-
1
-
-
48249113056
-
Translocation and unwinding mechanisms of RNA and DNA helicases
-
Pyle, A.M. Translocation and unwinding mechanisms of RNA and DNA helicases. Annu. Rev. Biophys. 37, 317-336 (2008).
-
(2008)
Annu. Rev. Biophys
, vol.37
, pp. 317-336
-
-
Pyle, A.M.1
-
2
-
-
0033786801
-
Structure and function of hexameric helicase
-
Patel, S.S. & Picha, K.M. Structure and function of hexameric helicases. Annu. Rev. Biochem. 69, 651-697 (2000).
-
(2000)
Annu. Rev. Biochem
, vol.69
, pp. 651-697
-
-
Patel, S.S.1
Picha, K.M.2
-
3
-
-
0037294467
-
Helicase mechanisms and the coupling of helicases within macromolecular machines Part II: Integration of helicases into cellular processes
-
Delagoutte, E. & von Hippel, P.H. Helicase mechanisms and the coupling of helicases within macromolecular machines. Part II: integration of helicases into cellular processes. Q. Rev. Biophys. 36, 1-69 (2003).
-
(2003)
Q. Rev. Biophys
, vol.36
, pp. 1-69
-
-
Delagoutte, E.1
Von Hippel, P.H.2
-
4
-
-
34548638261
-
Structure and mechanism of helicases and nucleic acid translocases
-
Singleton, M.R., Dillingham, M.S. & Wigley, D.B. Structure and mechanism of helicases and nucleic acid translocases. Annu. Rev. Biochem. 76, 23-50 (2007).
-
(2007)
Annu. Rev. Biochem
, vol.76
, pp. 23-50
-
-
Singleton, M.R.1
Dillingham, M.S.2
Wigley, D.B.3
-
5
-
-
33746375404
-
Mechanism of DNA translocation in a replicative hexameric helicase
-
Enemark, E.J. & Joshua-Tor, L. Mechanism of DNA translocation in a replicative hexameric helicase. Nature 442, 270-275 (2006).
-
(2006)
Nature
, vol.442
, pp. 270-275
-
-
Enemark, E.J.1
Joshua-Tor, L.2
-
6
-
-
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. Single-molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase. Cell 129, 1299-1309 (2007).
-
(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
-
7
-
-
4644261530
-
Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: Quantitative analysis of the rate of the dsDNA unwinding, processivity and kinetic step-size of the Escherichia coli DnaB helicase using rapid quench-fow method
-
Galletto, R., Jezewska, M.J. & Bujalowski, W. Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: quantitative analysis of the rate of the dsDNA unwinding, processivity and kinetic step-size of the Escherichia coli DnaB helicase using rapid quench-fow method. J. Mol. Biol. 343, 83-99 (2004).
-
(2004)
J. Mol. Biol
, vol.343
, pp. 83-99
-
-
Galletto, R.1
Jezewska, M.J.2
Bujalowski, W.3
-
8
-
-
38049186506
-
Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism
-
Lionnet, T., Spiering, M.M., Benkovic, S.J., Bensimon, D. & Croquette, V. Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism. Proc. Natl. Acad. Sci. USA 104, 19790-19795 (2007).
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 19790-19795
-
-
Lionnet, T.1
Spiering, M.M.2
Benkovic, S.J.3
Bensimon, D.4
Croquette, V.5
-
9
-
-
47049093279
-
Coupling of DNA unwinding to nucleotide hydrolysis in a ring-shaped helicase
-
Donmez, I. & Patel, S.S. Coupling of DNA unwinding to nucleotide hydrolysis in a ring-shaped helicase. EMBO J. 27, 1718-1726 (2008).
-
(2008)
EMBO J
, vol.27
, pp. 1718-1726
-
-
Donmez, I.1
Patel, S.S.2
-
10
-
-
0037073063
-
Rho-dependent termination and ATPases in transcript termination
-
Richardson, J.P. Rho-dependent termination and ATPases in transcript termination. Biochim. Biophys. Acta 1577, 251-260 (2002).
-
(2002)
Biochim. Biophys. Acta
, vol.1577
, pp. 251-260
-
-
Richardson, J.P.1
-
11
-
-
44249091644
-
Termination factor rho and its cofactors NusA and NusG silence foreign DNA in E. coli
-
Cardinale, C.J. et al. Termination factor rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science 320, 935-938 (2008).
