-
1
-
-
0031779081
-
RNA polymerase-promoter interaction: The comings and goings of RNA polymerase
-
deHaseth,P.L., Zupancic,M. and Record,M.T.Jr. (1998) RNA polymerase-promoter interaction: The comings and goings of RNA polymerase. J. Bacteriol., 180, 3019-3025.
-
(1998)
J. Bacteriol
, vol.180
, pp. 3019-3025
-
-
deHaseth, P.L.1
Zupancic, M.2
Record Jr., M.T.3
-
2
-
-
0036304755
-
R promoter: Large scale conformational changes in forming the kinetically significant intermediates
-
R promoter: large scale conformational changes in forming the kinetically significant intermediates. J. Mol. Biol., 319, 649-671.
-
(2002)
J. Mol. Biol
, vol.319
, pp. 649-671
-
-
Saecker, R.M.1
Tsodikov, O.V.2
McQuade, K.L.3
Schlax, P.E.4
Capp, M.W.5
Record Jr., M.T.6
-
3
-
-
0032491380
-
-
Craig,M.L., Tsodikov,O.V., McQuade,K.L., Schlax,P.E.Jr., Capp.M.W., Saecker,R.M. and Record,M.T.Jr. (1998) DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: Evidence that interactions with the start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol., 283, 741-756.
-
Craig,M.L., Tsodikov,O.V., McQuade,K.L., Schlax,P.E.Jr., Capp.M.W., Saecker,R.M. and Record,M.T.Jr. (1998) DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: Evidence that interactions with the start site and downstream DNA induce sequential conformational changes in polymerase and DNA. J. Mol. Biol., 283, 741-756.
-
-
-
-
4
-
-
0346120324
-
Simple fluorescence assays probing conformational changes of Escherichia coli RNA polymerase during transcription initiation
-
Sen,R. and Dasgupta,D. (2003) Simple fluorescence assays probing conformational changes of Escherichia coli RNA polymerase during transcription initiation. Meth. Enzymol., 370, 598-605.
-
(2003)
Meth. Enzymol
, vol.370
, pp. 598-605
-
-
Sen, R.1
Dasgupta, D.2
-
5
-
-
0037123602
-
Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex
-
Murakami,K.S., Masuda,S., Campbell,E.A., Muzzin,O. and Darst,S.A. (2002) Structural basis of transcription initiation: An RNA polymerase holoenzyme-DNA complex. Science, 296, 1285-1290.
-
(2002)
Science
, vol.296
, pp. 1285-1290
-
-
Murakami, K.S.1
Masuda, S.2
Campbell, E.A.3
Muzzin, O.4
Darst, S.A.5
-
7
-
-
0037123659
-
Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution
-
Murakami,K.S., Masuda,S. and Darst,S.A. (2002) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science, 296, 1280-1284.
-
(2002)
Science
, vol.296
, pp. 1280-1284
-
-
Murakami, K.S.1
Masuda, S.2
Darst, S.A.3
-
8
-
-
0037071844
-
Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6Å resolution
-
Vassylyev,D.G., Sekine,S.-I., Laptenko,O., Lee,J., Vassylyeva,M.N., Borukhov,S. and Yokoyama,S. (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6Å resolution. Nature, 417, 712-719.
-
(2002)
Nature
, vol.417
, pp. 712-719
-
-
Vassylyev, D.G.1
Sekine, S.-I.2
Laptenko, O.3
Lee, J.4
Vassylyeva, M.N.5
Borukhov, S.6
Yokoyama, S.7
-
9
-
-
0036203066
-
-
Campbell,E.A., Muzzin,O., Chlenov,M., Sun,J.L., Olson,C.A., Weimnan.O., Trester-Zedlitz,M.L. and Darst,S.A. (2002) Structure of the bacterial RNA polymerase promoter specificity δ subunit. Mol. Cell, 9 527-539.
