol. Biol. 257 1996 21 29
-
(1996)
J. Mol. Biol.
, vol.257
, pp. 21-29
-
-
Müller, J.1
Oehler, S.2
Müller-Hill, B.3
-
6
-
-
19444387811
-
Bacterial repression loops require enhanced DNA flexibility
-
DOI 10.1016/j.jmb.2005.04.035, PII S0022283605004559
-
N.A. Becker, J.D. Kahn, and L.J. Maher 3rd Bacterial repression loops require enhanced DNA flexibility J. Mol. Biol. 349 2005 716 730 (Pubitemid 40725950)
-
(2005)
Journal of Molecular Biology
, vol.349
, Issue.4
, pp. 716-730
-
-
Becker, N.A.1
Kahn, J.D.2
Maher III, L.J.3
-
7
-
-
66249118030
-
Concentration and length dependence of DNA looping in transcriptional regulation
-
L. Han, and H.G. Garcia R. Phillips Concentration and length dependence of DNA looping in transcriptional regulation PLoS ONE 4 2009 e5621
-
(2009)
PLoS ONE
, vol.4
, pp. 5621
-
-
Han, L.1
Garcia, H.G.2
Phillips, R.3
-
8
-
-
68349150612
-
First-principles calculation of DNA looping in tethered particle experiments
-
K.B. Towles, and J.F. Beausang P.C. Nelson First-principles calculation of DNA looping in tethered particle experiments Phys. Biol. 6 2009 025001
-
(2009)
Phys. Biol.
, vol.6
, pp. 025001
-
-
Towles, K.B.1
Beausang, J.F.2
Nelson, P.C.3
-
9
-
-
2142855754
-
DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor
-
H. Krämer, and M. Amouyal B. Müller-Hill DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor EMBO J. 7 1988 547 556
-
(1988)
EMBO J.
, vol.7
, pp. 547-556
-
-
Krämer, H.1
Amouyal, M.2
Müller-Hill, B.3
-
10
-
-
0033585029
-
Designed hyperstable Lac repressor.DNA loop topologies suggest alternative loop geometries
-
R.A. Mehta, and J.D. Kahn Designed hyperstable Lac repressor.DNA loop topologies suggest alternative loop geometries J. Mol. Biol. 294 1999 67 77
-
(1999)
J. Mol. Biol.
, vol.294
, pp. 67-77
-
-
Mehta, R.A.1
Kahn, J.D.2
-
11
-
-
0029004903
-
Crystal structure of lac repressor core tetramer and its implications for DNA looping
-
A.M. Friedman, T.O. Fischmann, and T.A. Steitz Crystal structure of lac repressor core tetramer and its implications for DNA looping Science 268 1995 1721 1727
-
(1995)
Science
, vol.268
, pp. 1721-1727
-
-
Friedman, A.M.1
Fischmann, T.O.2
Steitz, T.A.3
-
12
-
-
0029938053
-
Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
-
M. Lewis, and G. Chang P. Lu Crystal structure of the lactose operon repressor and its complexes with DNA and inducer Science 271 1996 1247 1254
-
(1996)
Science
, vol.271
, pp. 1247-1254
-
-
Lewis, M.1
Chang, G.2
Lu, P.3
-
13
-
-
0031002095
-
Conformation of Lac repressor tetramer in solution, bound and unbound to operator DNA
-
G.C. Ruben, and T.B. Roos Conformation of Lac repressor tetramer in solution, bound and unbound to operator DNA Microsc. Res. Tech. 36 1997 400 416 (Pubitemid 27194572)
-
(1997)
Microscopy Research and Technique
, vol.36
, Issue.5
, pp. 400-416
-
-
Ruben, G.C.1
Roos, T.B.2
-
14
-
-
38349193126
-
Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein
-
M. Taraban, and H. Zhan J. Trewhella Ligand-induced conformational changes and conformational dynamics in the solution structure of the lactose repressor protein J. Mol. Biol. 376 2008 466 481
-
(2008)
J. Mol. Biol.
, vol.376
, pp. 466-481
-
-
Taraban, M.1
Zhan, H.2
Trewhella, J.3
-
15
-
-
54749084305
-
Interconvertible lac repressor-DNA loops revealed by single-molecule experiments
-
O.K. Wong, and M. Guthold J. Gelles Interconvertible lac repressor-DNA loops revealed by single-molecule experiments PLoS Biol. 6 2008 e232
-
(2008)
PLoS Biol.
, vol.6
, pp. 232
-
-
Wong, O.K.1
Guthold, M.2
Gelles, J.3
-
16
-
-
43349099320
-
Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping
-
DOI 10.1093/nar/gkn071
-
D. Normanno, F. Vanzi, and F.S. Pavone Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping Nucleic Acids Res. 36 2008 2505 2513 (Pubitemid 351659566)
-
(2008)
Nucleic Acids Research
, vol.36
, Issue.8
, pp. 2505-2513
-
-
Normanno, D.1
Vanzi, F.2
Pavone, F.S.3
-
17
-
-
33746207766
-
Lac repressor hinge flexibility and DNA looping: Single molecule kinetics by tethered particle motion
-
F. Vanzi, and C. Broggio F.S. Pavone Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion Nucleic Acids Res. 34 2006 3409 3420
-
(2006)
Nucleic Acids Res.