-
(2008)
Science
, vol.320
, pp. 935-938
-
-
Cardinale, C.J.1
-
12
-
-
7644223774
-
Why is transcription coupled to translation in bacteria?
-
Gowrishankar, J. & Harinarayanan, R. Why is transcription coupled to translation in bacteria? Mol. Microbiol. 54, 598-603 (2004).
-
(2004)
Mol Microbiol
, vol.54
, pp. 598-603
-
-
Gowrishankar, J.1
Harinarayanan, R.2
-
13
-
-
0033120903
-
The structural basis for terminator recognition by the rho transcription termination factor
-
Bogden, C.E., Fass, D., Bergman, N., Nichols, M.D. & Berger, J.M. The structural basis for terminator recognition by the rho transcription termination factor. Mol. Cell 3, 487-493 (1999).
-
(1999)
Mol. Cell
, vol.3
, pp. 487-493
-
-
Bogden, C.E.1
Fass, D.2
Bergman, N.3
Nichols, M.D.4
Berger, J.M.5
-
14
-
-
33845940368
-
Sequence-specifc interactions in the RNA-binding domain of Escherichia coli transcription termination factor Rho
-
Hitchens, T.K., Zhan, Y., Richardson, L.V., Richardson, J.P. & Rule, G.S. Sequence-specifc interactions in the RNA-binding domain of Escherichia coli transcription termination factor Rho. J. Biol. Chem. 281, 33697-33703 (2006).
-
(2006)
J. Biol. Chem
, vol.281
, pp. 33697-33703
-
-
Hitchens, T.K.1
Zhan, Y.2
Richardson, L.V.3
Richardson, J.P.4
Rule, G.S.5
-
15
-
-
34548104113
-
Noncanonical interactions in the management of RNA structural blocks by the transcription termination rho helicase
-
Schwartz, A., Walmacq, C., Rahmouni, A.R. & Boudvillain, M. Noncanonical interactions in the management of RNA structural blocks by the transcription termination rho helicase. Biochemistry 46, 9366-9379 (2007).
-
(2007)
Biochemistry
, vol.46
, pp. 9366-9379
-
-
Schwartz, A.1
Walmacq, C.2
Rahmouni, A.R.3
Boudvillain, M.4
-
16
-
-
0030347278
-
13C resonance assignments and secondary structure determination of the RNA-binding domain of E. coli rho protein
-
Briercheck, D.M. et al. 1H, 15N and 13C resonance assignments and secondary structure determination of the RNA-binding domain of E. coli rho protein. J. Biomol. NMR 8, 429-444 (1996).
-
(1996)
J. Biomol. NMR
, vol.8
, pp. 429-444
-
-
Briercheck, D.M.1
-
17
-
-
0037119488
-
Mutations in the rho transcription termination factor that affect RNA tracking
-
Xu, Y., Kohn, H. & Widger, W.R. Mutations in the rho transcription termination factor that affect RNA tracking. J. Biol. Chem. 277, 30023-30030 (2002).
-
(2002)
J. Biol. Chem
, vol.277
, pp. 30023-30030
-
-
Xu, Y.1
Kohn, H.2
Widger, W.R.3
-
18
-
-
0035861978
-
Mutational changes of conserved residues in the Q-loop region of transcription factor rho greatly reduce secondary site RNA-binding
-
Wei, R.R. & Richardson, J.P. Mutational changes of conserved residues in the Q-loop region of transcription factor rho greatly reduce secondary site RNA-binding. J. Mol. Biol. 314, 1007-1015 (2001).
-
(2001)
J. Mol. Biol
, vol.314
, pp. 1007-1015
-
-
Wei, R.R.1
Richardson, J.P.2
-
19
-
-
0020490675
-
Activation of rho protein ATPase requires simultaneous interaction at two kinds of nucleic acid-binding sites
-
Richardson, J.P. Activation of rho protein ATPase requires simultaneous interaction at two kinds of nucleic acid-binding sites. J. Biol. Chem. 257, 5760-5766 (1982).
-
(1982)
J. Biol. Chem
, vol.257
, pp. 5760-5766
-
-
Richardson, J.P.1
-
20
-
-
0035958964
-
Identifcation of an RNA-binding Site in the ATP binding domain of Escherichia coli Rho by H2O2/Fe-EDTA cleavage protection studies
-
Wei, R.R. & Richardson, J.P. Identifcation of an RNA-binding Site in the ATP binding domain of Escherichia coli Rho by H2O2/Fe-EDTA cleavage protection studies. J. Biol. Chem. 276, 28380-28387 (2001).
