-
1
-
-
0023904316
-
Action at a distance along a DNA
-
Wang, J. C., and G. N. Giaever. 1988. Action at a distance along a DNA. Science. 240:300-304.
-
(1988)
Science
, vol.240
, pp. 300-304
-
-
Wang, J.C.1
Giaever, G.N.2
-
3
-
-
0037311664
-
Eukaryotic transcriptional regulatory complexes: Cooperativity from near and afar
-
Ogata, K., K. Sato, and T. H. Tahirov. 2003. Eukaryotic transcriptional regulatory complexes: cooperativity from near and afar. Curr. Opin. Struct. Biol. 13:40-48.
-
(2003)
Curr. Opin. Struct. Biol
, vol.13
, pp. 40-48
-
-
Ogata, K.1
Sato, K.2
Tahirov, T.H.3
-
4
-
-
85030583553
-
-
Nash, H. A. 1996. Site-specific recombination: integration, excition, resolution and inversion of defined DNA segments. In Escherichia coli and Salmonella. F. C. Neidhardt, editor. American Society for Microbiology, Washington DC. 2330-2376.
-
Nash, H. A. 1996. Site-specific recombination: integration, excition, resolution and inversion of defined DNA segments. In Escherichia coli and Salmonella. F. C. Neidhardt, editor. American Society for Microbiology, Washington DC. 2330-2376.
-
-
-
-
5
-
-
0030014783
-
DNA topoisomerases
-
Wang, J. C. 1996. DNA topoisomerases. Annu. Rev. Biochem. 65: 635-695.
-
(1996)
Annu. Rev. Biochem
, vol.65
, pp. 635-695
-
-
Wang, J.C.1
-
7
-
-
0035909991
-
DNA supercoiling allows enhancer action over a large distance
-
Liu, Y., V. Bondarenko, A. Ninfa, and V. M. Studitsky. 2001. DNA supercoiling allows enhancer action over a large distance. Proc. Natl. Acad. Sci. USA. 98:14883-14888.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 14883-14888
-
-
Liu, Y.1
Bondarenko, V.2
Ninfa, A.3
Studitsky, V.M.4
-
8
-
-
33645275997
-
Loops in DNA: An overview of experimental and theoretical approaches
-
Allemand, J. F., S. Cocco, N. Douarche, and G. Lia. 2006. Loops in DNA: An overview of experimental and theoretical approaches. Eur. Phys. J. 19:293-302.
-
(2006)
Eur. Phys. J
, vol.19
, pp. 293-302
-
-
Allemand, J.F.1
Cocco, S.2
Douarche, N.3
Lia, G.4
-
9
-
-
0030058275
-
Effect of supercoiling on the juxtaposition and relative orientation of DNA sites
-
Vologodskii, A., and N. R. Cozzarelli. 1996. Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. Biophys. J. 70:2548-2556.
-
(1996)
Biophys. J
, vol.70
, pp. 2548-2556
-
-
Vologodskii, A.1
Cozzarelli, N.R.2
-
11
-
-
0035134518
-
Diffusion-controlled intrachain reactions of supercoiled DNA: Brownian dynamics simulations
-
Klenin, K. V., and J. Langowski. 2001. Diffusion-controlled intrachain reactions of supercoiled DNA: Brownian dynamics simulations. Biophys. J. 80:69-74.
-
(2001)
Biophys. J
, vol.80
, pp. 69-74
-
-
Klenin, K.V.1
Langowski, J.2
-
12
-
-
0032479079
-
Going the distance: A current view of enhancer action
-
Blackwood, E. M., and J. T. Kadonaga. 1998. Going the distance: a current view of enhancer action. Science. 281:61-63.
-
(1998)
Science
, vol.281
, pp. 61-63
-
-
Blackwood, E.M.1
Kadonaga, J.T.2
-
13
-
-
0042387955
-
Communication over a large distance: Enhancers and insulators
-
Bondarenko, V. A., Y. V. Liu, Y. I. Jiang, and V. M. Studitsky. 2003. Communication over a large distance: enhancers and insulators. Biochem. Cell Biol. 81:241-251.
