-
1
-
-
65549116836
-
A nonlinear dynamic model of DNA with a sequence-dependent stacking term
-
Alexandrov, B.S., Gelev, V., Monisova, Y., Alexandrov, L.B.,Bishop, A.R., Rasmussen, K.Ø. and Usheva, A. (2009) A nonlinear dynamic model of DNA with a sequence-dependent stacking term. Nucleic Acids Res., 37, 2405-2410.
-
(2009)
Nucleic Acids Res.
, vol.37
, pp. 2405-2410
-
-
Alexandrov, B.S.1
Gelev, V.2
Monisova, Y.3
Alexandrov, L.B.4
Bishop, A.R.5
Rasmussen, K.O.6
Usheva, A.7
-
2
-
-
0033529089
-
Structural basis for initiation of transcription from an RNA polymerase-promoter complex
-
Cheetham, G.M., Jeruzalmi, D. and Steitz, T.A. (1999) Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature, 399, 80-83.
-
(1999)
Nature
, vol.399
, pp. 80-83
-
-
Cheetham, G.M.1
Jeruzalmi, D.2
Steitz, T.A.3
-
3
-
-
0034087616
-
Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II
-
Fiedler, U. and Marc Timmers, H.T. (2000) Peeling by binding or twisting by cranking: models for promoter opening and transcription initiation by RNA polymerase II. Bioessays, 22, 316-326.
-
(2000)
Bioessays
, vol.22
, pp. 316-326
-
-
Fiedler, U.1
Marc Timmers, H.T.2
-
4
-
-
63549108096
-
Toward a detailed description of the thermally induced dynamics of the core promoter
-
Alexandrov, B.S., Gelev, V., Yoo, S.W., Bishop, A.R.,Rasmussen, K.Ø. and Usheva, A. (2009) Toward a detailed description of the thermally induced dynamics of the core promoter. PLoS Comput. Biol., 5, e1000313.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Alexandrov, B.S.1
Gelev, V.2
Yoo, S.W.3
Bishop, A.R.4
Rasmussen, K.O.5
Usheva, A.6
-
5
-
-
0030472774
-
YY1 transcriptional initiator: protein interactions and association with a DNA site containing unpaired strands
-
Usheva, A. and Shenk, T. (1996) YY1 transcriptional initiator: protein interactions and association with a DNA site containing unpaired strands. Proc. Natl Acad. Sci. USA, 93, 13571-13576.
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 13571-13576
-
-
Usheva, A.1
Shenk, T.2
-
6
-
-
0028223852
-
TATA-binding protein-independent initiation: YY1, TFIIB, and RNA polymerase II direct basal transcription on supercoiled template DNA
-
Usheva, A. and Shenk, T. (1994) TATA-binding protein-independent initiation: YY1, TFIIB, and RNA polymerase II direct basal transcription on supercoiled template DNA. Cell, 76, 1115-1121.
-
(1994)
Cell
, vol.76
, pp. 1115-1121
-
-
Usheva, A.1
Shenk, T.2
-
7
-
-
0034718503
-
An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled
-
Leblanc, B.P., Benham, C.J. and Clark, D.J. (2000) An initiation element in the yeast CUP1 promoter is recognized by RNA polymerase II in the absence of TATA box-binding protein if the DNA is negatively supercoiled. Proc. Natl Acad. Sci. USA, 97, 10745-10750.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 10745-10750
-
-
Leblanc, B.P.1
Benham, C.J.2
Clark, D.J.3
-
8
-
-
0027168221
-
DNA topology and a minimal set of basal factors for transcription by RNA polymerase II
-
Parvin, J.D. and Sharp, P.A. (1993) DNA topology and a minimal set of basal factors for transcription by RNA polymerase II. Cell, 73, 533-540.
-
(1993)
Cell
, vol.73
, pp. 533-540
-
-
Parvin, J.D.1
Sharp, P.A.2
-
9
-
-
2342498193
-
DNA dynamically directs its own transcription initiation
-
Choi, C.H., Kalosakas, G., Rasmussen, K.Ø., Hiromura, M., Bishop, A.R. and Usheva, A. (2004) DNA dynamically directs its own transcription initiation. Nucleic Acids Res., 32, 1584-1590.
-
(2004)
Nucleic Acids Res.
, vol.32
, pp. 1584-1590
-
-
Choi, C.H.1
Kalosakas, G.2
Rasmussen, K.O.3
Hiromura, M.4
Bishop, A.R.5
Usheva, A.6
-
10
-
-
4243187319
-
Statistical mechanics of a nonlinear model for DNA denaturation
-
Peyrard, M. and Bishop, A.R. (1989) Statistical mechanics of a nonlinear model for DNA denaturation. Phys. Rev. Lett., 62, 2755-2758.
-
(1989)
Phys. Rev. Lett.
