-
1
-
-
0024284650
-
Recognition of a DNA operator by the repressor of phage 434: A view at high resolution
-
AGGARWAL, A., RODGERS, D. W., DROTTAR, M., PTASHNE, M. & HARRISON, S. C. (1988). Recognition of a DNA operator by the repressor of phage 434: a view at high resolution. Science 242, 899-907.
-
(1988)
Science
, vol.242
, pp. 899-907
-
-
Aggarwal, A.1
Rodgers, D.W.2
Drottar, M.3
Ptashne, M.4
Harrison, S.C.5
-
2
-
-
33747827908
-
Readout: Structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition
-
AHMAD, S., KONO, H., ARAúZO-BRAVO, M. J. & SARAI, A. (2006). Readout: structure-based calculation of direct and indirect readout energies and specificities for protein-DNA recognition. Nucleic Acids Research 34, W124-W127.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Ahmad, S.1
Kono, H.2
Araúzo-Bravo, M.J.3
Sarai, A.4
-
3
-
-
0032564447
-
Stretched and overwound DNA forms a Pauling-like structure with exposed bases
-
ALLEMAND, J.-F., BENSIMON, D., LAVERY, R. & CROQUETTE, V. (1998). Stretched and overwound DNA forms a Pauling-like structure with exposed bases. Proceedings of the National Academy of Sciences of the United States of America 95, 14152-14157.
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, pp. 14152-14157
-
-
Allemand, J.-F.1
Bensimon, D.2
Lavery, R.3
Croquette, V.4
-
4
-
-
0017835311
-
Supercoiling in closed circular DNA: Dependence upon ion type and concentration
-
ANDERSON, P. & BAUER, W. (1978). Supercoiling in closed circular DNA: dependence upon ion type and concentration. Biochemistry 17, 594-601.
-
(1978)
Biochemistry
, vol.17
, pp. 594-601
-
-
Anderson, P.1
Bauer, W.2
-
5
-
-
0026530492
-
Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-Mer
-
ANSARI, A. Z., CHAEL, M. L. & O'HALLORAN, T. V. (1992). Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-Mer. Nature 355, 87-89.
-
(1992)
Nature
, vol.355
, pp. 87-89
-
-
Ansari, A.Z.1
Chael, M.L.2
O'Halloran, T.V.3
-
6
-
-
0016304026
-
Structures for the poly-nucleotide complexes poly(dA) with poly(dT) and poly(dT) with poly(dA) with poly (dT)
-
ARNOTT, S. & SELSING, E. (1974). Structures for the poly-nucleotide complexes poly(dA) with poly(dT) and poly(dT) with poly(dA) with poly (dT). Journal of Molecular Biology 88, 509-521.
-
(1974)
Journal of Molecular Biology
, vol.88
, pp. 509-521
-
-
Arnott, S.1
Selsing, E.2
-
7
-
-
31544464136
-
Structural and dynamic basis of a supercoiling-responsive DNA element
-
BAE, S. H., YUN, S. H., SUN, D., LIM, H. M. & CHOI, B. S. (2006). Structural and dynamic basis of a supercoiling-responsive DNA element. Nucleic Acids Research 34, 254-261.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 254-261
-
-
Bae, S.H.1
Yun, S.H.2
Sun, D.3
Lim, H.M.4
Choi, B.S.5
-
8
-
-
0025298857
-
Supercoil-induced unusual DNA structures as tran-scriptional block
-
BAGGA, R., RAMESH, N. & BRAHMACHARI, S. K. (1990). Supercoil-induced unusual DNA structures as tran-scriptional block. Nucleic Acids Research 18, 3363-3369.
-
(1990)
Nucleic Acids Research
, vol.18
, pp. 3363-3369
-
-
Bagga, R.1
Ramesh, N.2
Brahmachari, S.K.3
-
9
-
-
66149110385
-
DNA sequence-directed organization of chromatin: Structure-based computational analysis of nucleosome-binding sequences
-
BALASUBRAMANIAN, S., XU, F. & OLSON, W. K. (2009). DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophysical Journal 96, 2245-2260.
-
(2009)
Biophysical Journal
, vol.96
, pp. 2245-2260
-
-
Balasubramanian, S.1
F, X.U.2
Olson, W.K.3
-
10
-
-
79953313413
-
Targeting G-quadruplexes in gene promoters: A novel anticancer strategy?
-
BALASUBRAMANIAN, S., HURLEY, L. H. & NEIDLE, S. (2011). Targeting G-quadruplexes in gene promoters: a novel anticancer strategy? Nature Reviews Drug Discovery 10, 261-275.
-
(2011)
Nature Reviews Drug Discovery
, vol.10
, pp. 261-275
-
-
Balasubramanian, S.1
Hurley, L.H.2
Neidle, S.3
-
11
-
-
39149138419
-
DNA double helices recognize mutual sequence homology in a protein free environment
-
BALDWIN, G. S., BROOKS, N. J., ROBSON, R. E., WYNVEEN, A., GOLDAR, A., LEIKIN, S., SEDDON, J.M. & KORNYSHEV, A. A. (2008). DNA double helices recognize mutual sequence homology in a protein free environment. Journal of Physical Chemistry B 112, 1060-1064.
-
(2008)
Journal of Physical Chemistry B
, vol.112
, pp. 1060-1064
-
-
Baldwin, G.S.1
Brooks, N.J.2
Robson, R.E.3
Wynveen, A.4
Goldar, A.5
Leikin, S.6
Seddon, J.M.7
Kornyshev, A.A.8
-
12
-
-
1042300668
-
Behavior of complex knots in single DNA molecules
-
BAO, X. R., LEE, H. J. & QUAKE, S. R. (2003). Behavior of complex knots in single DNA molecules. Physical Review Letters 91, 34.
-
(2003)
Physical Review Letters
, vol.91
, pp. 34
-
-
Bao, X.R.1
Lee, H.J.2
Quake, S.R.3
-
13
-
-
65349131971
-
The folding and unfolding of eukaryotic chromatin
-
BASSETT, A., COOPER, S., WU, C. & TRAVERS, A. (2009). The folding and unfolding of eukaryotic chromatin. Current Opinion in Genetics and Development 19, 159-165.
-
(2009)
Current Opinion in Genetics and Development
, vol.19
, pp. 159-165
-
-
Bassett, A.1
Cooper, S.2
C, W.U.3
Travers, A.4
-
15
-
-
34447323073
-
Energy coupling in type II topoisomerases: Why do they hydrolyze ATP?
-
BATES, A. D. & MAXWELL, A. (2007). Energy coupling in type II topoisomerases: why do they hydrolyze ATP? Biochemistry 46, 7929-7941.
-
(2007)
Biochemistry
, vol.46
, pp. 7929-7941
-
-
Bates, A.D.1
Maxwell, A.2
-
16
-
-
80055065448
-
The ancestral role of ATP hydrolysis in type II topoisome-rases: Prevention of DNA double-strand breaks
-
BATES, A. D., BERGER, J. M. & MAXWELL, A. (2011). The ancestral role of ATP hydrolysis in type II topoisome-rases: prevention of DNA double-strand breaks. Nucleic Acids Research 39, 6327-6339.
-
(2011)
Nucleic Acids Research
, vol.39
, pp. 6327-6339
-
-
Bates, A.D.1
Berger, J.M.2
Maxwell, A.3
-
17
-
-
0028049305
-
The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo
-
BEDNAR, J., FURRER, P., STASIAK, A., DUBOCHET, J., EGELMAN, E. H. & BATES, A. D. (1994). The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. Journal of Molecular Biology 235, 825-847.
-
(1994)
Journal of Molecular Biology
, vol.235
, pp. 825-847
-
-
Bednar, J.1
Furrer, P.2
Stasiak, A.3
Dubochet, J.4
Egelman, E.H.5
Bates, A.D.6
-
18
-
-
36148968944
-
A triplex-forming sequence from the human c-MYC promoter interferes with DNA transcription
-
BELOTSERKOVSKII, B.P., DE SILVA, E., TORNALETTI, S., WANG, G., VASQUEZ, K. M. & HANAWALT, P. C. (2007). A triplex-forming sequence from the human c-MYC promoter interferes with DNA transcription. Journal of Biological Chemistry 282, 32433-32441.
-
(2007)
Journal of Biological Chemistry
, vol.282
, pp. 32433-32441
-
-
Belotserkovskii, B.P.1
De Silva, E.2
Tornaletti, S.3
Wang, G.4
Vasquez, K.M.5
Hanawalt, P.C.6
-
20
-
-
0019887628
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory
-
BERG, O. G., WINTER, R. B. & VON HIPPEL, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20, 6929-6948.
-
(1981)
Biochemistry
, vol.20
, pp. 6929-6948
-
-
Berg, O.G.1
Winter, R.B.2
Von Hippel, P.H.3
-
22
-
-
0031447208
-
DNA condensation by multi-valent cations
-
BLOOMFIELD, V. A. (1997). DNA condensation by multi-valent cations. Biopolymers 44, 269-282.
-
(1997)
Biopolymers
, vol.44
, pp. 269-282
-
-
Bloomfield, V.A.1
-
23
-
-
33745612978
-
Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome
-
BLOT, N., MAVATHUR, R., GEERTZ, M., TRAVERS, A. & MUSKHELISHVILI, G. (2006). Homeostatic regulation of supercoiling sensitivity coordinates transcription of the bacterial genome. EMBO Reports 7, 710-715.
-
(2006)
EMBO Reports
, vol.7
, pp. 710-715
-
-
Blot, N.1
Mavathur, R.2
Geertz, M.3
Travers, A.4
Muskhelishvili, G.5
-
24
-
-
0025363121
-
Structure of plectonemically supercoiled DNA
-
BOLES, T. C., WHITE, J. H. & COZZARELLI, N. R. (1990). Structure of plectonemically supercoiled DNA. Journal of Molecular Biology 213, 931-951.
-
(1990)
Journal of Molecular Biology
, vol.213
, pp. 931-951
-
-
Boles, T.C.1
White, J.H.2
Cozzarelli, N.R.3
-
26
-
-
78650435917
-
Gene repression by minimal lac loops in vivo
-
BOND, L. M., PETERS, J. P., BECKER, N. A., KAHN, J. D. & MAHER, III, L. J. (2010). Gene repression by minimal lac loops in vivo. Nucleic Acids Research 38, 8072-8082.
-
(2010)
Nucleic Acids Research
, vol.38
, pp. 8072-8082
-
-
Bond, L.M.1
Peters, J.P.2
Becker, N.A.3
Kahn, J.D.4
Maher III, L.J.5
-
27
-
-
40349095138
-
Increased fluoroquinolone resistance with time in Escherichia coli from >17, 000 patients at a large county hospital as a function of culture site, age, sex, and location
-
BOYD, L. B., ATMAR, R. L., RANDALL, G. L., HAMILL, R. J., STEFFEN, D. & ZECHIEDRICH, L. (2008). Increased fluoroquinolone resistance with time in Escherichia coli from >17, 000 patients at a large county hospital as a function of culture site, age, sex, and location. BMC Infectious Diseases 8, 35.
-
(2008)
BMC Infectious Diseases
, vol.8
, pp. 35
-
-
Boyd, L.B.1
Atmar, R.L.2
Randall, G.L.3
Hamill, R.J.4
Steffen, D.5
Zechiedrich, L.6
-
28
-
-
77951821756
-
-
New York: Wiley
-
BROOKS, C. L., KARPLUS, M. & PETTITT, B. M. (1988). Advances in Chemical Physics, Proteins: A Theoretical Perspective on Dynamics, Structure, and Thermodynamics, Vol. 71. New York: Wiley.
-
(1988)
Advances in Chemical Physics, Proteins: A Theoretical Perspective on Dynamics, Structure, and Thermodynamics
, vol.71
-
-
Brooks, C.L.1
Karplus, M.2
Pettitt, B.M.3
-
30
-
-
34548576981
-
Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topo-isomerases
-
BURNIER, Y., WEBER, C., FLAMMINI, A. & STASIAK, A. (2007). Local selection rules that can determine specific pathways of DNA unknotting by type II DNA topo-isomerases. Nucleic Acids Research 35, 5223-5331.
-
(2007)
Nucleic Acids Research
, vol.35
, pp. 5223-5331
-
-
Burnier, Y.1
Weber, C.2
Flammini, A.3
Stasiak, A.4
-
31
-
-
85015087906
-
Ten years of tension: Single-molecule DNA mechanics
-
BUSTAMANTE, C., BRYANT, Z. & SMITH, S. B. (2003). Ten years of tension: single-molecule DNA mechanics. Nature 421, 423-427.
-
(2003)
Nature
, vol.421
, pp. 423-427
-
-
Bustamante, C.1
Bryant, Z.2
Smith, S.B.3
-
32
-
-
0001443491
-
Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants
-
CǍLUGǍREANU, G. (1961). Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants. Czechoslovak Mathematical Journal. 11, 588-625.
-
(1961)
Czechoslovak Mathematical Journal.
, vol.11
, pp. 588-625
-
-
Cǎlugǎreanu, G.1
-
33
-
-
33747802145
-
A thermodynamic signature for drug-DNA binding mode
-
CHAIRES, J. B. (2006). A thermodynamic signature for drug-DNA binding mode. Archives of Biochemistry and Biophysics 453, 26-31.