-
(2003)
Biochem. Cell Biol
, vol.81
, pp. 241-251
-
-
Bondarenko, V.A.1
Liu, Y.V.2
Jiang, Y.I.3
Studitsky, V.M.4
-
14
-
-
0028801067
-
Action at a distance: DNA-looping and initiation of transcription
-
Rippe, K., P. H. von Hippel, and J. Langowski. 1995. Action at a distance: DNA-looping and initiation of transcription. Trends Biochem. Sci. 20:500-506.
-
(1995)
Trends Biochem. Sci
, vol.20
, pp. 500-506
-
-
Rippe, K.1
von Hippel, P.H.2
Langowski, J.3
-
15
-
-
0030935280
-
RNA polymerase II holoenzyme recruitment is sufficient to remodel chromatin at the yeast PHO5 promoter
-
Gaudreau, L., A. Schmid, D. Blaschke, M. Ptashne, and W. Horz. 1997. RNA polymerase II holoenzyme recruitment is sufficient to remodel chromatin at the yeast PHO5 promoter. Cell. 89:55-62.
-
(1997)
Cell
, vol.89
, pp. 55-62
-
-
Gaudreau, L.1
Schmid, A.2
Blaschke, D.3
Ptashne, M.4
Horz, W.5
-
16
-
-
0032457658
-
The bacterial enhancer-binding protein NtrC as a molecular machine
-
Rombel, I., A. North, I. Hwang, C. Wyman, and S. Kustu. 1998. The bacterial enhancer-binding protein NtrC as a molecular machine. Cold Spring Harb. Symp. Quant. Biol. 63:157-166.
-
(1998)
Cold Spring Harb. Symp. Quant. Biol
, vol.63
, pp. 157-166
-
-
Rombel, I.1
North, A.2
Hwang, I.3
Wyman, C.4
Kustu, S.5
-
17
-
-
0033912262
-
The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor
-
Buck, M., M. T. Gallegos, D. J. Studholme, Y. Guo, and J. D. Gralla. 2000. The bacterial enhancer-dependent sigma(54) (sigma(N)) transcription factor. J. Bacteriol. 182:4129-4136.
-
(2000)
J. Bacteriol
, vol.182
, pp. 4129-4136
-
-
Buck, M.1
Gallegos, M.T.2
Studholme, D.J.3
Guo, Y.4
Gralla, J.D.5
-
18
-
-
0024598928
-
Function of a bacterial activator protein that binds to transcriptional enhancers
-
Popham, D. L., D. Szeto, J. Keener, and S. Kustu. 1989. Function of a bacterial activator protein that binds to transcriptional enhancers. Science. 243:629-635.
-
(1989)
Science
, vol.243
, pp. 629-635
-
-
Popham, D.L.1
Szeto, D.2
Keener, J.3
Kustu, S.4
-
19
-
-
0141514008
-
Rationally designed insulator-like elements can block enhancer action in vitro
-
Bondarenko, V. A., Y. I. Jiang, and V. M. Studitsky. 2003. Rationally designed insulator-like elements can block enhancer action in vitro. EMBO J. 22:4728-4737.
-
(2003)
EMBO J
, vol.22
, pp. 4728-4737
-
-
Bondarenko, V.A.1
Jiang, Y.I.2
Studitsky, V.M.3
-
20
-
-
0027359777
-
Oligomerization of NTRC at the glnA enhancer is required for transcriptional activation
-
Porter, S. C., A. K. North, A. B. Wedel, and S. Kustu. 1993. Oligomerization of NTRC at the glnA enhancer is required for transcriptional activation. Genes Dev. 7:2258-2273.
