-
1
-
-
28544432440
-
Direct observation of base-pair stepping by RNA polymerase
-
E.A. Abbondanzieri, W.J. Greenleaf, J.W. Shaevitz, R. Landick, and S.M. Block Direct observation of base-pair stepping by RNA polymerase Nature 438 2005 460 465
-
(2005)
Nature
, vol.438
, pp. 460-465
-
-
Abbondanzieri, E.A.1
Greenleaf, W.J.2
Shaevitz, J.W.3
Landick, R.4
Block, S.M.5
-
3
-
-
0023654911
-
Helicase action of dnaB protein during replication from the Escherichia coli chromosomal origin in vitro
-
T.A. Baker, B.E. Funnell, and A. Kornberg Helicase action of dnaB protein during replication from the Escherichia coli chromosomal origin in vitro J. Biol. Chem. 262 1987 6877 6885
-
(1987)
J. Biol. Chem.
, vol.262
, pp. 6877-6885
-
-
Baker, T.A.1
Funnell, B.E.2
Kornberg, A.3
-
4
-
-
84859615818
-
Single-molecule studies of DNA transcription using atomic force microscopy
-
D.J. Billingsley, W.A. Bonass, N. Crampton, J. Kirkham, and N.H. Thomson Single-molecule studies of DNA transcription using atomic force microscopy Phys. Biol. 9 2012 021001
-
(2012)
Phys. Biol.
, vol.9
, pp. 021001
-
-
Billingsley, D.J.1
Bonass, W.A.2
Crampton, N.3
Kirkham, J.4
Thomson, N.H.5
-
7
-
-
79951703348
-
Revisiting the central dogma one molecule at a time
-
C. Bustamante, W. Cheng, and Y.X. Mejia Revisiting the central dogma one molecule at a time Cell 144 2011 480 497
-
(2011)
Cell
, vol.144
, pp. 480-497
-
-
Bustamante, C.1
Cheng, W.2
Mejia, Y.X.3
-
8
-
-
84864770299
-
Opening and closing of the bacterial RNA polymerase clamp
-
A. Chakraborty, D. Wang, Y.W. Ebright, Y. Korlann, E. Kortkhonjia, T. Kim, S. Chowdhury, S. Wigneshweraraj, H. Irschik, and R. Jansen et al. Opening and closing of the bacterial RNA polymerase clamp Science 337 2012 591 595
-
(2012)
Science
, vol.337
, pp. 591-595
-
-
Chakraborty, A.1
Wang, D.2
Ebright, Y.W.3
Korlann, Y.4
Kortkhonjia, E.5
Kim, T.6
Chowdhury, S.7
Wigneshweraraj, S.8
Irschik, H.9
Jansen, R.10
-
9
-
-
0042733395
-
Direct interaction between Escherichia coli RNA polymerase and the zinc ribbon domains of DNA topoisomerase i
-
B. Cheng, C.X. Zhu, C. Ji, A. Ahumada, and Y.C. Tse-Dinh Direct interaction between Escherichia coli RNA polymerase and the zinc ribbon domains of DNA topoisomerase I J. Biol. Chem. 278 2003 30705 30710
-
(2003)
J. Biol. Chem.
, vol.278
, pp. 30705-30710
-
-
Cheng, B.1
Zhu, C.X.2
Ji, C.3
Ahumada, A.4
Tse-Dinh, Y.C.5
-
10
-
-
54249083606
-
A stochastic single-molecule event triggers phenotype switching of a bacterial cell
-
P.J. Choi, L. Cai, K. Frieda, and X.S. Xie A stochastic single-molecule event triggers phenotype switching of a bacterial cell Science 322 2008 442 446
-
(2008)
Science
, vol.322
, pp. 442-446
-
-
Choi, P.J.1
Cai, L.2
Frieda, K.3
Xie, X.S.4
-
12
-
-
78751659330
-
Nascent transcript sequencing visualizes transcription at nucleotide resolution
-
L.S. Churchman, and J.S. Weissman Nascent transcript sequencing visualizes transcription at nucleotide resolution Nature 469 2011 368 373
-
(2011)
Nature
, vol.469
, pp. 368-373
-
-
Churchman, L.S.1
Weissman, J.S.2
-
13
-
-
57849109058
-
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters
-
L.J. Core, J.J. Waterfall, and J.T. Lis Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters Science 322 2008 1845 1848
-
(2008)
Science
, vol.322
, pp. 1845-1848
-
-
Core, L.J.1
Waterfall, J.J.2
Lis, J.T.3
-
14
-
-
0034737593
-
Single-molecule study of transcriptional pausing and arrest by E. Coli RNA polymerase
-
R.J. Davenport, G.J. Wuite, R. Landick, and C. Bustamante Single-molecule study of transcriptional pausing and arrest by E. coli RNA polymerase Science 287 2000 2497 2500
-
(2000)
Science
, vol.287
, pp. 2497-2500
-
-
Davenport, R.J.1
Wuite, G.J.2
Landick, R.3
Bustamante, C.4
-
15
-
-
1542618333
-
Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium chromosome
-
S. Deng, R.A. Stein, and N.P. Higgins Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium chromosome Proc. Natl. Acad. Sci. USA 101 2004 3398 3403
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 3398-3403
-
-
Deng, S.1
Stein, R.A.2
Higgins, N.P.3
-
16
-
-
25144495578
-
Organization of supercoil domains and their reorganization by transcription
-
S. Deng, R.A. Stein, and N.P. Higgins Organization of supercoil domains and their reorganization by transcription Mol. Microbiol. 57 2005 1511 1521
-
(2005)
Mol. Microbiol.