, vol.62
, pp. 2755-2758
-
-
Peyrard, M.1
Bishop, A.R.2
-
11
-
-
17144404972
-
Entropy-driven DNA denaturation
-
Dauxois, T., Peyrard, M. and Bishop, A.R. (1993) Entropy-driven DNA denaturation. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics, 47, R44-R47.
-
(1993)
Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics
, vol.47
-
-
Dauxois, T.1
Peyrard, M.2
Bishop, A.R.3
-
12
-
-
33750595189
-
Bubble statistics and dynamics in double-stranded DNA
-
Alexandrov, B.S., Wille, L.T., Rasmussen, K.Ø., Bishop, A.R. and Blagoev, K.B. (2006) Bubble statistics and dynamics in double-stranded DNA. Phys. Rev. E, 74, 50901(R).
-
(2006)
Phys. Rev. E
, vol.74
-
-
Alexandrov, B.S.1
Wille, L.T.2
Rasmussen, K.O.3
Bishop, A.R.4
Blagoev, K.B.5
-
13
-
-
0014966634
-
Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences
-
Wells, R.D., Larson, J.E., Grant, R.C., Shortle, B.E. and Cantor, C.R. (1970) Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences. J. Mol. Biol., 54, 465-497.
-
(1970)
J. Mol. Biol.
, vol.54
, pp. 465-497
-
-
Wells, R.D.1
Larson, J.E.2
Grant, R.C.3
Shortle, B.E.4
Cantor, C.R.5
-
14
-
-
43449137856
-
Nature and magnitude of aromatic stacking of nucleic acid bases
-
Sponer, J., Riley, K.E. and Hobza, P. (2008) Nature and magnitude of aromatic stacking of nucleic acid bases. Phys. Chem. Chem. Phys., 10, 2595-2610.
-
(2008)
Phys. Chem. Chem. Phys.
, vol.10
, pp. 2595-2610
-
-
Sponer, J.1
Riley, K.E.2
Hobza, P.3
-
15
-
-
0033548682
-
High base pair opening rates in tracts of GC base pairs
-
Dornberger, U., Leijon, M. and Fritzsche, H. (1999) High base pair opening rates in tracts of GC base pairs. J. Biol. Chem., 274, 6957-6962.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 6957-6962
-
-
Dornberger, U.1
Leijon, M.2
Fritzsche, H.3
-
16
-
-
33750345805
-
Rational design of a super core promoter that enhances gene expression
-
Juven-Gershon, T., Cheng, S. and Kadonaga, J.T. (2006) Rational design of a super core promoter that enhances gene expression. Nat. Methods, 3, 917-922.
-
(2006)
Nat. Methods
, vol.3
, pp. 917-922
-
-
Juven-Gershon, T.1
Cheng, S.2
Kadonaga, J.T.3
-
17
-
-
0027261229
-
Lack of an initiator element is responsible for multiple transcriptional initiation sites of the TATA-less mouse thymidylate synthase promoter
-
Geng, Y. and Johnson, L.F. (1993) Lack of an initiator element is responsible for multiple transcriptional initiation sites of the TATA-less mouse thymidylate synthase promoter. Mol. Cell. Biol., 13, 4894-4903.
-
(1993)
Mol. Cell. Biol.
, vol.13
, pp. 4894-4903
-
-
Geng, Y.1
Johnson, L.F.2
-
18
-
-
0019333274
-
Multiple factors required for accurate initiation of transcription by purified RNA polymerase II
-
Matsui, T.S., Segallg, J., Weill, P.A. and Roeder, R.G. (1980) Multiple factors required for accurate initiation of transcription by purified RNA polymerase II. J. Biol. Chem., 255, 11992-11996.
-
(1980)
J. Biol. Chem.
, vol.255
, pp. 11992-11996
-
-
Matsui, T.S.1
Segallg, J.2
Weill, P.A.3
Roeder, R.G.4
-
19
-
-
44649193565
-
The RNA polymerase II core promoter - the gateway to transcription
-
Juven-Gershon, T., Hsu, J.Y., Theisen, J.W. and Kadonaga, J.T. (2008) The RNA polymerase II core promoter - the gateway to transcription. Opin. Cell Biol., 20, 253-259.
-
(2008)
Opin. Cell Biol.
, vol.20
, pp. 253-259
-
-
Juven-Gershon, T.1
Hsu, J.Y.2
Theisen, J.W.3
Kadonaga, J.T.4
-
20
-
-
0036346546
-
Synergistic activation of the TATA-less mouse thymidylate synthase promoter by the Ets transcription factor GABP and Sp1
-
Rudge, T.L. and Johnson, L.F. (2002) Synergistic activation of the TATA-less mouse thymidylate synthase promoter by the Ets transcription factor GABP and Sp1. Exp. Cell Res., 274, 45-50.
-
(2002)
Exp. Cell Res.