-
(1993)
Genes Dev
, vol.7
, pp. 2258-2273
-
-
Porter, S.C.1
North, A.K.2
Wedel, A.B.3
Kustu, S.4
-
21
-
-
0029166594
-
The bacterial enhancer-binding protein NTRC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation
-
Wedel, A., and S. Kustu. 1995. The bacterial enhancer-binding protein NTRC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation. Genes Dev. 9:2042-2052.
-
(1995)
Genes Dev
, vol.9
, pp. 2042-2052
-
-
Wedel, A.1
Kustu, S.2
-
22
-
-
0030894489
-
Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein
-
Wyman, C., I. Rombel, A. K. North, C. Bustamante, and S. Kustu. 1997. Unusual oligomerization required for activity of NtrC, a bacterial enhancer-binding protein. Science. 275:1658-1661.
-
(1997)
Science
, vol.275
, pp. 1658-1661
-
-
Wyman, C.1
Rombel, I.2
North, A.K.3
Bustamante, C.4
Kustu, S.5
-
23
-
-
0033609111
-
Physical evidence for a phosphorylation-dependent conformational change in the enhancer-binding protein NtrC
-
Hwang, I., T. Thorgeirsson, J. Lee, S. Kustu, and Y. K. Shin. 1999. Physical evidence for a phosphorylation-dependent conformational change in the enhancer-binding protein NtrC. Proc. Natl. Acad. Sci. USA. 96:4880-4885.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 4880-4885
-
-
Hwang, I.1
Thorgeirsson, T.2
Lee, J.3
Kustu, S.4
Shin, Y.K.5
-
24
-
-
0025035371
-
DNA-looping and enhancer activity: Association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter
-
Su, W., S. Porter, S. Kustu, and H. Echols. 1990. DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter. Proc. Natl. Acad. Sci. USA. 87:5504-5508.
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 5504-5508
-
-
Su, W.1
Porter, S.2
Kustu, S.3
Echols, H.4
-
25
-
-
0030748519
-
Transcriptional activation via DNA-looping: Visualization of intermediates in the activation pathway of E. coli RNA polymerase X sigma 54 holoenzyme by scanning force microscopy
-
Rippe, K., M. Guthold, P. H. von Hippel, and C. Bustamante. 1997. Transcriptional activation via DNA-looping: visualization of intermediates in the activation pathway of E. coli RNA polymerase X sigma 54 holoenzyme by scanning force microscopy. J. Mol. Biol. 270:125-138.
-
(1997)
J. Mol. Biol
, vol.270
, pp. 125-138
-
-
Rippe, K.1
Guthold, M.2
von Hippel, P.H.3
Bustamante, C.4
-
26
-
-
33845197966
-
Chromatin structure can strongly facilitate enhancer action over a distance
-
Rubtsov, M. A., Y. S. Polikanov, V. A. Bondarenko, Y. H. Wang, and V. M. Studitsky. 2006. Chromatin structure can strongly facilitate enhancer action over a distance. Proc. Natl. Acad. Sci. USA. 103:17690-17695.
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 17690-17695
-
-
Rubtsov, M.A.1
Polikanov, Y.S.2
Bondarenko, V.A.3
Wang, Y.H.4
Studitsky, V.M.5
-
27
-
-
0347381249
-
Assay of prokaryotic enhancer activity over a distance in vitro
-
Bondarenko, V., Y. V. Liu, A. J. Ninfa, and V. M. Studitsky. 2003. Assay of prokaryotic enhancer activity over a distance in vitro. Meth. Enzymol. 370:324-337.
-
(2003)
Meth. Enzymol
, vol.370
, pp. 324-337
-
-
Bondarenko, V.1
Liu, Y.V.2
Ninfa, A.J.3
Studitsky, V.M.4
-
28
-
-
85047672273
-
Supercoiling energy and nucleosome formation: The role of the arginine-rich histone kernel
-
Camerini-Otero, R. D., and G. Felsenfeld. 1977. Supercoiling energy and nucleosome formation: the role of the arginine-rich histone kernel. Nucleic Acids Res. 4:1159-1181.