-
(2006)
Archives of Biochemistry and Biophysics
, vol.453
, pp. 26-31
-
-
Chaires, J.B.1
-
34
-
-
13544272030
-
Distributions of Z-DNA and nuclear factor i in human chromosome 22: A model for coupled transcriptional regulation
-
CHAMP, P. C., MAURICE, S., VARGASON, J. M., CAMP, T. & HO, P. S. (2004). Distributions of Z-DNA and nuclear factor I in human chromosome 22: a model for coupled transcriptional regulation. Nucleic Acids Research 32, 6501-6510.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 6501-6510
-
-
Champ, P.C.1
Maurice, S.2
Vargason, J.M.3
Camp, T.4
Ho, P.S.5
-
35
-
-
0000264109
-
A contribution to the theory of electrocapilarity
-
CHAPMAN, D. L. (1913). A contribution to the theory of electrocapilarity. Philosiphical Magazine Series 25, 475-481.
-
(1913)
Philosiphical Magazine Series
, vol.25
, pp. 475-481
-
-
Chapman, D.L.1
-
36
-
-
0028345358
-
Comparison of plasmid topology among mesophilic and thermophilic eubacteria and archaebacteria
-
CHARBONNIER, F. & FORTERRE, P. (1994). Comparison of plasmid topology among mesophilic and thermophilic eubacteria and archaebacteria. Journal of Bacteriology 176, 1251-1259.
-
(1994)
Journal of Bacteriology
, vol.176
, pp. 1251-1259
-
-
Charbonnier, F.1
Forterre, P.2
-
38
-
-
0035914474
-
Electron and scanning force microscopy studies of alterations in super-coiled DNA tertiary structure
-
CHERNY, D. I. & JOVIN, T. M. (2001). Electron and scanning force microscopy studies of alterations in super-coiled DNA tertiary structure. Journal of Molecular Biology 313, 295-307.
-
(2001)
Journal of Molecular Biology
, vol.313
, pp. 295-307
-
-
Cherny, D.I.1
Jovin, T.M.2
-
39
-
-
2342518189
-
Spontaneous sharp bending of double-stranded DNA
-
CLOUTIER, T. E. & WIDOM, J. (2004). Spontaneous sharp bending of double-stranded DNA. Molecular Cell 14, 355-362.
-
(2004)
Molecular Cell
, vol.14
, pp. 355-362
-
-
Cloutier, T.E.1
Widom, J.2
-
41
-
-
22544467771
-
The structural basis for substrate specificity in DNA topoisomerase IV
-
CORBETT, K. D., SCHOEFFLER, A. J., THOMSEN, N. D. & BERGER, J. M. (2005). The structural basis for substrate specificity in DNA topoisomerase IV. Journal of Molecular Biology 351, 545-561.
-
(2005)
Journal of Molecular Biology
, vol.351
, pp. 545-561
-
-
Corbett, K.D.1
Schoeffler, A.J.2
Thomsen, N.D.3
Berger, J.M.4
-
42
-
-
34447136857
-
Holoenzyme assembly and ATP-mediated conforma-tional dynamics of topoisomerase VI
-
CORBETT, K. D., BENEDETTI, P. & BERGER, J. M. (2007). Holoenzyme assembly and ATP-mediated conforma-tional dynamics of topoisomerase VI. Nature Structural and Molecular Biology 14, 611-619.
-
(2007)
Nature Structural and Molecular Biology
, vol.14
, pp. 611-619
-
-
Corbett, K.D.1
Benedetti, P.2
Berger, J.M.3
-
43
-
-
0000559719
-
Primer on the topology and geometry of DNA super-coiling
-
eds. N. R. Cozzarelli & J. C. Wang Woodbury, NY: Cold Spring Harbor Laboratory Press
-
COZZARELLI, N. R., BOLES, T. C. & WHITE J. H. (1990). Primer on the topology and geometry of DNA super-coiling. In DNA Topology and Its Biological Effects (eds. N. R. Cozzarelli & J. C. Wang), pp. 139-184, Woodbury, NY: Cold Spring Harbor Laboratory Press.
-
(1990)
DNA Topology and Its Biological Effects
, pp. 139-184
-
-
Cozzarelli, N.R.1
Boles, T.C.2
White, J.H.3
-
44
-
-
33748335686
-
Giant proteins that move DNA: Bullies of the genomic playground
-
COZZARELLI, N. R., COST, G. J., NÖLLMANN, M., VIARD, T. & STRAY, J. E. (2006). Giant proteins that move DNA: bullies of the genomic playground. Nature Reviews Molecular Cell Biology 7, 580-588.
-
(2006)
Nature Reviews Molecular Cell Biology
, vol.7
, pp. 580-588
-
-
Cozzarelli, N.R.1
Cost, G.J.2
Nöllmann, M.3
Viard, T.4
Stray, J.E.5
-
45
-
-
0016850069
-
Kinky helix
-
CRICK, F. H. & KLUG, A. (1975). Kinky helix. Nature 255, 530-533.
-
(1975)
Nature
, vol.255
, pp. 530-533
-
-
Crick, F.H.1
Klug, A.2
-
46
-
-
0026796061
-
DNA bending, flexibility, and helical repeat by cyclization kinetics
-
CROTHERS, D. M., DRAK, J., KAHN, J. D. & LEVENE, S. D. (1992). DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods in Enzymology 212, 3-29.
-
(1992)
Methods in Enzymology
, vol.212
, pp. 3-29
-
-
Crothers, D.M.1
Drak, J.2
Kahn, J.D.3
Levene, S.D.4
-
47
-
-
15544376421
-
Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection
-
CROZAT, E., PHILIPPE, N., LENSKI, R. E., GEISELMANN, J. & SCHNEIDER, D. (2005). Long-term experimental evolution in Escherichia coli. XII. DNA topology as a key target of selection. Genetics 169, 523-532.
-
(2005)
Genetics
, vol.169
, pp. 523-532
-
-
Crozat, E.1
Philippe, N.2
Lenski, R.E.3
Geiselmann, J.4
Schneider, D.5
-
48
-
-
77955933105
-
Parallel genetic and phenotypic evolution of DNA su-perhelicity in experimental populations of Escherichia coli
-
CROZAT, E., WINKWORTH, C., GAFFÉ, J., HALLIN, P. F., RILEY, M. A., LENSKI, R. E. & SCHNEIDER, D. (2010). Parallel genetic and phenotypic evolution of DNA su-perhelicity in experimental populations of Escherichia coli. Molecular Biology and Evolution 27, 2113-2128.
-
(2010)
Molecular Biology and Evolution
, vol.27
, pp. 2113-2128
-
-
Crozat, E.1
Winkworth, C.2
Gaffé, J.3
Hallin, P.F.4
Riley, M.A.5
Lenski, R.E.6
Schneider, D.7
-
49
-
-
67649883207
-
Local and global effects of strong bending induced during molecular dynamics simulations
-
CURUKSU, J., ZACHARIAS, M., LAVERY, R. & ZAKRZEWSKA, K. (2009). Local and global effects of strong bending induced during molecular dynamics simulations. Nucleic Acids Research 37, 3766-3773.
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 3766-3773
-
-
Curuksu, J.1
Zacharias, M.2
Lavery, R.3
Zakrzewska, K.4
-
50
-
-
33749243974
-
Sequence-dependent effects in the cyclization of short DNA
-
CZAPLA, L., SWIGON, D. & OLSON, W. K. (2006). Sequence-dependent effects in the cyclization of short DNA. Journal of Chemical Theory and Computation 2, 685-695.
-
(2006)
Journal of Chemical Theory and Computation
, vol.2
, pp. 685-695
-
-
Czapla, L.1
Swigon, D.2
Olson, W.K.3
-
51
-
-
0032538282
-
Sequence-dependent extrusion of a small DNA hairpin at the N4 virion RNA polymerase promoters
-
DAI, X., KLOSTER, M. & ROTHMAN-DENES, L. B. (1998). Sequence-dependent extrusion of a small DNA hairpin at the N4 virion RNA polymerase promoters. Journal of Molecular Biology 283, 43-58.
-
(1998)
Journal of Molecular Biology
, vol.283
, pp. 43-58
-
-
Dai, X.1
Kloster, M.2
Rothman-Denes, L.B.3
-
52
-
-
46349088924
-
3D visualization software to analyze topological outcomes of topoisomerase reactions
-
DARCY, I. K., SCHAREIN, R. G. & STASIAK, A. (2008). 3D visualization software to analyze topological outcomes of topoisomerase reactions. Nucleic Acids Research 36, 3515-3521.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 3515-3521
-
-
Darcy, I.K.1
Scharein, R.G.2
Stasiak, A.3
-
53
-
-
0035868644
-
Topoisomerase IV, alone, unknots DNA in E. coli
-
DEIBLER, R. W., RAHMATI, S., & ZECHIEDRICH, E. L. (2001). Topoisomerase IV, alone, unknots DNA in E. coli. Genes and Development 15, 748-761.
-
(2001)
Genes and Development
, vol.15
, pp. 748-761
-
-
Deibler, R.W.1
Rahmati, S.2
Zechiedrich, E.L.3
-
54
-
-
34347368460
-
Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation
-
DEIBLER, R.W., MANN, J.K., SUMNERS, D.W.L. & ZECHIEDRICH, L. (2007). Hin-mediated DNA knotting and recombining promote replicon dysfunction and mutation. BMC Molecular Biology 8, 44.
-
(2007)
BMC Molecular Biology
, vol.8
, pp. 44
-
-
Deibler, R.W.1
Mann, J.K.2
Sumners, D.W.L.3
Zechiedrich, L.4
-
55
-
-
66249118371
-
Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles
-
DEMURTAS, D., AMZALLAG, A., RAWDON, E. J., MADDOCKS, J. H., DUBOCHET, J. & STASIAK, A. (2009). Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles. Nucleic Acids Research 37, 2882-2893.
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 2882-2893
-
-
Demurtas, D.1
Amzallag, A.2
Rawdon, E.J.3
Maddocks, J.H.4
Dubochet, J.5
Stasiak, A.6
-
57
-
-
76949089832
-
Bacterial nucleoid-associated proteins, nucleoid structure and gene expression
-
DILLON, S. C. & DORMAN, C. J. (2010). Bacterial nucleoid-associated proteins, nucleoid structure and gene expression. Nature Reviews Microbiology 8, 185-195.
-
(2010)
Nature Reviews Microbiology
, vol.8
, pp. 185-195
-
-
Dillon, S.C.1
Dorman, C.J.2
-
58
-
-
37549023863
-
Structural basis for gate-DNA recognition and bending by type IIa topoi-somerases
-
DONG, K. C. & BERGER, J. M. (2007). Structural basis for gate-DNA recognition and bending by type IIa topoi-somerases. Nature 450, 1201-1205.
-
(2007)
Nature
, vol.450
, pp. 1201-1205
-
-
Dong, K.C.1
Berger, J.M.2
-
59
-
-
84865249128
-
Regulation of transcription in bacteria by DNA supercoiling
-
ed. W. El-Sharoud Berlin: Springer
-
DORMAN, C. J. (2008). Regulation of transcription in bacteria by DNA supercoiling. In Bacterial Physiology: A Molecular Approach (ed. W. El-Sharoud), pp. 155-178. Berlin: Springer.
-
(2008)
Bacterial Physiology: A Molecular Approach
, pp. 155-178
-
-
Dorman, C.J.1
-
60
-
-
63349085395
-
Bacterial DNA topology and infectious disease
-
DORMAN, C. J. & CORCORAN, C. P. (2009). Bacterial DNA topology and infectious disease. Nucleic Acids Research. 37, 672-678.
-
(2009)
Nucleic Acids Research.
, vol.37
, pp. 672-678
-
-
Dorman, C.J.1
Corcoran, C.P.2
-
63
-
-
17244362931
-
Cyclization of short DNA fragments and bending fluctuations of the double helix
-
DU, Q., SMITH, C., SHIFFELDRIM, N., VOLOGODSKAIA, M. & VOLOGODSKII, A. (2005). Cyclization of short DNA fragments and bending fluctuations of the double helix. Proceedings of the National Academy of Sciences of the United States of America 102, 5397-5402.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 5397-5402
-
-
Du, Q.1
Smith, C.2
Shiffeldrim, N.3
Vologodskaia, M.4
Vologodskii, A.5
-
64
-
-
40249090005
-
Kinking the double helix by bending deformation
-
DU, Q., KOTLYAR, A. & VOLOGODSKII, A. (2008). Kinking the double helix by bending deformation. Nucleic Acids Research 36, 1120-1128.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 1120-1128
-
-
Du, Q.1
Kotlyar, A.2
Vologodskii, A.3
-
65
-
-
30144436268
-
RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP
-
DUMONT, S., CHENG, W., SEREBROV, V., BERAN, R. K., TINOCO, I., PYLE, A. M. & BUSTAMANTE, C. (2006). RNA translocation and unwinding mechanism of HCV NS3 helicase and its coordination by ATP. Nature 439, 105-108.
-
(2006)
Nature
, vol.439
, pp. 105-108
-
-
Dumont, S.1
Cheng, W.2
Serebrov, V.3
Beran, R.K.4
Tinoco, I.5
Pyle, A.M.6
Bustamante, C.7
-
66
-
-
63849304900
-
Similia similibus: Pairing of homologous chromosomes driven by the physicochemical properties of DNA
-
FALASCHI, A. (2008). Similia similibus: pairing of homologous chromosomes driven by the physicochemical properties of DNA. Human Frontiers Science Program Journal 2, 257-261.
-
(2008)
Human Frontiers Science Program Journal
, vol.2
, pp. 257-261
-
-
Falaschi, A.1
-
67
-
-
0006627150
-
A molecular simulation picture of DNA hydration around A-and B-DNA
-
FEIG, M. & PETTITT, B. M. (1988). A molecular simulation picture of DNA hydration around A-and B-DNA. Biopolymers 48, 199-209.