-
(2001)
J. Biol. Chem
, vol.276
, pp. 28380-28387
-
-
Wei, R.R.1
Richardson, J.P.2
-
21
-
-
0037559627
-
Structure of the rho transcription terminator. Mechanism of mRNA recognition and helicase loading
-
Skordalakes, E. & Berger, J.M. Structure of the rho transcription terminator. Mechanism of mRNA recognition and helicase loading. Cell 114, 135-146 (2003).
-
(2003)
Cell
, vol.114
, pp. 135-146
-
-
Skordalakes, E.1
Berger, J.M.2
-
22
-
-
33750477997
-
Structural insights into RNA-dependent ring closure and ATPase activation by the rho termination factor
-
Skordalakes, E. & Berger, J.M. Structural insights into RNA-dependent ring closure and ATPase activation by the rho termination factor. Cell 127, 553-564 (2006).
-
(2006)
Cell
, vol.127
, pp. 553-564
-
-
Skordalakes, E.1
Berger, J.M.2
-
23
-
-
0027156376
-
Escherichia coli transcription termination factor rho. I. ATPase activation by oligonucleotide cofactors
-
Wang, Y. & von Hippel, P.H. Escherichia coli transcription termination factor rho. I. ATPase activation by oligonucleotide cofactors. J. Biol. Chem. 268, 13940-13946 (1993).
-
(1993)
J. Biol. Chem.
, Issue.268
, pp. 13940-13946
-
-
Wang, Y.1
Von Hippel, P.H.2
-
24
-
-
33646489157
-
Testing the steric exclusion model for hexameric helicases: Substrate features that alter RNA-DNA unwinding by the transcription termination factor rho
-
Walmacq, C., Rahmouni, A.R. & Boudvillain, M. Testing the steric exclusion model for hexameric helicases: substrate features that alter RNA-DNA unwinding by the transcription termination factor rho. Biochemistry 45, 5885-5895 (2006).
-
(2006)
Biochemistry
, vol.45
, pp. 5885-5895
-
-
Walmacq, C.1
Rahmouni, A.R.2
Boudvillain, M.3
-
25
-
-
0029831394
-
Rho-dependent termination of transcription is governed primarily by the upstream rho utilization (rut) sequences of a terminator
-
Richardson, L.V. & Richardson, J.P. Rho-dependent termination of transcription is governed primarily by the upstream rho utilization (rut) sequences of a terminator. J. Biol. Chem. 271, 21597-21603 (1996).
-
(1996)
J. Biol. Chem
, vol.271
, pp. 21597-21603
-
-
Richardson, L.V.1
Richardson, J.P.2
-
26
-
-
84889266520
-
Nucleotide analog interference mapping and suppression: Specifc applications in studies of RNA tertiary structure, dynamic helicase mechanism and RNA-protein interactions
-
(eds. Hartmann, R.K., Bindereif, A., Schön, A. & Westhof, E.) Wiley-VCH, Weinheim
-
Fedorova, O., Boudvillain, M., Kawaoka, J. & Pyle, A.M. Nucleotide analog interference mapping and suppression: specifc applications in studies of RNA tertiary structure, dynamic helicase mechanism and RNA-protein interactions. in Handbook of RNA Biochemistry Vol. 1 (eds. Hartmann, R.K., Bindereif, A., Schön, A. & Westhof, E.) 259-293 (Wiley-VCH, Weinheim, 2005).
-
(2005)
Handbook of RNA Biochemistry
, vol.1
, pp. 259-293
-
-
Fedorova, O.1
Boudvillain, M.2
Kawaoka, J.3
Pyle, A.M.4
-
27
-
-
4344661527
-
Infuence of substrate composition on the helicase activity of transcription termination factor rho: Reduced processivity of rho hexamers during unwinding of RNA-DNA hybrid regions
-
Walmacq, C., Rahmouni, A.R. & Boudvillain, M. Infuence of substrate composition on the helicase activity of transcription termination factor rho: reduced processivity of rho hexamers during unwinding of RNA-DNA hybrid regions. J. Mol. Biol. 342, 403-420 (2004).