-
Campbell,E.A., Muzzin,O., Chlenov,M., Sun,J.L., Olson,C.A., Weimnan.O., Trester-Zedlitz,M.L. and Darst,S.A. (2002) Structure of the bacterial RNA polymerase promoter specificity δ subunit. Mol. Cell, 9 527-539.
-
-
-
-
10
-
-
0028333908
-
A promoter melting region in the primary sigma factor of Bacillus subtilis: Identification of functionally important aromatic amino acids
-
Juang,Y.-L. and Helmann,J.D. (1994) A promoter melting region in the primary sigma factor of Bacillus subtilis: Identification of functionally important aromatic amino acids. J. Mol. Biol., 235 1470-1488.
-
(1994)
J. Mol. Biol
, vol.235
, pp. 1470-1488
-
-
Juang, Y.-L.1
Helmann, J.D.2
-
11
-
-
0034705333
-
Aromatic amino acids in region 2.3 of Escherichia coli sigma 70 participate collectively in the formation of an RNA polymerase-promoter open complex
-
Panaghie,G., Aiyar,S.E., Bobb,K.L., Hayward,R.S. and deHaseth,P.L. (2000) Aromatic amino acids in region 2.3 of Escherichia coli sigma 70 participate collectively in the formation of an RNA polymerase-promoter open complex. J. Mol. Biol., 299, 1217-1230.
-
(2000)
J. Mol. Biol
, vol.299
, pp. 1217-1230
-
-
Panaghie, G.1
Aiyar, S.E.2
Bobb, K.L.3
Hayward, R.S.4
deHaseth, P.L.5
-
12
-
-
0035943648
-
70 in the nucleation and maintenance of the single-stranded DNA bubble in open RNA polymerase promoter complexes
-
70 in the nucleation and maintenance of the single-stranded DNA bubble in open RNA polymerase promoter complexes. J. Biol. Chem., 276, 31891-31896.
-
(2001)
J. Biol. Chem
, vol.276
, pp. 31891-31896
-
-
Tomsic, M.1
Tsujikawa, L.2
Panaghie, G.3
Wang, Y.4
Azok, J.5
deHaseth, P.L.6
-
14
-
-
0037133615
-
Interaction of RNA polymerase with forked DNA: Evidence for two kinetically significant intermediates on the pathway to the final complex
-
Tsujikawa,L., Tsodikov,O.V. and deHaseth,P.L. (2002) Interaction of RNA polymerase with forked DNA: Evidence for two kinetically significant intermediates on the pathway to the final complex. Proc. Natl Acad. Sci. USA, 99, 3493-3498.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 3493-3498
-
-
Tsujikawa, L.1
Tsodikov, O.V.2
deHaseth, P.L.3
-
16
-
-
20444491160
-
Mechanistic differences in promoter DNA melting by Thermus aquaticus and Escherichia coli RNA polymerases
-
Schroeder,L.A. and deHaseth,P.L. (2005) Mechanistic differences in promoter DNA melting by Thermus aquaticus and Escherichia coli RNA polymerases. J. Biol. Chem., 280, 17422-17429.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 17422-17429
-
-
Schroeder, L.A.1
deHaseth, P.L.2
-
17
-
-
0038606991
-
70 holoenzyme binding and isomerization using fork junction probes
-
70 holoenzyme binding and isomerization using fork junction probes. Nucleic Acids Res., 31, 2745-2750.
-
(2003)
Nucleic Acids Res
, vol.31
, pp. 2745-2750
-
-
Fenton, M.S.1
Gralla, J.D.2
-
18
-
-
18344418394
-
Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners
-
Helmann,J.D. and deHaseth,P.L. (1999) Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners. Biochemistry, 37, 5959-5967.