-
(1988)
Biopolymers
, vol.48
, pp. 199-209
-
-
Feig, M.1
Pettitt, B.M.2
-
68
-
-
77954376773
-
The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters
-
FERRÁNDIZ, M. J., MARTÍN-GALIANO, A. J., SCHVARTZMAN, J. B. & DE LA CAMPA, A. G. (2010). The genome of Streptococcus pneumoniae is organized in topology-reacting gene clusters. Nucleic Acids Research 38, 3570-3581.
-
(2010)
Nucleic Acids Research
, vol.38
, pp. 3570-3581
-
-
Ferrándiz, M.J.1
Martín-Galiano, A.J.2
Schvartzman, J.B.3
De La Campa, A.G.4
-
69
-
-
33645295275
-
Exploring writhe in supercoiled minicircle DNA
-
FOGG, J.M., KOLMAKOVA, N., REES, I., MAGONOV, S., HANSMA, H., PERONA, J. J. & ZECHIEDRICH, E. L. (2006). Exploring writhe in supercoiled minicircle DNA. Journal of Physics: Condensed Matter 18, S145-S159.
-
(2006)
Journal of Physics: Condensed Matter
, vol.18
-
-
Fogg, J.M.1
Kolmakova, N.2
Rees, I.3
Magonov, S.4
Hansma, H.5
Perona, J.J.6
Zechiedrich, E.L.7
-
70
-
-
79956291011
-
Differences between positively and negatively supercoiled DNA that top-oisomerases may distinguish
-
eds. C. J. Benham, S. Harvey, W. K. Olson, D. W. L. Sumners & D. Swigon New York: Springer
-
FOGG, J. M., CATANESE, JR, D. J., RANDALL, G. L., SWICK, M. C. & ZECHIEDRICH, L. (2009). Differences between positively and negatively supercoiled DNA that top-oisomerases may distinguish. In The Institute for Mathematics and its Applications Volumes in Mathematics and its Applications. Mathematics of DNA Structure, Function and Interactions, Vol. 150 (eds. C. J. Benham, S. Harvey, W. K. Olson, D. W. L. Sumners & D. Swigon), pp. 73-122. New York: Springer.
-
(2009)
The Institute for Mathematics and Its Applications Volumes in Mathematics and Its Applications. Mathematics of DNA Structure, Function and Interactions
, vol.150
, pp. 73-122
-
-
Fogg, J.M.1
Catanese, J.R.D.J.2
Randall, G.L.3
Swick, M.C.4
Zechiedrich, L.5
-
71
-
-
34247496263
-
Origin and evolution of DNA topoisomerases
-
FORTERRE, P., GRIBALDO, S., GADELLE, D. & SERRE, M. C. (2007). Origin and evolution of DNA topoisomerases. Biochimie 89, 427-446.
-
(2007)
Biochimie
, vol.89
, pp. 427-446
-
-
Forterre, P.1
Gribaldo, S.2
Gadelle, D.3
Serre, M.C.4
-
72
-
-
63349102030
-
Phylogenetics of DNA topoisomerases: Their origin and putative roles in the emergence of modern organisms
-
FORTERRE, P. & GADELLE, D. (2009). Phylogenetics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms. Nucleic Acids Research 37, 679-692.
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 679-692
-
-
Forterre, P.1
Gadelle, D.2
-
73
-
-
41949110996
-
Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules
-
FORTH, S., DEUFEL, C., SHEININ, M.Y., DANIELS, B., SETHNA, J. P. & WANG, M. D. (2008). Abrupt buckling transition observed during the plectoneme formation of individual DNA molecules. Physical Review Letters 100, 148301.
-
(2008)
Physical Review Letters
, vol.100
, pp. 148301
-
-
Forth, S.1
Deufel, C.2
Sheinin, M.Y.3
Daniels, B.4
Sethna, J.P.5
Wang, M.D.6
-
74
-
-
0016849392
-
In vitro recognition of carcinogen-induced local denaturation sites native DNA by S1 en-donuclease from Aspergillus oryzae
-
FUCHS, R. P. P. (1975). In vitro recognition of carcinogen-induced local denaturation sites native DNA by S1 en-donuclease from Aspergillus oryzae. Nature 257, 151-152.
-
(1975)
Nature
, vol.257
, pp. 151-152
-
-
Fuchs, R.P.P.1
-
76
-
-
33847164986
-
Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity
-
GARCIA, H.G., GRAYSON, P., HAN, L., INAMDAR, M., KONDEV, J., NELSON, P. C., PHILLIPS, R., WIDOM, J. & WIGGINS, P. A. (2007). Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Biopolymers 85, 115-130.
-
(2007)
Biopolymers
, vol.85
, pp. 115-130
-
-
Garcia, H.G.1
Grayson, P.2
Han, L.3
Inamdar, M.4
Kondev, J.5
Nelson, P.C.6
Phillips, R.7
Widom, J.8
Wiggins, P.A.9
-
77
-
-
0037335588
-
Base pair opening within B-DNA: Free energy pathways for GC and at pairs from umbrella sampling simulations
-
GIUDICE, E., VARNAI, P. & LAVERY, R. (2003). Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. Nucleic Acids Research 31, 1434-1443.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 1434-1443
-
-
Giudice, E.1
Varnai, P.2
Lavery, R.3
-
78
-
-
0000555535
-
Sur la constitution de la charge electrique a la surface d'un electrolyte
-
GOUY, G. J. (1910). Sur la constitution de la charge electrique a la surface d'un electrolyte. Journal de Physique 9, 457-468.
-
(1910)
Journal de Physique
, vol.9
, pp. 457-468
-
-
Gouy, G.J.1
-
79
-
-
0037451299
-
Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling
-
GOWERS, D. M. & HALFORD, S. E. (2003). Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling. EMBO Journal 22, 1410-1418.
-
(2003)
EMBO Journal
, vol.22
, pp. 1410-1418
-
-
Gowers, D.M.1
Halford, S.E.2
-
80
-
-
1442323773
-
Intermolecular and intramolecular readout mechanisms in protein-DNA recognition
-
GROMIHA, M. M., SIEBERS, J. G., SELVARAJ, S., KONO, H. & SARAI, A. (2004). Intermolecular and intramolecular readout mechanisms in protein-DNA recognition. Journal of Molecular Biology 337, 285-294.
-
(2004)
Journal of Molecular Biology
, vol.337
, pp. 285-294
-
-
Gromiha, M.M.1
Siebers, J.G.2
Selvaraj, S.3
Kono, H.4
Sarai, A.5
-
81
-
-
0030886293
-
Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse
-
GUO, F., GOPAUL, D. N. & VAN DUYNE, G. D. (1997). Structure of Cre recombinase complexed with DNA in a site-specific recombination synapse. Nature 389, 40-46.
-
(1997)
Nature
, vol.389
, pp. 40-46
-
-
Guo, F.1
Gopaul, D.N.2
Van Duyne, G.D.3
-
82
-
-
27144542066
-
Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases
-
HA, S. C., LOWENHAUPT, K., RICH, A., KIM, Y. G. & KIM, K. K. (2005). Crystal structure of a junction between B-DNA and Z-DNA reveals two extruded bases. Nature 437, 1183-1186.
-
(2005)
Nature
, vol.437
, pp. 1183-1186
-
-
Ha, S.C.1
Lowenhaupt, K.2
Rich, A.3
Kim, Y.G.4
Kim, K.K.5
-
83
-
-
3042579602
-
How do site-specific DNA-binding proteins find their targets?
-
HALFORD, S. E. & MARKO, J. F. (2004). How do site-specific DNA-binding proteins find their targets? Nucleic Acids Research 32, 3040-3052.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 3040-3052
-
-
Halford, S.E.1
Marko, J.F.2
-
84
-
-
2342640588
-
Enzyme-mediated DNA looping
-
HALFORD, S.E., WELSH, A.J. & SZCZELKUN, M.D. (2004). Enzyme-mediated DNA looping. Annual Review of Biophysics and Biomolecular Structure 33, 1-24.
-
(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
-
85
-
-
0011204402
-
Intramolecular DNA triplexes in supercoiled plasmids
-
HANVEY, J.C., SHIMIZU, M. & WELLS, R. D. (1988). Intramolecular DNA triplexes in supercoiled plasmids. Proceedings of the National Academy of Science of the United States of America 85, 6292-6296.
-
(1988)
Proceedings of the National Academy of Science of the United States of America
, vol.85
, pp. 6292-6296
-
-
Hanvey, J.C.1
Shimizu, M.2
Wells, R.D.3
-
86
-
-
80052187659
-
Direct measurement of DNA bending by type IIA top-oisomerases: Implications for non-equilibrium topology simplification
-
epub ahead of print
-
HARDIN, A. H., SARKAR, S.K., SEOL, Y., LIOU, G. F., OSHEROFF, N. & NEUMAN, K.C. (2011). Direct measurement of DNA bending by type IIA top-oisomerases: implications for non-equilibrium topology simplification. Nucleic Acids Research (epub ahead of print).
-
(2011)
Nucleic Acids Research
-
-
Hardin, A.H.1
Sarkar, S.K.2
Seol, Y.3
Liou, G.F.4
Osheroff, N.5
Neuman, K.C.6
-
87
-
-
38349173106
-
Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations
-
HARRIS, S. A., LAUGHTON, C. A. & LIVERPOOL, T. B. (2008). Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations. Nucleic Acids Research 36, 21-29.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 21-29
-
-
Harris, S.A.1
Laughton, C.A.2
Liverpool, T.B.3
-
88
-
-
79251604303
-
Quinolones: From antibiotics to autoinducers
-
HEEB, S., FLETCHER, M. P., CHHABRA, S. R., DIGGLE, S. P., WILLIAMS, P. & CÁMARA, M. (2011). Quinolones: from antibiotics to autoinducers. FEMS Microbiology Reviews 35, 247-274.
-
(2011)
FEMS Microbiology Reviews
, vol.35
, pp. 247-274
-
-
Heeb, S.1
Fletcher, M.P.2
Chhabra, S.R.3
Diggle, S.P.4
Williams, P.5
Cámara, M.6
-
89
-
-
0029116348
-
Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA
-
HERBERT, A., LOWENHAUPT, K., SPITZNER, J. & RICH, A. (1995). Chicken double-stranded RNA adenosine deaminase has apparent specificity for Z-DNA. Proceedings of the National Academy of Sciences of the United States of America 92, 7550-7554.
-
(1995)
Proceedings of the National Academy of Sciences of the United States of America
, vol.92
, pp. 7550-7554
-
-
Herbert, A.1
Lowenhaupt, K.2
Spitzner, J.3
Rich, A.4
-
90
-
-
0014210552
-
Catenated circular molecules in HeLa cell mitochondria
-
HUDSON, B. & VINOGRAD, J. (1967). Catenated circular molecules in HeLa cell mitochondria. Nature 216, 647-652.
-
(1967)
Nature
, vol.216
, pp. 647-652
-
-
Hudson, B.1
Vinograd, J.2
-
91
-
-
54249116230
-
Genetic regulatory mechanisms in the synthesis of proteins
-
JACOB, F. & MONOD, J. (1961). Genetic regulatory mechanisms in the synthesis of proteins. Journal of Molecular Biology 3, 318-356.
-
(1961)
Journal of Molecular Biology
, vol.3
, pp. 318-356
-
-
Jacob, F.1
Monod, J.2
-
92
-
-
0015918868
-
DNA replication of SV40-infected cells VII. Formation of SV40 catenated and circular dimers
-
JAENISCH, R. & LEVINE, A. J. (1973). DNA replication of SV40-infected cells VII. Formation of SV40 catenated and circular dimers. Journal of Molecular Biology 73, 199-212.
-
(1973)
Journal of Molecular Biology
, vol.73
, pp. 199-212
-
-
Jaenisch, R.1
Levine, A.J.2
-
93
-
-
0034435652
-
Structural and thermodynamic strategies for site-specific DNA binding proteins
-
JEN-JACOBSON, L., ENGLER, L. E. & JACOBSON, L. A. (2000). Structural and thermodynamic strategies for site-specific DNA binding proteins. Structure 8, 1015-1023.
-
(2000)
Structure
, vol.8
, pp. 1015-1023
-
-
Jen-Jacobson, L.1
Engler, L.E.2
Jacobson, L.A.3
-
94
-
-
0032573605
-
Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition
-
JIAN, H., SCHLICK, T. & VOLOGODSKII, A. (1998). Internal motion of supercoiled DNA: Brownian dynamics simulations of site juxtaposition. Journal of Molecular Biology 284, 287-296.
-
(1998)
Journal of Molecular Biology
, vol.284
, pp. 287-296
-
-
Jian, H.1
Schlick, T.2
Vologodskii, A.3
-
95
-
-
34250766751
-
Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase
-
JOHNSON, D. S., BAI, L., SMITH, B. Y., PATEL, S. S. & WANG, M. D. (2007). Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell 129, 1299-1309.
-
(2007)
Cell
, vol.129
, pp. 1299-1309
-
-
Johnson, D.S.1
Bai, L.2
Smith, B.Y.3
Patel, S.S.4
Wang, M.D.5
-
96
-
-
33749524793
-
B-DNA under stress: Over-and untwisting of DNA during molecular dynamics simulations
-
KANNAN, S., KOHLHOFF, K. & ZACHARIAS, M. (2006). B-DNA under stress: over-and untwisting of DNA during molecular dynamics simulations. Biophysical Journal 91, 2956-2965.
-
(2006)
Biophysical Journal
, vol.91
, pp. 2956-2965
-
-
Kannan, S.1
Kohlhoff, K.2
Zacharias, M.3
-
97
-
-
0034662998
-
Analysis of topoisomerase function in bacterial replication fork movement: Use of DNA microarrays
-
KHODURSKY, A. B., PETER, B. J., SCHMID, M. B., DERISI, J., BOTSTEIN, D., BROWN, P.O. & COZZARELLI, N.R. (2000). Analysis of topoisomerase function in bacterial replication fork movement: use of DNA microarrays. Proceedings of the National Academy of Sciences of the United States of America 97, 9419-9424.