, vol.34
, pp. 3409-3420
-
-
Vanzi, F.1
Broggio, C.2
Pavone, F.S.3
-
19
-
-
0037306915
-
Fluorescence resonance energy transfer over ∼130 basepairs in hyperstable Lac repressor-DNA loops
-
L.M. Edelman, R. Cheong, and J.D. Kahn Fluorescence resonance energy transfer over approximately 130 basepairs in hyperstable lac repressor-DNA loops Biophys. J. 84 2003 1131 1145 (Pubitemid 36133436)
-
(2003)
Biophysical Journal
, vol.84
, Issue.2
, pp. 1131-1145
-
-
Edelman, L.M.1
Cheong, R.2
Kahn, J.D.3
-
20
-
-
58749116653
-
Computational analysis of looping of a large family of highly bent DNA by LacI
-
T.D. Lillian, and S. Goyal N.C. Perkins Computational analysis of looping of a large family of highly bent DNA by LacI Biophys. J. 95 2008 5832 5842
-
(2008)
Biophys. J.
, vol.95
, pp. 5832-5842
-
-
Lillian, T.D.1
Goyal, S.2
Perkins, N.C.3
-
21
-
-
31544452261
-
Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI
-
DOI 10.1093/nar/gkj432
-
B. van den Broek, and F. Vanzi G.J. Wuite Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI Nucleic Acids Res. 34 2006 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
-
22
-
-
33744546367
-
DNA looping by two-site restriction endonucleases: Heterogeneous probability distributions for loop size and unbinding force
-
DOI 10.1093/nar/gkl382
-
G.J. Gemmen, R. Millin, and D.E. Smith DNA looping by two-site restriction endonucleases: heterogeneous probability size and unbinding force Nucleic Acids Res. 34 2006 2864 2877 (Pubitemid 44540415)
-
(2006)
Nucleic Acids Research
, vol.34
, Issue.10
, pp. 2864-2877
-
-
Gemmen, G.J.1
Millin, R.2
Smith, D.E.3
-
23
-
-
43149113705
-
Geometry of mediating protein affects the probability of loop formation in DNA
-
N.J. Agrawal, R. Radhakrishnan, and P.K. Purohit Geometry of mediating protein affects the probability of loop formation in DNA Biophys. J. 94 2008 3150 3158
-
(2008)
Biophys. J.
, vol.94
, pp. 3150-3158
-
-
Agrawal, N.J.1
Radhakrishnan, R.2
Purohit, P.K.3
-
25
-
-
55849089592
-
Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes
-
L. Saiz, and J.M.G. Vilar Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes PLoS ONE 2 2007 e355
-
(2007)
PLoS ONE
, vol.2
, pp. 355
-
-
Saiz, L.1
Vilar, J.M.G.2
-
27
-
-
34547852967
-
Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
-
Y. Zhang, and A.E. McEwen S.D. Levene Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping PLoS ONE 1 2006 e136
-
(2006)
PLoS ONE
, vol.1
, pp. 136
-
-
Zhang, Y.1
McEwen, A.E.2
Levene, S.D.3
-
29
-
-
33645086141
-
Modeling DNA loops using the theory of elasticity
-
A. Balaeff, L. Mahadevan, and K. Schulten Modeling DNA loops using the theory of elasticity Phys. Rev. E. 73 2006 031919
-
(2006)
Phys. Rev. E.
, vol.73
, pp. 031919
-
-
Balaeff, A.1
Mahadevan, L.2
Schulten, K.3
-
30
-
-
33845793417
-
Effect of supercoiling on formation of protein-mediated DNA loops
-
P.K. Purohit, and P.C. Nelson Effect of supercoiling on formation of protein-mediated DNA loops Phys. Rev. E. 74 2006 061907
-
(2006)
Phys. Rev. E.
, vol.74
, pp. 061907
-
-
Purohit, P.K.1
Nelson, P.C.2
-
32
-
-
0038298831
-
Theory of sequence-dependent DNA elasticity
-
B.D. Coleman, W.K. Olson, and D. Swigon Theory of sequence-dependent DNA elasticity J. Chem. Phys. 118 2003 7127 7140
-
(2003)
J. Chem. Phys.
, vol.118
, pp. 7127-7140
-
-
Coleman, B.D.1
Olson, W.K.2
Swigon, D.3
-
34
-
-
0037215722
-
Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization
-
Y. Zhang, and D.M. Crothers Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization Biophys. J. 84 2003 136 153 (Pubitemid 36026386)
-
(2003)
Biophysical Journal
, vol.84
, Issue.1
, pp. 136-153
-
-
Zhang, Y.1
Crothers, D.M.2
-
35
-
-
33645991551
-
Statistical-mechanical theory of DNA looping
-
Y. Zhang, and A.E. McEwen S.D. Levene Statistical-mechanical theory of DNA looping Biophys. J. 90 2006 1903 1912
-
(2006)
Biophys. J.