-
(1999)
Biochemistry
, vol.37
, pp. 5959-5967
-
-
Helmann, J.D.1
deHaseth, P.L.2
-
19
-
-
0035910043
-
A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding
-
Lim,H.M., Lee,H.J., Roy,S. and Adhya,S. (2001) A "master" in base unpairing during isomerization of a promoter upon RNA polymerase binding. Proc. Natl Acad. Sci. USA, 98, 14849-14852.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 14849-14852
-
-
Lim, H.M.1
Lee, H.J.2
Roy, S.3
Adhya, S.4
-
20
-
-
2342431849
-
An unsubstituted C2 hydrogen of Adenine is critical and sufficient at the -11 position of a promoter to signal base pair deformation
-
Lee,H.J., Lim,H.M. and Adhya,S. (2004) An unsubstituted C2 hydrogen of Adenine is critical and sufficient at the -11 position of a promoter to signal base pair deformation. J. Biol. Chem., 279, 16899-16902.
-
(2004)
J. Biol. Chem
, vol.279
, pp. 16899-16902
-
-
Lee, H.J.1
Lim, H.M.2
Adhya, S.3
-
21
-
-
0034633951
-
Sequence determinants for the recognition of the fork junction DNA containing the -10 region of promoter DNA by E. coli RNA polymerase
-
Matlock,D.L. and Heyduk,T. (2000) Sequence determinants for the recognition of the fork junction DNA containing the -10 region of promoter DNA by E. coli RNA polymerase. Biochemistry, 39, 12274-12283.
-
(2000)
Biochemistry
, vol.39
, pp. 12274-12283
-
-
Matlock, D.L.1
Heyduk, T.2
-
22
-
-
33744958373
-
A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting
-
Heyduk,E., Kuznedelov,K., Severinov,K. and Heyduk,T. (2006) A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting. J. Biol. Chem., 281, 12362-12369.
-
(2006)
J. Biol. Chem
, vol.281
, pp. 12362-12369
-
-
Heyduk, E.1
Kuznedelov, K.2
Severinov, K.3
Heyduk, T.4
-
23
-
-
0035979258
-
Function of the bacterial TATAAT -10 element as single-stranded DNA during RNA polymerase isomerization
-
Fenton,M.S. and Gralla,J.D. (2001) Function of the bacterial TATAAT -10 element as single-stranded DNA during RNA polymerase isomerization. Proc. Natl Acad. Sci. USA, 98, 9020-9025.
-
(2001)
Proc. Natl Acad. Sci. USA
, vol.98
, pp. 9020-9025
-
-
Fenton, M.S.1
Gralla, J.D.2
-
24
-
-
0023918675
-
Structure and function of bacterial sigma factors
-
Helmann,J.D. and Chamberlin,J. (1988) Structure and function of bacterial sigma factors. Annu. Rev. Biochem., 57, 839-872.
-
(1988)
Annu. Rev. Biochem
, vol.57
, pp. 839-872
-
-
Helmann, J.D.1
Chamberlin, J.2
-
25
-
-
1542741327
-
When a part is as good as the whole
-
deHaseth,P.L. and Nilsen,T.W. (2004) When a part is as good as the whole. Science, 303, 1307-1308.
-
(2004)
Science
, vol.303
, pp. 1307-1308
-
-
deHaseth, P.L.1
Nilsen, T.W.2
-
26
-
-
1442281182
-
Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting
-
Young,B.A., Gruber,T.M. and Gross,C.A. (2004) Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting. Science, 303, 1382-1384.
-
(2004)
Science
, vol.303
, pp. 1382-1384
-
-
Young, B.A.1
Gruber, T.M.2
Gross, C.A.3
-
27
-
-
0030576519
-
Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase
-
Roberts,J.W. and Roberts,C.W. (1996) Base-specific recognition of the nontemplate strand of promoter DNA by E. coli RNA polymerase. Cell, 86, 495-501.
-
(1996)
Cell
, vol.86
, pp. 495-501
-
-
Roberts, J.W.1
Roberts, C.W.2
-
28
-
-
0346120333
-
70 polypeptide overproduced at low temperature
-
70 polypeptide overproduced at low temperature. Methods in Enzymol., 370, 174-180.