-
(2000)
Proceedings of the National Academy of Sciences of the United States of America
, vol.97
, pp. 9419-9424
-
-
Khodursky, A.B.1
Peter, B.J.2
Schmid, M.B.3
Derisi, J.4
Botstein, D.5
Brown, P.O.6
Cozzarelli, N.R.7
-
98
-
-
0027483012
-
Co-crystal structure of TBP recognizing the minor groove of a TATA element
-
KIM, J. L., NIKOLOV, D. B. & BURLEY, S. K. (1993a). Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365, 520-527.
-
(1993)
Nature
, vol.365
, pp. 520-527
-
-
Kim, J.L.1
Nikolov, D.B.2
Burley, S.K.3
-
99
-
-
0027504913
-
Crystal structure of a yeast TBP/TATA-box complex
-
KIM, Y., GEIGER, J. H., HAHN, S. & SIGLER, P. B. (1993b). Crystal structure of a yeast TBP/TATA-box complex. Nature 365, 512-520.
-
(1993)
Nature
, vol.365
, pp. 512-520
-
-
Kim, Y.1
Geiger, J.H.2
Hahn, S.3
Sigler, P.B.4
-
100
-
-
0028010888
-
HhaI methyltransferase flips its target base out of the DNA helix
-
KLIMASAUSKAS, S., KUMAR, S., ROBERTS, R. J. & CHENG, X. (1994). HhaI methyltransferase flips its target base out of the DNA helix. Cell 76, 357-369.
-
(1994)
Cell
, vol.76
, pp. 357-369
-
-
Klimasauskas, S.1
Kumar, S.2
Roberts, R.J.3
Cheng, X.4
-
101
-
-
0033120215
-
Structure-based prediction of DNA target sites by regulatory proteins
-
KONO, H. & SARAI, A. (1999). Structure-based prediction of DNA target sites by regulatory proteins. Proteins 35, 114-131.
-
(1999)
Proteins
, vol.35
, pp. 114-131
-
-
Kono, H.1
Sarai, A.2
-
103
-
-
0032518220
-
Recognition of DNA structure by 434 repressor
-
KOUDELKA, G. B. (1998). Recognition of DNA structure by 434 repressor. Nucleic Acids Research 26, 669-675.
-
(1998)
Nucleic Acids Research
, vol.26
, pp. 669-675
-
-
Koudelka, G.B.1
-
104
-
-
0026595235
-
DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 repressor
-
KOUDELKA, G. B. & CARLSON, P. (1992). DNA twisting and the effects of non-contacted bases on affinity of 434 operator for 434 repressor. Nature 355, 89-91.
-
(1992)
Nature
, vol.355
, pp. 89-91
-
-
Koudelka, G.B.1
Carlson, P.2
-
105
-
-
0023187152
-
Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and cro
-
KOUDELKA, G. B., HARRISON, S. C. & PTASHNE, M. (1987). Effect of non-contacted bases on the affinity of 434 operator for 434 repressor and cro. Nature 326, 886-888.
-
(1987)
Nature
, vol.326
, pp. 886-888
-
-
Koudelka, G.B.1
Harrison, S.C.2
Ptashne, M.3
-
106
-
-
34347231949
-
Supercoil-driven DNA structures regulate genetic transactions
-
KOUZINE, F. & LEVENS, D. (2007). Supercoil-driven DNA structures regulate genetic transactions. Frontiers in Bioscience 12, 4409-4423.
-
(2007)
Frontiers in Bioscience
, vol.12
, pp. 4409-4423
-
-
Kouzine, F.1
Levens, D.2
-
107
-
-
7544242666
-
The dynamic response of upstream DNA to transcription-generated torsional stress
-
KOUZINE, F., LIU, J., SANFORD, S., CHUNG, H.-J. & LEVENS, D. (2004). The dynamic response of upstream DNA to transcription-generated torsional stress. Nature Structural and Molecular Biology 11, 1092-1100.
-
(2004)
Nature Structural and Molecular Biology
, vol.11
, pp. 1092-1100
-
-
Kouzine, F.1
Liu, J.2
Sanford, S.3
Chung, H.-J.4
Levens, D.5
-
108
-
-
38849132828
-
The functional response of upstream DNA to dynamic supercoiling in vivo
-
KOUZINE, F., SANFORD, S., ELISHA-FEIL, Z. & LEVENS, D. (2008). The functional response of upstream DNA to dynamic supercoiling in vivo. Nature Structural and Molecular Biology 15, 146-154.
-
(2008)
Nature Structural and Molecular Biology
, vol.15
, pp. 146-154
-
-
Kouzine, F.1
Sanford, S.2
Elisha-Feil, Z.3
Levens, D.4
-
109
-
-
0030901608
-
Measurement of unrestrained negative supercoiling and topological domain size in living human cells
-
KRAMER, P. R. & SINDEN, R. R. (1997). Measurement of unrestrained negative supercoiling and topological domain size in living human cells. Biochemistry 36, 3151-3158.
-
(1997)
Biochemistry
, vol.36
, pp. 3151-3158
-
-
Kramer, P.R.1
Sinden, R.R.2
-
110
-
-
0018628599
-
Escherichia coli mutants thermosensitive for deoxyribonucleic acid gyrase subunit A: Effects on deoxyribonucleic acid replication, transcription and bacteriophage growth
-
KREUZER, K. N. & COZZARELLI, N. R. (1979). Escherichia coli mutants thermosensitive for deoxyribonucleic acid gyrase subunit A: effects on deoxyribonucleic acid replication, transcription and bacteriophage growth. Journal of Bacteriology 140, 424-435.
-
(1979)
Journal of Bacteriology
, vol.140
, pp. 424-435
-
-
Kreuzer, K.N.1
Cozzarelli, N.R.2
-
111
-
-
0011066764
-
Ü ber die gestalt fadenförmiger moleküle in Lösungen
-
KUHN, W. (1934). Ü ber die gestalt fadenförmiger moleküle in Lösungen, Kolloid-Z. 68, 2.
-
(1934)
Kolloid-Z.
, vol.68
, pp. 2
-
-
Kuhn, W.1
-
112
-
-
0015901068
-
A catenated DNA molecule as an intermediate in the replication of the resistance transfer factor RK6 in Escherichia coli
-
KUPERSZTOCH, Y. M. & HELINSKI, D. R. (1973). A catenated DNA molecule as an intermediate in the replication of the resistance transfer factor RK6 in Escherichia coli. Biochemical and Biophysical Research Communications 54, 1451-1459.
-
(1973)
Biochemical and Biophysical Research Communications
, vol.54
, pp. 1451-1459
-
-
Kupersztoch, Y.M.1
Helinski, D.R.2
-
113
-
-
33749259954
-
Kinking occurs during molecular dynamics simulations of small DNA minicircles
-
LANKAS, F., LAVERY, R. & MADDOCKS, J. H. (2006). Kinking occurs during molecular dynamics simulations of small DNA minicircles. Structure 14, 1527-1534.
-
(2006)
Structure
, vol.14
, pp. 1527-1534
-
-
Lankas, F.1
Lavery, R.2
Maddocks, J.H.3
-
114
-
-
0242290881
-
DNA basepair step deformability inferred from molecular dynamics simulations
-
LANKAS, F., SPONER, J., LANGOWSKI, J. & CHEATHAM, T. E. (2003). DNA basepair step deformability inferred from molecular dynamics simulations. Biophysical Journal 85, 2872-2883.
-
(2003)
Biophysical Journal
, vol.85
, pp. 2872-2883
-
-
Lankas, F.1
Sponer, J.2
Langowski, J.3
Cheatham, T.E.4
-
115
-
-
0018311913
-
Extracellular nu-cleases of Alteromonas espejiana BAL 31.IV. The single strand-specific deoxyriboendonuclease activity as a probe for regions of altered secondary structure in negatively and positively supercoiled closed circular DNA
-
LAU, P. P. & GRAY, JR, H. B. (1979). Extracellular nu-cleases of Alteromonas espejiana BAL 31.IV. The single strand-specific deoxyriboendonuclease activity as a probe for regions of altered secondary structure in negatively and positively supercoiled closed circular DNA. Nucleic Acids Research 6, 331-357.
-
(1979)
Nucleic Acids Research
, vol.6
, pp. 331-357
-
-
Lau, P.P.1
Gray, J.R.H.B.2
-
116
-
-
18344386476
-
Structural transitions of a twisted and stretched DNA molecule
-
LÉGER, J.F., ROMANO, G., SARKAR, A., ROBERT, J., BOURDIEU, L., CHATENAY, D. & MARKO, J. F. (1999). Structural transitions of a twisted and stretched DNA molecule. Physical Review Letters 83, 1066-1069.
-
(1999)
Physical Review Letters
, vol.83
, pp. 1066-1069
-
-
Léger, J.F.1
Romano, G.2
Sarkar, A.3
Robert, J.4
Bourdieu, L.5
Chatenay, D.6
Marko, J.F.7
-
117
-
-
0017650804
-
A sensitive endonuclease probe for lesions in deoxyribonucleic acid helix structure produced by carcinogenic or mutagenic agents
-
LEGERSKI, R.J., GRAY, JR, H.B. & ROBBERSON, D.L. (1977). A sensitive endonuclease probe for lesions in deoxyribonucleic acid helix structure produced by carcinogenic or mutagenic agents. Journal of Biological Chemistry 252, 8740-8746.
-
(1977)
Journal of Biological Chemistry
, vol.252
, pp. 8740-8746
-
-
Legerski, R.J.1
Gray, J.R.H.B.2
Robberson, D.L.3
-
118
-
-
40149095913
-
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm
-
LI, X. Y., MACARTHUR, S., BOURGON, R., NIX, D., POLLARD, D. A., IYER, V.N., HECHMER, A., SIMIRENKO, L., STAPLETON, M., HENDRIKS, C. L., CHU, H. C., OGAWA, N., INWOOD, W., SEMENTCHENKO, V., BEATON, A., WEISZMANN, R., CELNIKER, S.E., KNOWLES, D.W., GINGERAS, T., SPEED, T.P., EISEN, M.B. & BIGGIN, M. D. (2008). Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biology 6, e27.
-
(2008)
PLoS Biology
, vol.6
-
-
Li, X.Y.1
MacArthur, S.2
Bourgon, R.3
Nix, D.4
Pollard, D.A.5
Iyer, V.N.6
Hechmer, A.7
Simirenko, L.8
Stapleton, M.9
Hendriks, C.L.10
Chu, H.C.11
Ogawa, N.12
Inwood, W.13
Sementchenko, V.14
Beaton, A.15
Weiszmann, R.16
Celniker, S.E.17
Knowles, D.W.18
Gingeras, T.19
Speed, T.P.20
Eisen, M.B.21
Biggin, M.D.22
more..
-
119
-
-
0025819447
-
Local DNA topology and gene expression: The case of the leu-500 promoter
-
LILLEY, D. M. J. & HIGGINS, C. F. (1991). Local DNA topology and gene expression: the case of the leu-500 promoter. Molecular Microbiology 5, 779-783.
-
(1991)
Molecular Microbiology
, vol.5
, pp. 779-783
-
-
Lilley, D.M.J.1
Higgins, C.F.2
-
120
-
-
0041817952
-
Effect of varying the supercoiling of DNA on transcription and its regulation
-
LIM, H. M., LEWIS, D. E., LEE, H. J., LIU, M. & ADHYA, S. (2003). Effect of varying the supercoiling of DNA on transcription and its regulation. Biochemistry 42, 10718-10725.
-
(2003)
Biochemistry
, vol.42
, pp. 10718-10725
-
-
Lim, H.M.1
Lewis, D.E.2
Lee, H.J.3
Liu, M.4
Adhya, S.5
-
121
-
-
83755205430
-
Cooperative kinking at distant sites in mechanically stressed DNA
-
published online ahead of print
-
LIONBERGER, T. A., DEMURTAS, D., WITZ, G., DORIER, J., LILLIAN, T., MEYHÖFER, E. & STASIAK, A. (2011). Cooperative kinking at distant sites in mechanically stressed DNA. Nucleic Acids Research published online ahead of print.
-
(2011)
Nucleic Acids Research
-
-
Lionberger, T.A.1
Demurtas, D.2
Witz, G.3
Dorier, J.4
Lillian, T.5
Meyhöfer, E.6
Stasiak, A.7
-
122
-
-
0016860269
-
On the degree of unwinding of the DNA helix by ethidium. II. Studies by electron microscopy
-
LIU, L. F. & WANG, J. C. (1975). On the degree of unwinding of the DNA helix by ethidium. II. Studies by electron microscopy. Biochimica et Biophysica Acta 395, 401-412.
-
(1975)
Biochimica et Biophysica Acta
, vol.395
, pp. 401-412
-
-
Liu, L.F.1
Wang, J.C.2
-
124
-
-
33746253988
-
Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases
-
LIU, Z., MANN, J. K., ZECHIEDRICH, E. L. & CHAN, H. S. (2006a). Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases. Journal of Molecular Biology 361, 268-285.
-
(2006)
Journal of Molecular Biology
, vol.361
, pp. 268-285
-
-
Liu, Z.1
Mann, J.K.2
Zechiedrich, E.L.3
Chan, H.S.4
-
125
-
-
33646186254
-
Inferring global topology from local juxtaposition geometry: Interlinking polymer rings and ramifications for topoisomerase action
-
LIU, Z., ZECHIEDRICH, E. L. & CHAN, H. S. (2006b). Inferring global topology from local juxtaposition geometry: interlinking polymer rings and ramifications for topoisomerase action. Biophysical Journal 90, 2344-2355.