, vol.57
, pp. 1511-1521
-
-
Deng, S.1
Stein, R.A.2
Higgins, N.P.3
-
17
-
-
0026555506
-
Control of bacterial DNA supercoiling
-
K. Drlica Control of bacterial DNA supercoiling Mol. Microbiol. 6 1992 425 433
-
(1992)
Mol. Microbiol.
, vol.6
, pp. 425-433
-
-
Drlica, K.1
-
18
-
-
33645052194
-
Growth inhibition mediated by excess negative supercoiling: The interplay between transcription elongation, R-loop formation and DNA topology
-
M. Drolet Growth inhibition mediated by excess negative supercoiling: the interplay between transcription elongation, R-loop formation and DNA topology Mol. Microbiol. 59 2006 723 730
-
(2006)
Mol. Microbiol.
, vol.59
, pp. 723-730
-
-
Drolet, M.1
-
19
-
-
0033852525
-
Activation and silencing of leu-500 promoter by transcription-induced DNA supercoiling in the Salmonella chromosome
-
D. El Hanafi, and L. Bossi Activation and silencing of leu-500 promoter by transcription-induced DNA supercoiling in the Salmonella chromosome Mol. Microbiol. 37 2000 583 594
-
(2000)
Mol. Microbiol.
, vol.37
, pp. 583-594
-
-
El Hanafi, D.1
Bossi, L.2
-
20
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
M.B. Elowitz, and S. Leibler A synthetic oscillatory network of transcriptional regulators Nature 403 2000 335 338
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
22
-
-
0038756088
-
Cooperation between RNA polymerase molecules in transcription elongation
-
V. Epshtein, and E. Nudler Cooperation between RNA polymerase molecules in transcription elongation Science 300 2003 801 805
-
(2003)
Science
, vol.300
, pp. 801-805
-
-
Epshtein, V.1
Nudler, E.2
-
23
-
-
0024278509
-
DNA gyrase on the bacterial chromosome. Oxolinic acid-induced DNA cleavage in the dnaA-gyrB region
-
R.J. Franco, and K. Drlica DNA gyrase on the bacterial chromosome. Oxolinic acid-induced DNA cleavage in the dnaA-gyrB region J. Mol. Biol. 201 1988 229 233
-
(1988)
J. Mol. Biol.
, vol.201
, pp. 229-233
-
-
Franco, R.J.1
Drlica, K.2
-
24
-
-
84857311371
-
Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation
-
L.J. Friedman, and J. Gelles Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation Cell 148 2012 679 689
-
(2012)
Cell
, vol.148
, pp. 679-689
-
-
Friedman, L.J.1
Gelles, J.2
-
25
-
-
28944434119
-
Real-time kinetics of gene activity in individual bacteria
-
I. Golding, J. Paulsson, S.M. Zawilski, and E.C. Cox Real-time kinetics of gene activity in individual bacteria Cell 123 2005 1025 1036
-
(2005)
Cell
, vol.123
, pp. 1025-1036
-
-
Golding, I.1
Paulsson, J.2
Zawilski, S.M.3
Cox, E.C.4
-
26
-
-
30144434477
-
Mechanochemical analysis of DNA gyrase using rotor bead tracking
-
J. Gore, Z. Bryant, M.D. Stone, M. Nöllmann, N.R. Cozzarelli, and C. Bustamante Mechanochemical analysis of DNA gyrase using rotor bead tracking Nature 439 2006 100 104
-
(2006)
Nature
, vol.439
, pp. 100-104
-
-
Gore, J.1
Bryant, Z.2
Stone, M.D.3
Nöllmann, M.4
Cozzarelli, N.R.5
Bustamante, C.6
-
27
-
-
0030131125
-
Cooperative relaxation of supercoils and periodic transcriptional initiation within polymerase batteries
-
P. Guptasarma Cooperative relaxation of supercoils and periodic transcriptional initiation within polymerase batteries BioEssays 18 1996 325 332
-
(1996)
BioEssays
, vol.18
, pp. 325-332
-
-
Guptasarma, P.1
-
28
-
-
25144476232
-
A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure
-
C.D. Hardy, and N.R. Cozzarelli A genetic selection for supercoiling mutants of Escherichia coli reveals proteins implicated in chromosome structure Mol. Microbiol. 57 2005 1636 1652
-
(2005)
Mol. Microbiol.