-
(2004)
J. Mol. Biol
, vol.342
, pp. 403-420
-
-
Walmacq, C.1
Rahmouni, A.R.2
Boudvillain, M.3
-
28
-
-
0141865611
-
General methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding
-
Lucius, A.L., Maluf, N.K., Fischer, C.J. & Lohman, T.M. General methods for analysis of sequential "n-step" kinetic mechanisms: application to single turnover kinetics of helicase-catalyzed DNA unwinding. Biophys. J. 85, 2224-2239 (2003).
-
(2003)
Biophys. J
, vol.85
, pp. 2224-2239
-
-
Lucius, A.L.1
Maluf, N.K.2
Fischer, C.J.3
Lohman, T.M.4
-
29
-
-
0033150681
-
A chemogenetic approach to RNA function/structure analysis
-
Strobel, S.A. A chemogenetic approach to RNA function/structure analysis. Curr. Opin. Struct. Biol. 9, 346-352 (1999).
-
(1999)
Curr. Opin. Struct. Biol
, vol.9
, pp. 346-352
-
-
Strobel, S.A.1
-
30
-
-
0038601943
-
The functional anatomy of an intrinsic transcription terminator
-
Schwartz, A., Rahmouni, A.R. & Boudvillain, M. The functional anatomy of an intrinsic transcription terminator. EMBO J. 22, 3385-3394 (2003).
-
(2003)
EMBO J
, vol.22
, pp. 3385-3394
-
-
Schwartz, A.1
Rahmouni, A.R.2
Boudvillain, M.3
-
31
-
-
0030727765
-
The ups and downs of nucleic acid duplex stability: Structure-stability studies on chemically-modifed DNA:RNA duplexes
-
Freier, S.M. & Altmann, K.H. The ups and downs of nucleic acid duplex stability: structure-stability studies on chemically-modifed DNA:RNA duplexes. Nucleic Acids Res. 25, 4429-4443 (1997).
-
(1997)
Nucleic Acids Res
, vol.25
, pp. 4429-4443
-
-
Freier, S.M.1
Altmann, K.H.2
-
32
-
-
0028904989
-
Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2'-hydroxyl effects
-
Wang, S. & Kool, E.T. Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2'-hydroxyl effects. Biochemistry 34, 4125-4132 (1995).
-
(1995)
Biochemistry
, vol.34
, pp. 4125-4132
-
-
Wang, S.1
Kool, E.T.2
-
33
-
-
0024425738
-
Deoxynucleotide-containing oligoribonucleotide duplexes: Stability and susceptibility to RNase V1 and RNase H
-
Wyatt, J.R. & Walker, G.T. Deoxynucleotide-containing oligoribonucleotide duplexes: stability and susceptibility to RNase V1 and RNase H. Nucleic Acids Res. 17, 7833-7842 (1989).
-
(1989)
Nucleic Acids Res
, vol.17
, pp. 7833-7842
-
-
Wyatt, J.R.1
Walker, G.T.2
-
34
-
-
0030454007
-
Mutagenesis of a stacking contact in the MS2 coat protein-RNA complex
-
LeCuyer, K.A., Behlen, L.S. & Uhlenbeck, O.C. Mutagenesis of a stacking contact in the MS2 coat protein-RNA complex. EMBO J. 15, 6847-6853 (1996).
-
(1996)
EMBO J
, vol.15
, pp. 6847-6853
-
-
Lecuyer, K.A.1
Behlen, L.S.2
Uhlenbeck, O.C.3
-
35
-
-
0032066341
-
An engineered ribonuclease preferring phosphorothioate RNA
-
Loverix, S., Winquist, A., Stromberg, R. & Steyaert, J. An engineered ribonuclease preferring phosphorothioate RNA. Nat. Struct. Biol. 5, 365-368 (1998).
-
(1998)
Nat. Struct. Biol
, vol.5
, pp. 365-368
-
-
Loverix, S.1
Winquist, A.2
Stromberg, R.3
Steyaert, J.4
-
36
-
-
0032571245
-
Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase i by phosphorothioates
-
Brautigam, C.A. & Steitz, T.A. Structural principles for the inhibition of the 3′-5′ exonuclease activity of Escherichia coli DNA polymerase I by phosphorothioates. J. Mol. Biol. 277, 363-377 (1998).
-
(1998)
J. Mol. Biol
, vol.277
, pp. 363-377
-
-
Brautigam, C.A.1
Steitz, T.A.2
-
37
-
-
0034674037
-
Phosphorothioate substitution can substantially alter RNA conformation
-
Smith, J.S. & Nikonowicz, E.P. Phosphorothioate substitution can substantially alter RNA conformation. Biochemistry 39, 5642-5652 (2000).