-
(2006)
Biophysical Journal
, vol.90
, pp. 2344-2355
-
-
Liu, Z.1
Zechiedrich, E.L.2
Chan, H.S.3
-
126
-
-
33646779199
-
The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression
-
LIU, J., KOUZINE, F., NIE, Z., CHUNG, H. J., ELISHA-FEIL, Z., WEBER, A., ZHAO, K. & LEVENS, D. (2006c). The FUSE/FBP/FIR/TFIIH system is a molecular machine programming a pulse of c-myc expression. EMBO Journal 25, 2119-2130.
-
(2006)
EMBO Journal
, vol.25
, pp. 2119-2130
-
-
Liu, J.1
Kouzine, F.2
Nie, Z.3
Chung, H.J.4
Elisha-Feil, Z.5
Weber, A.6
Zhao, K.7
Levens, D.8
-
127
-
-
63349102536
-
The why and how of DNA unlinking
-
LIU, Z., DEIBLER, R. W., CHAN, H. S. & ZECHIEDRICH, L. (2009). The why and how of DNA unlinking. Nucleic Acids Research 37, 661-671.
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 661-671
-
-
Liu, Z.1
Deibler, R.W.2
Chan, H.S.3
Zechiedrich, L.4
-
128
-
-
77749337752
-
Local site preference rationalizes disentangling by DNA top-oisomerases
-
LIU, Z., ZECHIEDRICH, L. & CHAN, H. S. (2010a). Local site preference rationalizes disentangling by DNA top-oisomerases. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 81, 031902.
-
(2010)
Physical Review E: Statistical, Nonlinear and Soft Matter Physics
, vol.81
, pp. 031902
-
-
Liu, Z.1
Zechiedrich, L.2
Chan, H.S.3
-
129
-
-
77954625173
-
Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisome-rases
-
LIU, Z., ZECHIEDRICH, L. & CHAN, H. S. (2010b). Action at hooked or twisted-hooked DNA juxtapositions rationalizes unlinking preference of type-2 topoisome-rases. Journal of Molecular Biology 400, 963-982.
-
(2010)
Journal of Molecular Biology
, vol.400
, pp. 963-982
-
-
Liu, Z.1
Zechiedrich, L.2
Chan, H.S.3
-
130
-
-
45249118115
-
Supercoiling and denaturation of DNA loops
-
LIVERPOOL, T. B., HARRIS, S. A. & LAUGHTON, C. A. (2008). Supercoiling and denaturation of DNA loops. Physical Review Letters 100, 238103.
-
(2008)
Physical Review Letters
, vol.100
, pp. 238103
-
-
Liverpool, T.B.1
Harris, S.A.2
Laughton, C.A.3
-
131
-
-
0021112063
-
Positively super-coiled plasmid DNA is produced by treatment of Echerichia coli with DNA gyrase inhibitors
-
LOCKSHON, D. & MORRIS, D. R. (1983). Positively super-coiled plasmid DNA is produced by treatment of Echerichia coli with DNA gyrase inhibitors. Nucleic Acids Research 11, 2999-3017.
-
(1983)
Nucleic Acids Research
, vol.11
, pp. 2999-3017
-
-
Lockshon, D.1
Morris, D.R.2
-
132
-
-
0343167931
-
DNA topology and the thermal stress response, a tale from mesophiles and hyperthermophiles
-
LÓPEZ-GARĆIA, P. & FORTERRE, P. (2000). DNA topology and the thermal stress response, a tale from mesophiles and hyperthermophiles. Bioessays 22, 738-746.
-
(2000)
Bioessays
, vol.22
, pp. 738-746
-
-
López-Garćia, P.1
Forterre, P.2
-
133
-
-
3042855283
-
The LEF-1 high-mobility group undergoes a disorder-to-order transition upon formation of a complex with cognate DNA
-
LOVE, J. J., LI, X., CHUNG, J., DYSON, H. J. & WRIGHT, P. E. (2004). The LEF-1 high-mobility group undergoes a disorder-to-order transition upon formation of a complex with cognate DNA. Biochemistry 43, 8725-8734.
-
(2004)
Biochemistry
, vol.43
, pp. 8725-8734
-
-
Love, J.J.1
Li, X.2
Chung, J.3
Dyson, H.J.4
Wright, P.E.5
-
134
-
-
0028353171
-
Conjugative transposition: Tn916 integrase contains two independent DNA binding domains that recognize different DNA sequences
-
LU, F. & CHURCHWARD, G. (1994). Conjugative transposition: Tn916 integrase contains two independent DNA binding domains that recognize different DNA sequences. EMBO Journal 13, 1541-1548.
-
(1994)
EMBO Journal
, vol.13
, pp. 1541-1548
-
-
Lu, F.1
Churchward, G.2
-
135
-
-
1842411320
-
Crystal structure of the nucleosome core partice at 2.8 A resolution
-
LUGER, K., MÄDER, A. W., RICHMOND, R. K., SARGENT, D. F. & RICHMOND, T. J. (1997). Crystal structure of the nucleosome core partice at 2.8 A resolution. Nature 389, 251-260.
-
(1997)
Nature
, vol.389
, pp. 251-260
-
-
Luger, K.1
Mäder, A.W.2
Richmond, R.K.3
Sargent, D.F.4
Richmond, T.J.5
-
136
-
-
0028787255
-
Preferential binding of human topoisomerase i to superhelical DNA
-
MADDEN, K. R., STEWART, L. & CHAMPOUX, J. J. (1995). Preferential binding of human topoisomerase I to superhelical DNA. EMBO Journal 14, 5399-5409.
-
(1995)
EMBO Journal
, vol.14
, pp. 5399-5409
-
-
Madden, K.R.1
Stewart, L.2
Champoux, J.J.3
-
137
-
-
33846467150
-
A systems approach to measuring the binding energy landscapes of transcription factors
-
MAERKL, S. J. & QUAKE, S. R. (2007). A systems approach to measuring the binding energy landscapes of transcription factors. Science 315, 233-237.
-
(2007)
Science
, vol.315
, pp. 233-237
-
-
Maerkl, S.J.1
Quake, S.R.2
-
139
-
-
0036286851
-
Solvation and hydration of proteins and nucleic acids: A theoretical view of simulation and experiment
-
MAKAROV, V., FEIG, M. & PETTITT, B. M. (2002). Solvation and hydration of proteins and nucleic acids: a theoretical view of simulation and experiment. Accounts of Chemical Research 35, 376-384.
-
(2002)
Accounts of Chemical Research
, vol.35
, pp. 376-384
-
-
Makarov, V.1
Feig, M.2
Pettitt, B.M.3
-
140
-
-
11644276439
-
Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties
-
MANNING, G. S. (1969a). Limiting laws and counterion condensation in polyelectrolyte solutions. I. Colligative properties. Journal of Chemical Physics 51, 924-933.
-
(1969)
Journal of Chemical Physics
, vol.51
, pp. 924-933
-
-
Manning, G.S.1
-
141
-
-
20544473509
-
Limiting laws and counterion condensation in polyelectrolyte solutions. II. Self-diffusion of the small ions
-
MANNING, G. S. (1969b). Limiting laws and counterion condensation in polyelectrolyte solutions. II. Self-diffusion of the small ions. Journal of Chemical Physics 51, 934-938.
-
(1969)
Journal of Chemical Physics
, vol.51
, pp. 934-938
-
-
Manning, G.S.1
-
143
-
-
84964407711
-
Micromechanics of single supercoiled DNA molecules
-
eds. C. J. Benham, S. Harvey, W. K. Olson, D. W. L. Sumners & D. Swigon New York: Springer
-
MARKO, J. F. (2009). Micromechanics of single supercoiled DNA molecules. In The Institute for Mathematics and its Applications Volumes in Mathematics and its Applications. Mathematics of DNA Structure, Function and Interactions, vol. 150 (eds. C. J. Benham, S. Harvey, W. K. Olson, D. W. L. Sumners & D. Swigon), pp. 225-250. New York: Springer.
-
(2009)
The Institute for Mathematics and Its Applications Volumes in Mathematics and Its Applications. Mathematics of DNA Structure, Function and Interactions
, vol.150
, pp. 225-250
-
-
Marko, J.F.1
-
144
-
-
84901741978
-
Microscopic DNA fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force-field choice
-
EDS. N. Russo, D. R. Salahub & M. Witko Dordrecht: Kluwer Academic Press
-
MARKO, J.F., FEIG, M. & PETTITT, B.M. (2003). Microscopic DNA fluctuations are in accord with macroscopic DNA stretching elasticity without strong dependence on force-field choice. In Metal-Ligand Interactions: Molecular-, Nano-, Micro-, and Macrosystems in Complex Environments (EDS. N. Russo, D. R. Salahub & M. Witko), pp. 193-204. Dordrecht: Kluwer Academic Press.
-
(2003)
Metal-Ligand Interactions: Molecular-, Nano-, Micro-, and Macrosystems in Complex Environments
, pp. 193-204
-
-
Marko, J.F.1
Feig, M.2
Pettitt, B.M.3
-
146
-
-
0006744255
-
A new configuration of deoxyribonucleic acid
-
MARVIN, D. A., SPENCER, M., WILKINS, M. H. & HAMILTON, L. D. (1958). A new configuration of deoxyribonucleic acid. Nature 182, 387-388.
-
(1958)
Nature
, vol.182
, pp. 387-388
-
-
Marvin, D.A.1
Spencer, M.2
Wilkins, M.H.3
Hamilton, L.D.4
-
147
-
-
33749134234
-
High-throughput assays for DNA gyrase and other topoisomerases
-
MAXWELL, A., BURTON, N. P. & O'HAGAN, N. (2006). High-throughput assays for DNA gyrase and other topoisomerases. Nucleic Acids Research 34, e104.
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Maxwell, A.1
Burton, N.P.2
O'Hagan, N.3
-
149
-
-
0025847716
-
Structural alteration in alternating adenine-thymine sequences in positively supercoiled DNA
-
MCCLELLAN, J. A. & LILLEY, D. M. J. (1991). Structural alteration in alternating adenine-thymine sequences in positively supercoiled DNA. Journal of Molecular Biology 219, 145-149.
-
(1991)
Journal of Molecular Biology
, vol.219
, pp. 145-149
-
-
McClellan, J.A.1
Lilley, D.M.J.2
-
150
-
-
0031880930
-
Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation
-
MERLITZ, H., RIPPE, K., KLENIN, K. V. & LANGOWSKI, J. (1998). Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation. Biophysical Journal 74, 773-779.
-
(1998)
Biophysical Journal
, vol.74
, pp. 773-779
-
-
Merlitz, H.1
Rippe, K.2
Klenin, K.V.3
Langowski, J.4
-
151
-
-
79956013643
-
Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA
-
epub ahead of print
-
MITCHELL, J. S., LAUGHTON, C. A. & HARRIS, S. A. (2011). Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA. Nucleic Acids Research, epub ahead of print.
-
(2011)
Nucleic Acids Research
-
-
Mitchell, J.S.1
Laughton, C.A.2
Harris, S.A.3
-
152
-
-
0020430519
-
Studies on sequence recognition by type II restriction and modification enzymes
-
MODRICH, P. (1982). Studies on sequence recognition by type II restriction and modification enzymes. CRC Critical Reviews in Biochemistry 13, 287-323.
-
(1982)
CRC Critical Reviews in Biochemistry
, vol.13
, pp. 287-323
-
-
Modrich, P.1
-
153
-
-
0038007052
-
Archaeal genome organization and stress responses: Implications for the origin and evolution of cellular life
-
MUSGRAVE, D., ZHANG, X. & DINGER, M. (2003). Archaeal genome organization and stress responses: implications for the origin and evolution of cellular life. Astrobiology 2, 241-253.
-
(2003)
Astrobiology
, vol.2
, pp. 241-253
-
-
Musgrave, D.1
Zhang, X.2
Dinger, M.3
-
154
-
-
77949706153
-
General organisational principles of the transcriptional regulation system: A tree or a circle ?
-
MUSKHELISHVILI, G., SOBETZKO, P., GEERTZ, M. & BERGER, M. (2010). General organisational principles of the transcriptional regulation system: a tree or a circle ? Molecular BioSystems 6, 662-676.
-
(2010)
Molecular BioSystems
, vol.6
, pp. 662-676
-
-
Muskhelishvili, G.1
Sobetzko, P.2
Geertz, M.3
Berger, M.4
-
156
-
-
66349135629
-
Mechanisms of chiral discrimination by topoisomerase IV
-
NEUMAN, K.C., CHARVIN, G., BENSIMON, D. & CROQUETTE, V. (2009). Mechanisms of chiral discrimination by topoisomerase IV. Proceedings of the National Academy of Sciences of the United States of America 106, 6986-6992.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 6986-6992
-
-
Neuman, K.C.1
Charvin, G.2
Bensimon, D.3
Croquette, V.4
-
157
-
-
52649126241
-
DNA super-coiling-dependent gene regulation in Chlamydia
-
NIEHUS, E., CHENG, E. & TAN, M. (2008). DNA super-coiling-dependent gene regulation in Chlamydia. Journal of Bacteriology 190, 6419-6427.
-
(2008)
Journal of Bacteriology
, vol.190
, pp. 6419-6427
-
-
Niehus, E.1
Cheng, E.2
Tan, M.3
-
158
-
-
0015821566
-
A catenated intermediate in plasmid replication
-
NOVICK, R. P., SMITH, K., SHEEHY, R. J. & MURPHY, R. J. (1973). A catenated intermediate in plasmid replication. Biochemical and Biophysical Research Communications 54, 1460-1469.