-
(2003)
Methods in Enzymol
, vol.370
, pp. 174-180
-
-
Zhi, H.1
Jin, D.J.2
-
29
-
-
0346750969
-
70 in nucleation and maintenance of the single stranded bubble in RNA polymerase-promoter open complexes
-
70 in nucleation and maintenance of the single stranded bubble in RNA polymerase-promoter open complexes. Methods in Enzymol., 370, 553-567.
-
(2003)
Methods in Enzymol
, vol.370
, pp. 553-567
-
-
deHaseth, P.L.1
Tsujikawa, L.2
-
30
-
-
0043123261
-
Inactivation and destruction of Escherichia coli RNA polymerase open transcription complex: Recommendations for footprinting experiments
-
Lozinski,T. and Wierzchowski,K.L. (2003) Inactivation and destruction of Escherichia coli RNA polymerase open transcription complex: recommendations for footprinting experiments. Anal. Biochem., 320, 239-251.
-
(2003)
Anal. Biochem
, vol.320
, pp. 239-251
-
-
Lozinski, T.1
Wierzchowski, K.L.2
-
31
-
-
0034192263
-
DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: A systematic study
-
Burr,T., Mitchell,J., Kolb,A., Minchin,S. and Busby,S. (2000) DNA sequence elements located immediately upstream of the -10 hexamer in Escherichia coli promoters: A systematic study. Nucleic Acids Res. 28, 1864-1870.
-
(2000)
Nucleic Acids Res
, vol.28
, pp. 1864-1870
-
-
Burr, T.1
Mitchell, J.2
Kolb, A.3
Minchin, S.4
Busby, S.5
-
33
-
-
0023662558
-
Promoter recognition by Escherichia coli RNA polymerase: Effects of base substitution in the -10 and -35 regions
-
Szoke,P.A., Allen,T.A. and deHaseth,P.L. (1987) Promoter recognition by Escherichia coli RNA polymerase: Effects of base substitution in the -10 and -35 regions. Biochemistry, 26, 6188-6194.
-
(1987)
Biochemistry
, vol.26
, pp. 6188-6194
-
-
Szoke, P.A.1
Allen, T.A.2
deHaseth, P.L.3
-
34
-
-
0348011827
-
On the use of 2-aminopurine as a probe for base pair opening during transcription initiation
-
Roy,S. (2003) On the use of 2-aminopurine as a probe for base pair opening during transcription initiation. Methods in Enzymol., 370, 568-576.
-
(2003)
Methods in Enzymol
, vol.370
, pp. 568-576
-
-
Roy, S.1
-
35
-
-
0030446799
-
Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase
-
Ujvari,A. and Martin,C.T. (1996) Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase. Biochemistry, 35, 14574-14582.
-
(1996)
Biochemistry
, vol.35
, pp. 14574-14582
-
-
Ujvari, A.1
Martin, C.T.2
-
36
-
-
0037168467
-
RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNA
-
Tsujikawa,L., Strainic,M.G., Watrob,H., Barkley,M.D. and deHaseth,P.L. (2002) RNA polymerase alters the mobility of an A-residue crucial to polymerase-induced melting of promoter DNA. Biochemistry, 41 15334-15341.
-
(2002)
Biochemistry
, vol.41
, pp. 15334-15341
-
-
Tsujikawa, L.1
Strainic, M.G.2
Watrob, H.3
Barkley, M.D.4
deHaseth, P.L.5
-
37
-
-
33645896417
-
Rapid binding of T7 RNA polymerase is followed by simultaneous bending and opening of the promoter DNA
-
Tang,G.-Q. and Patel,S.S. (2006) Rapid binding of T7 RNA polymerase is followed by simultaneous bending and opening of the promoter DNA. Biochemistry, 45, 4947-4956.