-
(1977)
Nucleic Acids Res
, vol.4
, pp. 1159-1181
-
-
Camerini-Otero, R.D.1
Felsenfeld, G.2
-
29
-
-
0037459086
-
Topological measurement of an A-tract bend angle: Variation of duplex winding. Topological measurement of an A-tract bend angle: comparison of the bent and straightened states
-
Tchernaenko, V., H. R. Halvorson, L. C. Lutter, M. Radlinska, C. Drabik, and J. Bujnicki. 2003. Topological measurement of an A-tract bend angle: variation of duplex winding. Topological measurement of an A-tract bend angle: comparison of the bent and straightened states. J. Mol. Biol. 326:751-760.
-
(2003)
J. Mol. Biol
, vol.326
, pp. 751-760
-
-
Tchernaenko, V.1
Halvorson, H.R.2
Lutter, L.C.3
Radlinska, M.4
Drabik, C.5
Bujnicki, J.6
-
30
-
-
0015211548
-
Partial alteration of secondary structure in native superhelical DNA
-
Dean, W. W., and J. Lebowitz. 1971. Partial alteration of secondary structure in native superhelical DNA. Nat. New Biol. 231:5-8.
-
(1971)
Nat. New Biol
, vol.231
, pp. 5-8
-
-
Dean, W.W.1
Lebowitz, J.2
-
31
-
-
0018447729
-
Fluctuations in superhelical DNA
-
Vologodskii, A. V., A. V. Lukashin, V. V. Anshelevich, and M. D. Frank-Kamenetskii. 1979. Fluctuations in superhelical DNA. Nucleic Acids Res. 6:967-982.
-
(1979)
Nucleic Acids Res
, vol.6
, pp. 967-982
-
-
Vologodskii, A.V.1
Lukashin, A.V.2
Anshelevich, V.V.3
Frank-Kamenetskii, M.D.4
-
32
-
-
0027740297
-
The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA
-
Bauer, W. R., and C. J. Benham. 1993. The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA. J. Mol. Biol. 234:1184-1196.
-
(1993)
J. Mol. Biol
, vol.234
, pp. 1184-1196
-
-
Bauer, W.R.1
Benham, C.J.2
-
33
-
-
0041817952
-
Effect of varying the supercoiling of DNA on transcription and its regulation
-
Lim, H. M., D. E. Lewis, H. J. Lee, M. Liu, and S. Adhya. 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
-
34
-
-
11344266685
-
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
-
Peter, B. J., J. Arsuaga, A. M. Breier, A. B. Khodursky, P. O. Brown, and N. R. Cozzarelli. 2004. Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli. Genome Biol. 5:R87.
-
(2004)
Genome Biol
, 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
-
36
-
-
0026764407
-
Activator-independent formation of a closed complex between sigma 54- holoenzyme and nifH and nifU promoters of Klebsiella pneumoniae
-
Buck, M., and W. Cannon. 1992. Activator-independent formation of a closed complex between sigma 54- holoenzyme and nifH and nifU promoters of Klebsiella pneumoniae. Mol. Microbiol. 6:1625-1630.
-
(1992)
Mol. Microbiol
, vol.6
, pp. 1625-1630
-
-
Buck, M.1
Cannon, W.2
-
37
-
-
0036464552
-
Action of prokaryotic enhancer over a distance does not require continued presence of promoter-bound sigma54 subunit
-
Bondarenko, V., Y. Liu, A. Ninfa, and V. M. Studitsky. 2002. Action of prokaryotic enhancer over a distance does not require continued presence of promoter-bound sigma54 subunit. Nucleic Acids Res. 30:636-642.
-
(2002)
Nucleic Acids Res
, vol.30
, pp. 636-642
-
-
Bondarenko, V.1
Liu, Y.2
Ninfa, A.3
Studitsky, V.M.4
|