-
(1973)
Biochemical and Biophysical Research Communications
, vol.54
, pp. 1460-1469
-
-
Novick, R.P.1
Smith, K.2
Sheehy, R.J.3
Murphy, R.J.4
-
159
-
-
0032530555
-
DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
-
OLSON, W. K., GORIN, A. A., LU, X. J., HOCK, L. M. & ZHURKIN, V. B. (1998). DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. Proceedings of the National Academy of Sciences of the United States of America 95, 11163-11168.
-
(1998)
Proceedings of the National Academy of Sciences of the United States of America
, vol.95
, pp. 11163-11168
-
-
Olson, W.K.1
Gorin, A.A.2
Lu, X.J.3
Hock, L.M.4
Zhurkin, V.B.5
-
160
-
-
0032896707
-
Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations
-
PACK, G. R., WONG, L. & LAMM, G. (1999). Divalent cations and the electrostatic potential around DNA: Monte Carlo and Poisson-Boltzmann calculations. Biopolymers 49, 575-590.
-
(1999)
Biopolymers
, vol.49
, pp. 575-590
-
-
Pack, G.R.1
Wong, L.2
Lamm, G.3
-
161
-
-
65249089637
-
Local DNA topography correlates with functional noncoding regions of the human genome
-
PARKER, S. C., HANSEN, L., ABAAN, H. O., TULLIUS, T. D. & MARGULIES, E. H. (2009). Local DNA topography correlates with functional noncoding regions of the human genome. Science 324, 389-392.
-
(2009)
Science
, vol.324
, pp. 389-392
-
-
Parker, S.C.1
Hansen, L.2
Abaan, H.O.3
Tullius, T.D.4
Margulies, E.H.5
-
162
-
-
0033602242
-
Structure of a DNA-bound ultrabithorax-extradenticle homeodomain complex
-
PASSNER, J.M., RYOO, H.D., SHEN, L., MANN, R. S. & AGGARWAL, A. K. (1999). Structure of a DNA-bound ultrabithorax-extradenticle homeodomain complex. Nature 397, 714-719.
-
(1999)
Nature
, vol.397
, pp. 714-719
-
-
Passner, J.M.1
Ryoo, H.D.2
Shen, L.3
Mann, R.S.4
Aggarwal, A.K.5
-
163
-
-
77953583981
-
Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site
-
PATEL, A., YAKOVLEVA, L., SHUMAN, S. & MONDRAGÓN, A. (2010). Crystal structure of a bacterial topoisomerase IB in complex with DNA reveals a secondary DNA binding site. Structure 18, 725-733.
-
(2010)
Structure
, vol.18
, pp. 725-733
-
-
Patel, A.1
Yakovleva, L.2
Shuman, S.3
Mondragón, A.4
-
165
-
-
42449095007
-
Towards a molecular dynamics consensus view of B-DNA flexibility
-
PÉREZ, A., LANKAS, F., LUQUE, F. J. & OROZCO, M. (2008). Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Research 36, 2379-2394.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 2379-2394
-
-
Pérez, A.1
Lankas, F.2
Luque, F.J.3
Orozco, M.4
-
166
-
-
0032544699
-
The structure of supercoiled intermediates in DNA replication
-
PETER, B. J., ULLSPERGER, C., HIASA, H., MARIANS, K. J. & COZZARELLI, N. R. (1998). The structure of supercoiled intermediates in DNA replication. Cell 94, 819-827.
-
(1998)
Cell
, vol.94
, pp. 819-827
-
-
Peter, B.J.1
Ullsperger, C.2
Hiasa, H.3
Marians, K.J.4
Cozzarelli, N.R.5
-
167
-
-
11344266685
-
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
-
PETER, B.J., ARSUAGA, J., BREIER, A.M., KHODURSKY, A. B., BROWN, P. O. & COZZARELLI, N. R. (2004). Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biology 5, R87.
-
(2004)
Genome Biology
, vol.5
-
-
Peter, B.J.1
Arsuaga, J.2
Breier, A.M.3
Khodursky, A.B.4
Brown, P.O.5
Cozzarelli, N.R.6
-
168
-
-
4444221565
-
UCSF Chimera - A visualization system for exploratory research and analysis
-
PETTERSEN, E. F., GODDARD, T. D., HUANG, C. C., COUCH, G. S., GREENBLATT, D. M., MENG, E. C. & FERRIN, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry 25, 1605-1612.
-
(2004)
Journal of Computational Chemistry
, vol.25
, pp. 1605-1612
-
-
Pettersen, E.F.1
Goddard, T.D.2
Huang, C.C.3
Couch, G.S.4
Greenblatt, D.M.5
Meng, E.C.6
Ferrin, T.E.7
-
169
-
-
0033729723
-
Multimerization-cyclization of DNA fragments as a method of conformational analysis
-
PODTELEZHNIKOV, A.A., MAO, C., SEEMAN, N.C. & VOLOGODSKII, A. (2000). Multimerization-cyclization of DNA fragments as a method of conformational analysis. Biophysical Journal 79, 2692-2704.
-
(2000)
Biophysical Journal
, vol.79
, pp. 2692-2704
-
-
Podtelezhnikov, A.A.1
Mao, C.2
Seeman, N.C.3
Vologodskii, A.4
-
170
-
-
0030458354
-
T7 RNA polymerase cannot transcribe through a highly knotted DNA template
-
PORTUGAL, J. & RODIGUEZ-CAMPOS, A. (1996). T7 RNA polymerase cannot transcribe through a highly knotted DNA template. Nucleic Acids Research 24, 4890-4894.
-
(1996)
Nucleic Acids Research
, vol.24
, pp. 4890-4894
-
-
Portugal, J.1
Rodiguez-Campos, A.2
-
171
-
-
0035902590
-
Topological challenges to DNA replication: Conformations at the fork
-
POSTOW, L., CRISONA, N. J., PETER, B. J., HARDY, C. D. & COZZARELLI, N. R. (2001). Topological challenges to DNA replication: conformations at the fork. Proceedings of the National Academy of Sciences of the United States of America 98, 8219-8226.
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, pp. 8219-8226
-
-
Postow, L.1
Crisona, N.J.2
Peter, B.J.3
Hardy, C.D.4
Cozzarelli, N.R.5
-
172
-
-
3142774839
-
Topological domain structure of the Escherichia coli chromosome
-
POSTOW, L., HARDY, C.D., ARSUAGA, J. & COZZARELLI, N. R. (2004). Topological domain structure of the Escherichia coli chromosome. Genes and Development 18, 1766-1779.
-
(2004)
Genes and Development
, vol.18
, pp. 1766-1779
-
-
Postow, L.1
Hardy, C.D.2
Arsuaga, J.3
Cozzarelli, N.R.4
-
173
-
-
33748290192
-
Classification of protein-DNA complexes based on structural descriptors
-
PRABAKARAN, P., SIEBERS, J.G., AHMAD, S., GROMIHA, M. M., SINGARAYAN, M.G. & SARAI, A. (2006). Classification of protein-DNA complexes based on structural descriptors. Structure 14, 1355-1367.
-
(2006)
Structure
, vol.14
, pp. 1355-1367
-
-
Prabakaran, P.1
Siebers, J.G.2
Ahmad, S.3
Gromiha, M.M.4
Singarayan, M.G.5
Sarai, A.6
-
174
-
-
33645279594
-
Electrostatics of DNA-DNA juxtapositions: Consequences for type II topo-isomerase function
-
RANDALL, G.L., PETTITT, B.M., BUCK, G.R. & ZECHIEDRICH, E. L. (2006). Electrostatics of DNA-DNA juxtapositions: consequences for type II topo-isomerase function. Journal of Physics: Condensed Matter 18, S173-S185.
-
(2006)
Journal of Physics: Condensed Matter
, vol.18
-
-
Randall, G.L.1
Pettitt, B.M.2
Buck, G.R.3
Zechiedrich, E.L.4
-
175
-
-
70449711324
-
In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form
-
RANDALL, G. L., ZECHIEDRICH, L. & PETTITT, B. M. (2009). In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form. Nucleic Acids Research 37, 5568-5577.
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 5568-5577
-
-
Randall, G.L.1
Zechiedrich, L.2
Pettitt, B.M.3
-
176
-
-
0029068629
-
The crystal structure of HaeIII methyl-transferase covalently complexed to DNA: An extra-helical cytosine and rearranged base pairing
-
REINISCH, K. M., CHEN, L., VERDINE, G. L. & LIPSCOMB, W. N. (1995). The crystal structure of HaeIII methyl-transferase covalently complexed to DNA: an extra-helical cytosine and rearranged base pairing. Cell 82, 143-153.
-
(1995)
Cell
, vol.82
, pp. 143-153
-
-
Reinisch, K.M.1
Chen, L.2
Verdine, G.L.3
Lipscomb, W.N.4
-
177
-
-
33751218319
-
Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
-
REVYAKIN, A., LIU, C., EBRIGHT, R. H. & STRICK, T. R. (2006).
-
(2006)
Science
, vol.314
, pp. 1139-1143
-
-
Revyakin, A.1
Liu, C.2
Ebright, R.H.3
Strick, T.R.4
-
178
-
-
0037803571
-
Z-DNA: The long road to biological function
-
RICH, A. & ZHANG, S. (2003). Z-DNA: the long road to biological function. Nature Reviews Genetics 4, 566-572.
-
(2003)
Nature Reviews Genetics
, vol.4
, pp. 566-572
-
-
Rich, A.1
Zhang, S.2
-
179
-
-
0037992395
-
The structure of DNA in the nucleosome core
-
RICHMOND, T. J. & DAVEY, C. A. (2003). The structure of DNA in the nucleosome core. Nature 423, 145-150.
-
(2003)
Nature
, vol.423
, pp. 145-150
-
-
Richmond, T.J.1
Davey, C.A.2
-
180
-
-
0029068245
-
On base flipping
-
ROBERTS, R. J. (1995). On base flipping. Cell 82, 9-12.
-
(1995)
Cell
, vol.82
, pp. 9-12
-
-
Roberts, R.J.1
-
181
-
-
33748885240
-
The worldwide emergence of plasmid-mediated quinolone resistance
-
ROBICSEK, A., JACOBY, G. A. & HOOPER, D. C. (2006). The worldwide emergence of plasmid-mediated quinolone resistance. Lancet Infectious Diseases 6, 629-640.
-
(2006)
Lancet Infectious Diseases
, vol.6
, pp. 629-640
-
-
Robicsek, A.1
Jacoby, G.A.2
Hooper, D.C.3
-
182
-
-
70350686719
-
The role of DNA shape in proteinDNA recognition
-
ROHS, R., WEST, S. M., SOSINSKY, A., LIU, P., MANN, R. S. & HONIG, B. (2009). The role of DNA shape in proteinDNA recognition. Nature 461, 1248-1253.
-
(2009)
Nature
, vol.461
, pp. 1248-1253
-
-
Rohs, R.1
West, S.M.2
Sosinsky, A.3
Liu, P.4
Mann, R.S.5
Honig, B.6
-
183
-
-
77950519937
-
Origins of specificity in proteinDNA recognition
-
ROHS, R., JIN, X., WEST, S. M., JOSHI, R., HONIG, B. & MANN, R. S. (2010). Origins of specificity in proteinDNA recognition. Annual Review of Biochemistry 79, 233-269.
-
(2010)
Annual Review of Biochemistry
, vol.79
, pp. 233-269
-
-
Rohs, R.1
Jin, X.2
West, S.M.3
Joshi, R.4
Honig, B.5
Mann, R.S.6
-
184
-
-
70349748589
-
Tetramer opening in LacI-mediated DNA looping
-
RUTKAUSKAS, D., ZHAN, H., MATTHEWS, K.S., PAVONE, F. S. & VANZI, F. (2009). Tetramer opening in LacI-mediated DNA looping. Proceedings of the National Academy of Sciences of the United States of America 106, 16627-16632.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 16627-16632
-
-
Rutkauskas, D.1
Zhan, H.2
Matthews, K.S.3
Pavone, F.S.4
Vanzi, F.5
-
185
-
-
0030758268
-
Simplification of DNA topology below equilibrium values by type II topo-isomerases
-
RYBENKOV, V.V., ULLSPERGER, C., VOLOGODSKII, A. & COZZARELLI, N. R. (1997a). Simplification of DNA topology below equilibrium values by type II topo-isomerases. Science 277, 690-693.
-
(1997)
Science
, vol.277
, pp. 690-693
-
-
Rybenkov, V.V.1
Ullsperger, C.2
Vologodskii, A.3
Cozzarelli, N.R.4
-
186
-
-
0030740986
-
The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling
-
RYBENKOV, V.V., VOLOGODSKII, A.V. & COZZARELLI, N. R. (1997b). The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. Nucleic Acids Research 25, 1412-1418.
-
(1997)
Nucleic Acids Research
, vol.25
, pp. 1412-1418
-
-
Rybenkov, V.V.1
Vologodskii, A.V.2
Cozzarelli, N.R.3
-
187
-
-
0017055337
-
Formation of catenated molecules by replication of colicin E1 plasmid DNA in cell extracts
-
SAKAKIBARA, Y., SUZUKI, K. & TOMIZAWA, J.-I. (1976). Formation of catenated molecules by replication of colicin E1 plasmid DNA in cell extracts. Journal of Molecular Biology 108, 569-582.
-
(1976)
Journal of Molecular Biology
, vol.108
, pp. 569-582
-
-
Sakakibara, Y.1
Suzuki, K.2
Tomizawa, J.-I.3
-
188
-
-
0029968822
-
Improved nearest-neighbor parameters for predicting DNA duplex stability
-
SANTALUCIA, J., ALLAWAI, H.T. & SENEVIRATNE, P.A. (1996). Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555-3562.