-
(2006)
Biochemistry
, vol.45
, pp. 4947-4956
-
-
Tang, G.-Q.1
Patel, S.S.2
-
38
-
-
0032483348
-
Stimulation of open complex formation by nicks and apurinic sites suggests a role for nucleation of DNA melting in Escherichia coli promoter function
-
Li,X.-Y. and McClure,W.R. (1998) Stimulation of open complex formation by nicks and apurinic sites suggests a role for nucleation of DNA melting in Escherichia coli promoter function. J. Biol. Chem. 273, 23558-23566.
-
(1998)
J. Biol. Chem
, vol.273
, pp. 23558-23566
-
-
Li, X.-Y.1
McClure, W.R.2
-
39
-
-
0032546530
-
Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence
-
Gelfand,C.G., Plum,G.E., Grollman,A.P., Johnson,F. and Breslauer,K.J. (1998) Thermodynamic consequences of an abasic lesion in duplex DNA are strongly dependent on base sequence. Biochemistry, 37, 7321-7327.
-
(1998)
Biochemistry
, vol.37
, pp. 7321-7327
-
-
Gelfand, C.G.1
Plum, G.E.2
Grollman, A.P.3
Johnson, F.4
Breslauer, K.J.5
-
40
-
-
0027230594
-
Compilation of E.coli mRNA promoter sequences
-
Lisser,S. and Margalit,H. (1993) Compilation of E.coli mRNA promoter sequences. Nucleic Acids Res., 21, 1507-1516.
-
(1993)
Nucleic Acids Res
, vol.21
, pp. 1507-1516
-
-
Lisser, S.1
Margalit, H.2
-
41
-
-
33644670811
-
Escherichia coli RNA polymerase contacts outside the -10 promoter element are not essential for promoter melting
-
Niedziela-Majka,A. and Heyduk,T. (2005) Escherichia coli RNA polymerase contacts outside the -10 promoter element are not essential for promoter melting. J. Biol. Chem., 280, 38219-38227.
-
(2005)
J. Biol. Chem
, vol.280
, pp. 38219-38227
-
-
Niedziela-Majka, A.1
Heyduk, T.2
-
42
-
-
0024474697
-
4 as a probe for lac promoter DNA melting and mechanism in vivo
-
4 as a probe for lac promoter DNA melting and mechanism in vivo. J. Biol. Chem., 264 8074-8081.
-
(1989)
J. Biol. Chem
, vol.264
, pp. 8074-8081
-
-
Sasse-Dwight, S.1
Gralla, J.D.2
-
43
-
-
0030736323
-
Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state
-
Jen-Jacobson,J.J. (1997) Protein-DNA recognition complexes: Conservation of structure and binding energy in the transition state. Biopolymers 44, 153-180.
-
(1997)
Biopolymers
, vol.44
, pp. 153-180
-
-
Jen-Jacobson, J.J.1
-
44
-
-
0022409539
-
Thermodynamic origins of specificity in the lac Repressor-Operator interaction
-
Mossing,M.M. and Record,M.T.Jr. (1985) Thermodynamic origins of specificity in the lac Repressor-Operator interaction. J. Mol. Biol. 186, 295-305.
-
(1985)
J. Mol. Biol
, vol.186
, pp. 295-305
-
-
Mossing, M.M.1
Record Jr., M.T.2
-
45
-
-
0024355282
-
70 subunit of RNA polymerase with altered promoter specificity
-
70 subunit of RNA polymerase with altered promoter specificity. J. Mol. Biol., 206, 579-590.
-
(1989)
J. Mol. Biol
, vol.206
, pp. 579-590
-
-
Gardella, T.1
Moyle, H.2
Susskind, M.M.3
-
46
-
-
0021891874
-
Mechanism and control of transcription initiation in prokaryotes
-
McClure,W.R. (1985) Mechanism and control of transcription initiation in prokaryotes. Annu. Rev. Biochem., 54, 171-204.
-
(1985)
Annu. Rev. Biochem
, vol.54
, pp. 171-204
-
-
McClure, W.R.1
|