-
(2000)
Biochemistry
, vol.39
, pp. 5642-5652
-
-
Smith, J.S.1
Nikonowicz, E.P.2
-
38
-
-
35748950148
-
Transcription termination factor rho can displace streptavidin from biotinylated RNA
-
Schwartz, A., Margeat, E., Rahmouni, A.R. & Boudvillain, M. Transcription termination factor rho can displace streptavidin from biotinylated RNA. J. Biol. Chem. 282, 31469-31476 (2007).
-
(2007)
J. Biol. Chem
, vol.282
, pp. 31469-31476
-
-
Schwartz, A.1
Margeat, E.2
Rahmouni, A.R.3
Boudvillain, M.4
-
39
-
-
58749087869
-
Intersubunit coordination in a homomeric ring ATPase
-
Mofftt, J.R. et al. Intersubunit coordination in a homomeric ring ATPase. Nature (2009).
-
(2009)
Nature
-
-
Mofftt, J.R.1
-
40
-
-
34547595373
-
Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase
-
Myong, S., Bruno, M.M., Pyle, A.M. & Ha, T. Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase. Science 317, 513-516 (2007).
-
(2007)
Science
, vol.317
, pp. 513-516
-
-
Myong, S.1
Bruno, M.M.2
Pyle, A.M.3
Ha, T.4
-
41
-
-
33751212468
-
Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
-
Kapanidis, A.N. et al. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314, 1144-1147 (2006).
-
(2006)
Science
, vol.314
, pp. 1144-1147
-
-
Kapanidis, A.N.1
-
42
-
-
0035803474
-
T7 promoter release mediated by DNA scrunching
-
Brieba, L.G. & Sousa, R. T7 promoter release mediated by DNA scrunching. EMBO J. 20, 6826-6835 (2001).
-
(2001)
EMBO J
, vol.20
, pp. 6826-6835
-
-
Brieba, L.G.1
Sousa, R.2
-
43
-
-
4644358568
-
Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: The effect of the 3′ arm and the stability of the dsDNA on the unwinding activity of the Escherichia coli DnaB helicase
-
DOI 10.1016/j.jmb.2004.07.056, PII S0022283604008848
-
Galletto, R., Jezewska, M.J. & Bujalowski, W. Unzipping mechanism of the double-stranded DNA unwinding by a hexameric helicase: the effect of the 3′ arm and the stability of the dsDNA on the unwinding activity of the Escherichia coli DnaB helicase. J. Mol. Biol. 343, 101-114 (2004). (Pubitemid 39277451)
-
(2004)
Journal of Molecular Biology
, vol.343
, Issue.1
, pp. 101-114
-
-
Galletto, R.1
Jezewska, M.J.2
Bujalowski, W.3
-
44
-
-
34547118809
-
Nucleic acid unwinding by hepatitis C virus and bacteriophage t7 helicases is sensitive to base pair stability
-
Donmez, I., Rajagopal, V., Jeong, Y.J. & Patel, S.S. Nucleic acid unwinding by hepatitis C virus and bacteriophage t7 helicases is sensitive to base pair stability. J. Biol. Chem. 282, 21116-21123 (2007).
-
(2007)
J. Biol. Chem
, vol.282
, pp. 21116-21123
-
-
Donmez, I.1
Rajagopal, V.2
Jeong, Y.J.3
Patel, S.S.4
-
45
-
-
50649101517
-
Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA
-
Dutta, D., Chalissery, J. & Sen, R. Transcription termination factor rho prefers catalytically active elongation complexes for releasing RNA. J. Biol. Chem. 283, 20243-20251 (2008).
-
(2008)
J. Biol. Chem
, vol.283
, pp. 20243-20251
-
-
Dutta, D.1
Chalissery, J.2
Sen, R.3
-
46
-
-
33645514260
-
Role of DNA bubble rewinding in enzymatic transcription termination
-
Park, J.S. & Roberts, J.W. Role of DNA bubble rewinding in enzymatic transcription termination. Proc. Natl. Acad. Sci. USA 103, 4870-4875 (2006).
-
(2006)
Proc. Natl. Acad. Sci. USA
, vol.103
, pp. 4870-4875
-
-
Park, J.S.1
Roberts, J.W.2
|