-
(1996)
Biochemistry
, vol.35
, pp. 3555-3562
-
-
Santalucia, J.1
Allawai, H.T.2
Seneviratne, P.A.3
-
189
-
-
0035333546
-
Structural transitions in DNA driven by external force and torque
-
SARKAR, A., LÉGER, J. F., CHATENAY, D. & MARKO, J. F. (2001). Structural transitions in DNA driven by external force and torque. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 63, 051903.
-
(2001)
Physical Review E: Statistical, Nonlinear and Soft Matter Physics
, vol.63
, pp. 051903
-
-
Sarkar, A.1
Léger, J.F.2
Chatenay, D.3
Marko, J.F.4
-
190
-
-
0026644556
-
Trefoil knotting revealed by molecular dynamics simulations of super-coiled DNA
-
SCHLICK, T. & OLSON, W. K. (1992). Trefoil knotting revealed by molecular dynamics simulations of super-coiled DNA. Science 257, 1110-1115.
-
(1992)
Science
, vol.257
, pp. 1110-1115
-
-
Schlick, T.1
Olson, W.K.2
-
191
-
-
0033814887
-
The expression of the Escherichia coli fis gene is dependent on the superhelical density of DNA
-
SCHNEIDER, R., TRAVERS, A. & MUSKHELISHVILI, G. (2000). The expression of the Escherichia coli fis gene is dependent on the superhelical density of DNA. Molecular Microbiology 38, 167-175.
-
(2000)
Molecular Microbiology
, vol.38
, pp. 167-175
-
-
Schneider, R.1
Travers, A.2
Muskhelishvili, G.3
-
192
-
-
50649101663
-
DNA topoisome-rases: Harnessing and constraining energy to govern chromosome topology
-
SCHOEFFLER, A. & BERGER, J. (2008). DNA topoisome-rases: harnessing and constraining energy to govern chromosome topology. Quarterly Review of Biophysics 41, 61.
-
(2008)
Quarterly Review of Biophysics
, vol.41
, pp. 61
-
-
Schoeffler, A.1
Berger, J.2
-
193
-
-
3142665836
-
A topological view of the replicon
-
SCHVARTZMAN, J. B. & STASIAK, A. (2004). A topological view of the replicon. EMBO Reports 5, 256-261.
-
(2004)
EMBO Reports
, vol.5
, pp. 256-261
-
-
Schvartzman, J.B.1
Stasiak, A.2
-
194
-
-
0033546005
-
Crystal structure of the Za domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA
-
SCHWARTZ, T., ROULD, M. A., LOWENHAUPT, K., HERBERT, A. & RICH, A. (1999). Crystal structure of the Za domain of the human editing enzyme ADAR1 bound to left-handed Z-DNA. Science 284, 1841-1845.
-
(1999)
Science
, vol.284
, pp. 1841-1845
-
-
Schwartz, T.1
Rould, M.A.2
Lowenhaupt, K.3
Herbert, A.4
Rich, A.5
-
195
-
-
33747500567
-
A genomic code for nucleosome positioning
-
SEGAL, E., FONDUFE-MITTENDORF, Y., CHEN, L., THÅSTRÖM, A., FIELD, Y., MOORE, I. K., WANG, J. P. & WIDOM, J. (2006). A genomic code for nucleosome positioning. Nature 442, 772-778.
-
(2006)
Nature
, vol.442
, pp. 772-778
-
-
Segal, E.1
Fondufe-Mittendorf, Y.2
Chen, L.3
Thåström, A.4
Field, Y.5
Moore, I.K.6
Wang, J.P.7
Widom, J.8
-
196
-
-
4444343959
-
Identifying DNA-binding proteins using structural motifs and the electrostatic potential
-
SHANAHAN, H. P., GARCIA, M. A., JONES, S. & THORNTON, J. (2004). Identifying DNA-binding proteins using structural motifs and the electrostatic potential. Nucleic Acids Research 32, 4732-4741.
-
(2004)
Nucleic Acids Research
, vol.32
, pp. 4732-4741
-
-
Shanahan, H.P.1
Garcia, M.A.2
Jones, S.3
Thornton, J.4
-
197
-
-
0021847771
-
Statistical mechanics of DNA topoisomers. The helical worm-like chain
-
SHIMADA, J. & YAMAKAWA, H. (1985). Statistical mechanics of DNA topoisomers. The helical worm-like chain. Journal of Molecular Biology 184, 319-329.
-
(1985)
Journal of Molecular Biology
, vol.184
, pp. 319-329
-
-
Shimada, J.1
Yamakawa, H.2
-
198
-
-
27144503807
-
DNA twists and flips
-
SINDEN, R. R. (2005). DNA twists and flips. Nature 437, 1097-1098.
-
(2005)
Nature
, vol.437
, pp. 1097-1098
-
-
Sinden, R.R.1
-
199
-
-
23244432464
-
Target search of N sliding proteins on a DNA
-
SOKOLOV, I. M., METZLER, R., PANT, K. & WILLIAMS, M. C. (2005). Target search of N sliding proteins on a DNA. Biophysical Journal 89, 895-902.
-
(2005)
Biophysical Journal
, vol.89
, pp. 895-902
-
-
Sokolov, I.M.1
Metzler, R.2
Pant, K.3
Williams, M.C.4
-
200
-
-
85115911245
-
On the writhing number of a non-closed curves
-
eds. J. A. Calvo, K. C. Millett, E. J. Rawdon & A. Stasiak Singapore: World Scientific Publishing
-
STAROSTIN, E. L. (2005). On the writhing number of a non-closed curves. In Physical and Numerical Models in Knot Theory Including Applications to the Life Sciences (eds. J. A. Calvo, K. C. Millett, E. J. Rawdon & A. Stasiak), pp. 525-545. Singapore: World Scientific Publishing.
-
(2005)
Physical and Numerical Models in Knot Theory Including Applications to the Life Sciences
, pp. 525-545
-
-
Starostin, E.L.1
-
201
-
-
0038226895
-
DNA sequence and structure: Direct and indirect recognition in proteinDNA binding
-
STEFFEN, N. R., MURPHY, S. D., TOLLERI, L., HATFIELD, G. W. & LATHROP, R. H. (2002). DNA sequence and structure: direct and indirect recognition in proteinDNA binding. Bioinformatics 18 (Suppl. 1), S22-S30.
-
(2002)
Bioinformatics
, vol.18
, Issue.SUPPL. 1
-
-
Steffen, N.R.1
Murphy, S.D.2
Tolleri, L.3
Hatfield, G.W.4
Lathrop, R.H.5
-
202
-
-
77950934795
-
The shape of the DNA minor groove directs binding by the DNA-bending protein FIS
-
STELLA, S., CASCIO, D. & JOHNSON, R. C. (2010). The shape of the DNA minor groove directs binding by the DNA-bending protein FIS. Genes and Development 24, 814-826.
-
(2010)
Genes and Development
, vol.24
, pp. 814-826
-
-
Stella, S.1
Cascio, D.2
Johnson, R.C.3
-
203
-
-
0035842899
-
Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes
-
STRICK, R., STRISSEL, P. L., GAVRILOV, K. & LEVI-SETTI, R. (2001). Cation-chromatin binding as shown by ion microscopy is essential for the structural integrity of chromosomes. Journal of Cell Biology 155, 899-910.
-
(2001)
Journal of Cell Biology
, vol.155
, pp. 899-910
-
-
Strick, R.1
Strissel, P.L.2
Gavrilov, K.3
Levi-Setti, R.4
-
204
-
-
0031895463
-
Behavior of supercoiled DNA
-
STRICK, T.R., ALLEMAND, J.-F., BENSIMON, D. & CROQUETTE, V. (1998). Behavior of supercoiled DNA. Biophysical Journal 74, 2016-2028.
-
(1998)
Biophysical Journal
, vol.74
, pp. 2016-2028
-
-
Strick, T.R.1
Allemand, J.-F.2
Bensimon, D.3
Croquette, V.4
-
205
-
-
0033908445
-
Stress-induced structural transitions in DNA and proteins
-
STRICK, T.R., ALLEMAND, J.F., BENSIMON, D. & CROQUETTE, V. (2000). Stress-induced structural transitions in DNA and proteins. Annual Review of Biophysics and Biomolecular Structure 29, 523-543.
-
(2000)
Annual Review of Biophysics and Biomolecular Structure
, vol.29
, pp. 523-543
-
-
Strick, T.R.1
Allemand, J.F.2
Bensimon, D.3
Croquette, V.4
-
206
-
-
58549101862
-
How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases
-
STUCHINSKAYA, T., MITCHENALL, L. A., SCHOEFFLER, A. J., CORBETT, K.D., BERGER, J.M., BATES, A.D. & MAXWELL, A. (2009). How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases. Journal of Molecular Biology 385, 1397-1408.
-
(2009)
Journal of Molecular Biology
, vol.385
, pp. 1397-1408
-
-
Stuchinskaya, T.1
Mitchenall, L.A.2
Schoeffler, A.J.3
Corbett, K.D.4
Berger, J.M.5
Bates, A.D.6
Maxwell, A.7
-
207
-
-
0029090187
-
Analysis of the mechanism of DNA recombination using tangles
-
SUMNERS, D. W., ERNST, C., SPENGLER, S. J. & COZZARELLI, N. R. (1995). Analysis of the mechanism of DNA recombination using tangles. Quarterly Review of Biophysics 28, 253-313.
-
(1995)
Quarterly Review of Biophysics
, vol.28
, pp. 253-313
-
-
Sumners, D.W.1
Ernst, C.2
Spengler, S.J.3
Cozzarelli, N.R.4
-
208
-
-
49149093021
-
Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids
-
SVOZIL, D., SPONER, J.E., MARCHAN, I., PÉREZ, A., CHEATHAM, T. E., FORTI, F., LUQUE, F. J., OROZCO, M. & SPONER, J. (2008). Geometrical and electronic structure variability of the sugar-phosphate backbone in nucleic acids. The Journal of Physical Chemistry B 112, 8188-8197.
-
(2008)
The Journal of Physical Chemistry B
, vol.112
, pp. 8188-8197
-
-
Svozil, D.1
Sponer, J.E.2
Marchan, I.3
Pérez, A.4
Cheatham, T.E.5
Forti, F.6
Luque, F.J.7
Orozco, M.8
Sponer, J.9
-
209
-
-
33745595880
-
Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation
-
SWIGON, D., COLEMAN, B. D. & OLSON, W. K. (2006). Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. Proceedings of the National Academy of Sciences of the United States of America 103, 9879-9884.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, pp. 9879-9884
-
-
Swigon, D.1
Coleman, B.D.2
Olson, W.K.3
-
210
-
-
33845621535
-
Ambient occlusion and edge cueing for enhancing real time molecular visualization
-
TARINI, M., CIGNONI, P. & MONTANI, C. (2006). Ambient occlusion and edge cueing for enhancing real time molecular visualization. IEEE Transactions on Visualization and Computer Graphics 12, 1237-1244.
-
(2006)
IEEE Transactions on Visualization and Computer Graphics
, vol.12
, pp. 1237-1244
-
-
Tarini, M.1
Cignoni, P.2
Montani, C.3
-
211
-
-
34447644439
-
A novel roll-and-slide mechanism of DNA folding in chromatin: Implications for nucelosme positioning
-
TOLSTORUKOV, M.Y., COLASANTI, A.V., MCCANDLISH, D. M., OLSON, W. K. & ZHURKIN, V. B. (2007). A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucelosme positioning. Journal of Molecular Biology 371, 725-738.
-
(2007)
Journal of Molecular Biology
, vol.371
, pp. 725-738
-
-
Tolstorukov, M.Y.1
Colasanti, A.V.2
McCandlish, D.M.3
Olson, W.K.4
Zhurkin, V.B.5
-
212
-
-
13444288385
-
DNA super-coiling - A global transcriptional regulator for entero-bacterial growth?
-
TRAVERS, A. & MUSKHELISHVILI, G. (2005). DNA super-coiling-a global transcriptional regulator for entero-bacterial growth? Nature Reviews Microbiology 3, 157-169.
-
(2005)
Nature Reviews Microbiology
, vol.3
, pp. 157-169
-
-
Travers, A.1
Muskhelishvili, G.2
-
213
-
-
33947265929
-
A common topology for bacterial and eukaryotic transcription initiation?
-
TRAVERS, A. & MUSKHELISHVILI, G. (2007). A common topology for bacterial and eukaryotic transcription initiation? EMBO Reports 8, 147-151.
-
(2007)
EMBO Reports
, vol.8
, pp. 147-151
-
-
Travers, A.1
Muskhelishvili, G.2
-
214
-
-
57349153045
-
How DNA coiling enhances target localization by proteins
-
VAN DEN BROEK, B., LOMHOLT, M. A., KALISCH, S. M., METZLER, R. & WUITE, G. J. (2008). How DNA coiling enhances target localization by proteins. Proceedings of the National Academy of Sciences of the United States of America 105, 15738-15742.
-
(2008)
Proceedings of the National Academy of Sciences of the United States of America
, vol.105
, pp. 15738-15742
-
-
Van Den Broek, B.1
Lomholt, M.A.2
Kalisch, S.M.3
Metzler, R.4
Wuite, G.J.5
-
215
-
-
76049087668
-
Oscillations in supercoiling drive circadian gene expression in cyanobacteria
-
VIJAYAN, V., ZUZOW, R. & O'SHEA, E.K. (2009). Oscillations in supercoiling drive circadian gene expression in cyanobacteria. Proceedings of the National Academy of Sciences of the United States of America 106, 22564-22568.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 22564-22568
-
-
Vijayan, V.1
Zuzow, R.2
O'Shea, E.K.3
-
216
-
-
33646131847
-
Brownian dynamics simulation of knot diffusion along a stretched DNA molecule
-
VOLOGODSKII, A. (2006). Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. Biophysical Journal 90, 1594-1597.