, vol.57
, pp. 1636-1652
-
-
Hardy, C.D.1
Cozzarelli, N.R.2
-
29
-
-
84878203143
-
Are gene loops the cause of transcriptional noise?
-
D. Hebenstreit Are gene loops the cause of transcriptional noise? Trends Genet. 29 2013 333 338
-
(2013)
Trends Genet.
, vol.29
, pp. 333-338
-
-
Hebenstreit, D.1
-
30
-
-
33744981369
-
Sequence-resolved detection of pausing by single RNA polymerase molecules
-
K.M. Herbert, A. La Porta, B.J. Wong, R.A. Mooney, K.C. Neuman, R. Landick, and S.M. Block Sequence-resolved detection of pausing by single RNA polymerase molecules Cell 125 2006 1083 1094
-
(2006)
Cell
, vol.125
, pp. 1083-1094
-
-
Herbert, K.M.1
La Porta, A.2
Wong, B.J.3
Mooney, R.A.4
Neuman, K.C.5
Landick, R.6
Block, S.M.7
-
32
-
-
0020480662
-
The binding of gyrase to DNA: Analysis by retention by nitrocellulose filters
-
N.P. Higgins, and N.R. Cozzarelli The binding of gyrase to DNA: analysis by retention by nitrocellulose filters Nucleic Acids Res. 10 1982 6833 6847
-
(1982)
Nucleic Acids Res.
, vol.10
, pp. 6833-6847
-
-
Higgins, N.P.1
Cozzarelli, N.R.2
-
33
-
-
0004952211
-
Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity
-
N.P. Higgins, C.L. Peebles, A. Sugino, and N.R. Cozzarelli Purification of subunits of Escherichia coli DNA gyrase and reconstitution of enzymatic activity Proc. Natl. Acad. Sci. USA 75 1978 1773 1777
-
(1978)
Proc. Natl. Acad. Sci. USA
, vol.75
, pp. 1773-1777
-
-
Higgins, N.P.1
Peebles, C.L.2
Sugino, A.3
Cozzarelli, N.R.4
-
34
-
-
84873413265
-
Single-molecule analysis of gene expression using two-color RNA labeling in live yeast
-
S. Hocine, P. Raymond, D. Zenklusen, J.A. Chao, and R.H. Singer Single-molecule analysis of gene expression using two-color RNA labeling in live yeast Nat. Methods 10 2013 119 121
-
(2013)
Nat. Methods
, vol.10
, pp. 119-121
-
-
Hocine, S.1
Raymond, P.2
Zenklusen, D.3
Chao, J.A.4
Singer, R.H.5
-
35
-
-
68149120313
-
Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II
-
C. Hodges, L. Bintu, L. Lubkowska, M. Kashlev, and C. Bustamante Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II Science 325 2009 626 628
-
(2009)
Science
, vol.325
, pp. 626-628
-
-
Hodges, C.1
Bintu, L.2
Lubkowska, L.3
Kashlev, M.4
Bustamante, C.5
-
36
-
-
34447322451
-
Extracellular RNA constitutes a natural procoagulant cofactor in blood coagulation
-
C. Kannemeier, A. Shibamiya, F. Nakazawa, H. Trusheim, C. Ruppert, P. Markart, Y. Song, E. Tzima, E. Kennerknecht, and M. Niepmann et al. Extracellular RNA constitutes a natural procoagulant cofactor in blood coagulation Proc. Natl. Acad. Sci. USA 104 2007 6388 6393
-
(2007)
Proc. Natl. Acad. Sci. USA
, vol.104
, pp. 6388-6393
-
-
Kannemeier, C.1
Shibamiya, A.2
Nakazawa, F.3
Trusheim, H.4
Ruppert, C.5
Markart, P.6
Song, Y.7
Tzima, E.8
Kennerknecht, E.9
Niepmann, M.10
-
37
-
-
33751212468
-
Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
-
A.N. Kapanidis, E. Margeat, S.O. Ho, E. Kortkhonjia, S. Weiss, and R.H. Ebright Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism Science 314 2006 1144 1147
-
(2006)
Science
, vol.314
, pp. 1144-1147
-
-
Kapanidis, A.N.1
Margeat, E.2
Ho, S.O.3
Kortkhonjia, E.4
Weiss, S.5
Ebright, R.H.6
-
38
-
-
25444489027
-
Phenotypic diversity, population growth, and information in fluctuating environments
-
E. Kussell, and S. Leibler Phenotypic diversity, population growth, and information in fluctuating environments Science 309 2005 2075 2078
-
(2005)
Science
, vol.309
, pp. 2075-2078
-
-
Kussell, E.1
Leibler, S.2
-
39
-
-
33846914726
-
The regulatory roles and mechanism of transcriptional pausing
-
R. Landick The regulatory roles and mechanism of transcriptional pausing Biochem. Soc. Trans. 34 2006 1062 1066
-
(2006)
Biochem. Soc. Trans.