, vol.274
, pp. 45-50
-
-
Rudge, T.L.1
Johnson, L.F.2
-
21
-
-
33744805985
-
Genome-wide analysis of mammalian promoter architecture and evolution
-
Carninci, P., Sandelin, A., Lenhard, B., Katayama, S., Shimokawa, K., Ponjavic, J., Semple, C.A., Taylor, M.S., Engström, P.G., Frith, M.C. et al. (2006) Genome-wide analysis of mammalian promoter architecture and evolution. Nat. Genet., 38, 626-635.
-
(2006)
Nat. Genet.
, vol.38
, pp. 626-635
-
-
Carninci, P.1
Sandelin, A.2
Lenhard, B.3
Katayama, S.4
Shimokawa, K.5
Ponjavic, J.6
Semple, C.A.7
Taylor, M.S.8
Engström, P.G.9
Frith, M.C.10
-
22
-
-
0001719758
-
Low-frequency Raman spectra of guanosine and nucleotides in ordered states: origin of the lowest-frequency mode
-
Urabe, H., Sugawara, Y., Tsukakoshi, M. and Kasuya, T. (1991) Low-frequency Raman spectra of guanosine and nucleotides in ordered states: origin of the lowest-frequency mode. J. Chem. Phys., 95, 5519.
-
(1991)
J. Chem. Phys.
, vol.95
, pp. 5519
-
-
Urabe, H.1
Sugawara, Y.2
Tsukakoshi, M.3
Kasuya, T.4
-
23
-
-
0037038534
-
Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy
-
Fischer, B.M., Walther, M. and Uhd Jepsen, P. (2002) Far-infrared vibrational modes of DNA components studied by terahertz time-domain spectroscopy. Phys. Med. Biol., 47, 3807-3814.
-
(2002)
Phys. Med. Biol.
, vol.47
, pp. 3807-3814
-
-
Fischer, B.M.1
Walther, M.2
Uhd Jepsen, P.3
-
24
-
-
0027988648
-
Local modes in a DNA polymer with hydrogen bond defect
-
Saxena, V.K. and Van Zandt, L.L. (1994) Local modes in a DNA polymer with hydrogen bond defect. Biophys. J., 67, 2448-2453
-
(1994)
Biophys. J.
, vol.67
, pp. 2448-2453
-
-
Saxena, V.K.1
Van Zandt, L.L.2
-
25
-
-
77749272463
-
-
LA-UR 09-03248, arXiv:0910.5294v1
-
Alexandrov, B.S., Gelev, V., Bishop, A.R., Usheva, A. and Rasmussen, K.Ø. DNA breathing dynamics in the presence of a terahertz field. LA-UR 09-03248, arXiv:0910.5294v1.
-
DNA breathing dynamics in the presence of a terahertz field
-
-
Alexandrov, B.S.1
Gelev, V.2
Bishop, A.R.3
Usheva, A.4
Rasmussen, K.O.5
-
26
-
-
0000104103
-
Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains
-
Campa, A. and Giansanti, A. (1998) Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains. Phys. Rev. E, 58, 3585.
-
(1998)
Phys. Rev. E
, vol.58
, pp. 3585
-
-
Campa, A.1
Giansanti, A.2
-
27
-
-
63649104268
-
Pre-melting dynamics of DNA and its relation to specific functions
-
Alexandrov, B.S., Voulgarakis, N., Rasmussen, K.Ø., Usheva, A. and Bishop, A.R. (2009) Pre-melting dynamics of DNA and its relation to specific functions. J. Phys. Condens. Matter, 21, 034107.
-
(2009)
J. Phys. Condens. Matter
, vol.21
, pp. 034107
-
-
Alexandrov, B.S.1
Voulgarakis, N.2
Rasmussen, K.O.3
Usheva, A.4
Bishop, A.R.5
-
28
-
-
33745337111
-
Probing the mechanical unzipping of DNA
-
Voulgarakis, N.K., Redondo, A., Bishop, A.R. and Rasmussen, K.Ø. (2006) Probing the mechanical unzipping of DNA. Phys. Rev. Lett., 96, 248101.
-
(2006)
Phys. Rev. Lett.
, vol.96
, pp. 248101
-
-
Voulgarakis, N.K.1
Redondo, A.2
Bishop, A.R.3
Rasmussen, K.O.4
-
29
-
-
18144371205
-
Bubble nucleation and cooperativity in DNA melting
-
Ares, S., Voulgarakis, N.K., Rasmussen, K.Ø. and Bishop, A.R. (2005) Bubble nucleation and cooperativity in DNA melting. Phys. Rev. Lett., 94, 035504.
-
(2005)
Phys. Rev. Lett.
, vol.94
, pp. 035504
-
-
Ares, S.1
Voulgarakis, N.K.2
Rasmussen, K.O.3
Bishop, A.R.4
|