-
(2006)
Biophysical Journal
, vol.90
, pp. 1594-1597
-
-
Vologodskii, A.1
-
217
-
-
0030058275
-
Effect of supercoiling on the juxtaposition and relative orientation of DNA sites
-
VOLOGODSKII, A. & COZZARELLI, N. R. (1996). Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. Biophysical Journal 70, 2548-2556.
-
(1996)
Biophysical Journal
, vol.70
, pp. 2548-2556
-
-
Vologodskii, A.1
Cozzarelli, N.R.2
-
218
-
-
0035853134
-
Mechanism of topology simplification by type II DNA topoisomerases
-
VOLOGODSKII, A., ZHANG, W., RYBENKOV, V.V., PODTELEZHNIKOV, A.A., SUBRAMANIAN, D., GRIFFITH, J. D. & COZZARELLI, N. R. (2001). Mechanism of topology simplification by type II DNA topoisomerases. Proceedings of the National Academy of Sciences of the United States of America 98, 3045-3049.
-
(2001)
Proceedings of the National Academy of Sciences of the United States of America
, vol.98
, pp. 3045-3049
-
-
Vologodskii, A.1
Zhang, W.2
Rybenkov, V.V.3
Podtelezhnikov, A.A.4
Subramanian, D.5
Griffith, J.D.6
Cozzarelli, N.R.7
-
219
-
-
0026489194
-
Conformational and thermodynamic properties of supercoiled DNA
-
VOLOGODSKII, A.V., LEVENE, S.D., KLENIN, K.V., FRANK-KAMENETSKII, M. & COZZARELLI, N.R. (1992). Conformational and thermodynamic properties of supercoiled DNA. Journal of Molecular Biology 227, 1224-1243.
-
(1992)
Journal of Molecular Biology
, vol.227
, pp. 1224-1243
-
-
Vologodskii, A.V.1
Levene, S.D.2
Klenin, K.V.3
Frank-Kamenetskii, M.4
Cozzarelli, N.R.5
-
220
-
-
0018689799
-
Molecular structure of a left-handed double helical DNA fragment at atomic resolution
-
WANG, A. H., QUIGLEY, G. J., KOLPAK, F. J., CRAWFORD, J. L., VAN BOOM, J. H., VAN DER MAREL, G. & RICH, A. (1979). Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282, 680-686.
-
(1979)
Nature
, vol.282
, pp. 680-686
-
-
Wang, A.H.1
Quigley, G.J.2
Kolpak, F.J.3
Crawford, J.L.4
Van Boom, J.H.5
Van Der Marel, G.6
Rich, A.7
-
221
-
-
33744944261
-
Non-B DNA structure-induced genetic instability
-
WANG, G. & VASQUEZ, K. M. (2006). Non-B DNA structure-induced genetic instability. Mutation Research 598, 103-119.
-
(2006)
Mutation Research
, vol.598
, pp. 103-119
-
-
Wang, G.1
Vasquez, K.M.2
-
222
-
-
0032582494
-
Force and velocity measured for single molecules of RNA polymerase
-
WANG, M. D., SCHNITZER, M. J., YIN, H., LANDICK, R., GELLES, J. & BLOCK, S. M. (1998). Force and velocity measured for single molecules of RNA polymerase. Science 282, 902-907.
-
(1998)
Science
, vol.282
, pp. 902-907
-
-
Wang, M.D.1
Schnitzer, M.J.2
Yin, H.3
Landick, R.4
Gelles, J.5
Block, S.M.6
-
223
-
-
77955452799
-
Double-stranded DNA homology produces a physical signature
-
WANG, X., ZHANG, X., MAO, C. & SEEMAN, N. C. (2010). Double-stranded DNA homology produces a physical signature. Proceedings of the National Academy of Sciences of the United States of America 107, 12547-12552.
-
(2010)
Proceedings of the National Academy of Sciences of the United States of America
, vol.107
, pp. 12547-12552
-
-
Wang, X.1
Zhang, X.2
Mao, C.3
Seeman, N.C.4
-
224
-
-
0017903590
-
Supercoiling of DNA and nuclear conformation during the cell-cycle
-
WARREN, A. C. & COOK, P. R. (1978). Supercoiling of DNA and nuclear conformation during the cell-cycle. Journal of Cell Science. 30, 211-226.
-
(1978)
Journal of Cell Science.
, vol.30
, pp. 211-226
-
-
Warren, A.C.1
Cook, P.R.2
-
225
-
-
33750829427
-
On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension
-
WERESZCZYNSKI, J. & ANDRICIOAEI, I. (2006). On structural transitions, thermodynamic equilibrium, and the phase diagram of DNA and RNA duplexes under torque and tension. Proceedings of the National Academy of Sciences of the United States of America 103, 16200-16205.
-
(2006)
Proceedings of the National Academy of Sciences of the United States of America
, vol.103
, pp. 16200-16205
-
-
Wereszczynski, J.1
Andricioaei, I.2
-
226
-
-
0000751914
-
Self-linking and the Gauss integral in higher dimensions
-
WHITE, J. H. (1969). Self-linking and the Gauss integral in higher dimensions. American Journal of Mathematics 91, 693-728.
-
(1969)
American Journal of Mathematics
, vol.91
, pp. 693-728
-
-
White, J.H.1
-
227
-
-
41349084347
-
Exact theory of kinkable elastic polymers
-
WIGGINS, P. A., PHILLIPS, R. & NELSON, P. C. (2005). Exact theory of kinkable elastic polymers. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 71, 1-19.
-
(2005)
Physical Review E: Statistical, Nonlinear and Soft Matter Physics
, vol.71
, pp. 1-19
-
-
Wiggins, P.A.1
Phillips, R.2
Nelson, P.C.3
-
228
-
-
0019867850
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli Lac repressor-operator interaction: Kinetic measurements and conclusions
-
WINTER, R. B., BERG, O. G. & VON HIPPEL, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli Lac repressor-operator interaction: kinetic measurements and conclusions. Biochemistry 20, 6961-6977.
-
(1981)
Biochemistry
, vol.20
, pp. 6961-6977
-
-
Winter, R.B.1
Berg, O.G.2
Von Hippel, P.H.3
-
229
-
-
0019816896
-
Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor-operator interaction: Equilibrium measurements
-
WINTER, R. B. & VON HIPPEL, P. H. (1981). Diffusion-driven mechanisms of protein translocation on nucleic acids. 2. The Escherichia coli repressor-operator interaction: equilibrium measurements. Biochemistry 20, 6948-6960.
-
(1981)
Biochemistry
, vol.20
, pp. 6948-6960
-
-
Winter, R.B.1
Von Hippel, P.H.2
-
230
-
-
79952793415
-
Second-order selection for evolvability in a large Escherichia coli population
-
WOODS, R. J., BARRICK, J. E., COOPER, T. F., SHRESTHA, U., KAUTH, M. R. & LENSKI, R. E. (2011). Second-order selection for evolvability in a large Escherichia coli population. Science 331, 1433-1436.
-
(2011)
Science
, vol.331
, pp. 1433-1436
-
-
Woods, R.J.1
Barrick, J.E.2
Cooper, T.F.3
Shrestha, U.4
Kauth, M.R.5
Lenski, R.E.6
-
231
-
-
0032749078
-
Intrinsically unstructured proteins: Re-assessing the protein structure-function paradigm
-
WRIGHT, P. E. & DYSON, H. J. (1999). Intrinsically unstructured proteins: re-assessing the protein structure-function paradigm. Journal of Molecular Biology 293, 321-331.
-
(1999)
Journal of Molecular Biology
, vol.293
, pp. 321-331
-
-
Wright, P.E.1
Dyson, H.J.2
-
232
-
-
0034594940
-
Single-molecule studies of the effect of template tension on T7 DNA polymerase activity
-
WUITE, G. J., SMITH, S.B., YOUNG, M., KELLER, D. & BUSTMANTE, C. (2000). Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404, 103-106.
-
(2000)
Nature
, vol.404
, pp. 103-106
-
-
Wuite, G.J.1
Smith, S.B.2
Young, M.3
Keller, D.4
Bustmante, C.5
-
233
-
-
55249095348
-
Helical coherence of DNA in crystals and solution
-
WYNVEEN, A., LEE, D. J., KORNYSHEV, A. A. & LEIKIN, S. (2008). Helical coherence of DNA in crystals and solution. Nucleic Acids Research 36, 5540-5551.
-
(2008)
Nucleic Acids Research
, vol.36
, pp. 5540-5551
-
-
Wynveen, A.1
Lee, D.J.2
Kornyshev, A.A.3
Leikin, S.4
-
234
-
-
0030817948
-
Winding of the DNA helix by divalent metal ions
-
XU, Y. C. & BREMER, H. (1997). Winding of the DNA helix by divalent metal ions. Nucleic Acids Research 25, 4067-4071.
-
(1997)
Nucleic Acids Research
, vol.25
, pp. 4067-4071
-
-
Xu, Y.C.1
Bremer, H.2
-
235
-
-
27944487890
-
Statistics of loop formation along double helix DNAs
-
YAN, J., KAWAMURA, R. & MARKO, J. F. (2005). Statistics of loop formation along double helix DNAs. Physical Review E: Statistical, Nonlinear and Soft Matter Physics 71, 061905.
-
(2005)
Physical Review E: Statistical, Nonlinear and Soft Matter Physics
, vol.71
, pp. 061905
-
-
Yan, J.1
Kawamura, R.2
Marko, J.F.3
-
236
-
-
19544379865
-
Localized single-stranded bubble mechanism for cyclization of short double helix DNA
-
YAN, J. & MARKO, J. F. (2004). Localized single-stranded bubble mechanism for cyclization of short double helix DNA. Physical Review Letters 93, 108108.
-
(2004)
Physical Review Letters
, vol.93
, pp. 108108
-
-
Yan, J.1
Marko, J.F.2
-
237
-
-
78549235443
-
Topoisomerases and site-specific re-combinases: Similarities in structure and mechanism
-
YANG, W. (2010). Topoisomerases and site-specific re-combinases: similarities in structure and mechanism. Criticial Reviews in Biochemistry and Molecular Biology 45, 520-534.
-
(2010)
Criticial Reviews in Biochemistry and Molecular Biology
, vol.45
, pp. 520-534
-
-
Yang, W.1
-
238
-
-
0029416931
-
Transcription against an applied force
-
YIN, H., WANG, M. D., SVOBODA, K., LANDICK, R., BLOCK, S. M. & GELLES, J. (1995). Transcription against an applied force. Science 270, 1653-1657.
-
(1995)
Science
, vol.270
, pp. 1653-1657
-
-
Yin, H.1
Wang, M.D.2
Svoboda, K.3
Landick, R.4
Block, S.M.5
Gelles, J.6
-
239
-
-
0025647116
-
Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers
-
ZECHIEDRICH, E. L. & OSHEROFF, N. (1990). Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers. The EMBO Journal 9, 4555-4562.
-
(1990)
The EMBO Journal
, vol.9
, pp. 4555-4562
-
-
Zechiedrich, E.L.1
Osheroff, N.2
-
240
-
-
0034677898
-
Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli
-
ZECHIEDRICH, E. L., KHODURSKY, A. B., BACHELLIER, S., SCHNEIDER, R., CHEN, D., LILLEY, D. M. & COZZARELLI, N. R. (2000). Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli. Journal of Biological Chemistry 275, 8103-8113.
-
(2000)
Journal of Biological Chemistry
, vol.275
, pp. 8103-8113
-
-
Zechiedrich, E.L.1
Khodursky, A.B.2
Bachellier, S.3
Schneider, R.4
Chen, D.5
Lilley, D.M.6
Cozzarelli, N.R.7
-
241
-
-
77953553225
-
Topoisomerase IB-DNA interactions: X marks the spot
-
ZECHIEDRICH, L. & OSHEROFF, N. (2010). Topoisomerase IB-DNA interactions: X marks the spot. Structure 18, 661-663.
-
(2010)
Structure
, vol.18
, pp. 661-663
-
-
Zechiedrich, L.1
Osheroff, N.2
-
242
-
-
0037215722
-
Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization
-
ZHANG, Y. & CROTHERS, D. M. (2003). Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. Biophysical Journal 84, 136-153.
-
(2003)
Biophysical Journal
, vol.84
, pp. 136-153
-
-
Zhang, Y.1
Crothers, D.M.2
-
243
-
-
33645991551
-
Statistical-mechanical theory of DNA looping
-
ZHANG, Y., MCEWEN, A. E., CROTHERS, D. M. & LEVENE, S. D. (2006). Statistical-mechanical theory of DNA looping. Biophysical Journal 90, 1903-1912.
-
(2006)
Biophysical Journal
, vol.90
, pp. 1903-1912
-
-
Zhang, Y.1
McEwen, A.E.2
Crothers, D.M.3
Levene, S.D.4
-
244
-
-
73749085274
-
Non-B DNA structure-induced genetic instability and evolution
-
ZHAO, J., BACOLLA, A., WANG, G. & VASQUEZ, K.M. (2010). Non-B DNA structure-induced genetic instability and evolution. Cellular and Molecular Life Sciences 67, 43-62.
-
(2010)
Cellular and Molecular Life Sciences
, vol.67
, pp. 43-62
-
-
Zhao, J.1
Bacolla, A.2
Wang, G.3
Vasquez, K.M.4
|