, vol.90
, pp. 1903-1912
-
-
Zhang, Y.1
McEwen, A.E.2
Levene, S.D.3
-
36
-
-
0029066852
-
Modeling superhelical DNA: Recent analytical and dynamic approaches
-
T. Schlick Modeling superhelical DNA: recent analytical and dynamic approaches Curr. Opin. Struct. Biol. 5 1995 245 262
-
(1995)
Curr. Opin. Struct. Biol.
, vol.5
, pp. 245-262
-
-
Schlick, T.1
-
37
-
-
0030005131
-
Simulating DNA at low resolution
-
DOI 10.1016/S0959-440X(96)80082-0
-
W.K. Olson Simulating DNA at low resolution Curr. Opin. Struct. Biol. 6 1996 242 256 (Pubitemid 26128830)
-
(1996)
Current Opinion in Structural Biology
, vol.6
, Issue.2
, pp. 242-256
-
-
Olson, W.K.1
-
38
-
-
0000323998
-
A continuum rod model of sequence-dependent DNA structure
-
R.S. Manning, J.H. Maddocks, and J.D. Kahn A continuum rod model of sequence-dependent DNA structure J. Chem. Phys. 105 1996 5626 5646 (Pubitemid 126748226)
-
(1996)
Journal of Chemical Physics
, vol.105
, Issue.13
, pp. 5626-5646
-
-
Manning, R.S.1
Maddocks, J.H.2
Kahn, J.D.3
-
41
-
-
20344370700
-
Nonlinear dynamics and loop formation in Kirchhoff rods with implications to the mechanics of DNA and cables
-
DOI 10.1016/j.jcp.2005.03.027, PII S002199910500183X
-
S. Goyal, N.C. Perkins, and C.L. Lee Nonlinear dynamics and loop formation in Kirchhoff rods with implications to the mechanics of DNA and cables J. Comput. Phys. 209 2005 371 389 (Pubitemid 40792371)
-
(2005)
Journal of Computational Physics
, vol.209
, Issue.1
, pp. 371-389
-
-
Goyal, S.1
Perkins, N.C.2
Lee, C.L.3
-
42
-
-
37349076968
-
Intrinsic curvature of DNA influences LacR-mediated looping
-
DOI 10.1529/biophysj.107.112268
-
S. Goyal, and T. Lillian N.C. Perkins Intrinsic curvature of DNA influences LacR-mediated looping Biophys. J. 93 2007 4342 4359 (Pubitemid 350294481)
-
(2007)
Biophysical Journal
, vol.93
, Issue.12
, pp. 4342-4359
-
-
Goyal, S.1
Lillian, T.2
Blumberg, S.3
Meiners, J.-C.4
Meyhofer, E.5
Perkins, N.C.6
-
43
-
-
0035850731
-
A standard reference frame for the description of nucleic acid base-pair geometry
-
DOI 10.1006/jmbi.2001.4987
-
W.K. Olson, and M. Bansal H.M. Berman A standard reference frame for the description of nucleic acid base-pair geometry J. Mol. Biol. 313 2001 229 237 (Pubitemid 33001177)
-
(2001)
Journal of Molecular Biology
, vol.313
, Issue.1
, pp. 229-237
-
-
Olson, W.K.1
Bansal, M.2
Burley, S.K.3
Dickerson, R.E.4
Gerstein, M.5
Harvey, S.C.6
Heinemann, U.7
Lu, X.-J.8
Neidle, S.9
Shakked, Z.10
Sklenar, H.11
Suzuki, M.12
Tung, C.-S.13
Westhof, E.14
Wolberger, C.15
Berman, H.M.16
-
44
-
-
0034668195
-
Computation of writhe in modeling of supercoiled DNA
-
K. Klenin, and J. Langowski Computation of writhe in modeling of supercoiled DNA Biopolymers 54 2000 307 317
-
(2000)
Biopolymers
, vol.54
, pp. 307-317
-
-
Klenin, K.1
Langowski, J.2
-
45
-
-
78649931178
-
Electrostatics and self-contact in an elastic rod approximation for DNA
-
T.D. Lillian, and N.C. Perkins Electrostatics and self-contact in an elastic rod approximation for DNA J. Comput. Nonlinear Dyn. 6 2011 011008
-
(2011)
J. Comput. Nonlinear Dyn.
, vol.6
, pp. 011008
-
-
Lillian, T.D.1
Perkins, N.C.2
|