, vol.34
, pp. 1062-1066
-
-
Landick, R.1
-
40
-
-
79955407832
-
Real-time observation of transcription initiation and elongation on an endogenous yeast gene
-
D.R. Larson, D. Zenklusen, B. Wu, J.A. Chao, and R.H. Singer Real-time observation of transcription initiation and elongation on an endogenous yeast gene Science 332 2011 475 478
-
(2011)
Science
, vol.332
, pp. 475-478
-
-
Larson, D.R.1
Zenklusen, D.2
Wu, B.3
Chao, J.A.4
Singer, R.H.5
-
41
-
-
84055179007
-
Dividing a supercoiled DNA molecule into two independent topological domains
-
F. Leng, B. Chen, and D.D. Dunlap Dividing a supercoiled DNA molecule into two independent topological domains Proc. Natl. Acad. Sci. USA 108 2011 19973 19978
-
(2011)
Proc. Natl. Acad. Sci. USA
, vol.108
, pp. 19973-19978
-
-
Leng, F.1
Chen, B.2
Dunlap, D.D.3
-
42
-
-
79960630264
-
Central dogma at the single-molecule level in living cells
-
G.W. Li, and X.S. Xie Central dogma at the single-molecule level in living cells Nature 475 2011 308 315
-
(2011)
Nature
, vol.475
, pp. 308-315
-
-
Li, G.W.1
Xie, X.S.2
-
43
-
-
0041817952
-
Effect of varying the supercoiling of DNA on transcription and its regulation
-
H.M. Lim, D.E. Lewis, H.J. Lee, M. Liu, and S. Adhya Effect of varying the supercoiling of DNA on transcription and its regulation Biochemistry 42 2003 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
-
44
-
-
77958163968
-
Bending the rules of transcriptional repression: Tightly looped DNA directly represses T7 RNA polymerase
-
T.A. Lionberger, and E. Meyhöfer Bending the rules of transcriptional repression: tightly looped DNA directly represses T7 RNA polymerase Biophys. J. 99 2010 1139 1148
-
(2010)
Biophys. J.
, vol.99
, pp. 1139-1148
-
-
Lionberger, T.A.1
Meyhöfer, E.2
-
45
-
-
79551537838
-
A transgenic mouse for in vivo detection of endogenous labeled mRNA
-
T. Lionnet, K. Czaplinski, X. Darzacq, Y. Shav-Tal, A.L. Wells, J.A. Chao, H.Y. Park, V. de Turris, M. Lopez-Jones, and R.H. Singer A transgenic mouse for in vivo detection of endogenous labeled mRNA Nat. Methods 8 2011 165 170
-
(2011)
Nat. Methods
, vol.8
, pp. 165-170
-
-
Lionnet, T.1
Czaplinski, K.2
Darzacq, X.3
Shav-Tal, Y.4
Wells, A.L.5
Chao, J.A.6
Park, H.Y.7
De Turris, V.8
Lopez-Jones, M.9
Singer, R.H.10
-
46
-
-
0023433855
-
Supercoiling of the DNA template during transcription
-
L.F. Liu, and J.C. Wang Supercoiling of the DNA template during transcription Proc. Natl. Acad. Sci. USA 84 1987 7024 7027
-
(1987)
Proc. Natl. Acad. Sci. USA
, vol.84
, pp. 7024-7027
-
-
Liu, L.F.1
Wang, J.C.2
-
47
-
-
0027467896
-
Anchoring of DNA to the bacterial cytoplasmic membrane through cotranscriptional synthesis of polypeptides encoding membrane proteins or proteins for export: A mechanism of plasmid hypernegative supercoiling in mutants deficient in DNA topoisomerase i
-
A.S. Lynch, and J.C. Wang Anchoring of DNA to the bacterial cytoplasmic membrane through cotranscriptional synthesis of polypeptides encoding membrane proteins or proteins for export: a mechanism of plasmid hypernegative supercoiling in mutants deficient in DNA topoisomerase I J. Bacteriol. 175 1993 1645 1655
-
(1993)
J. Bacteriol.
, vol.175
, pp. 1645-1655
-
-
Lynch, A.S.1
Wang, J.C.2
-
48
-
-
84879682825
-
Transcription under torsion
-
J. Ma, L. Bai, and M.D. Wang Transcription under torsion Science 340 2013 1580 1583
-
(2013)
Science
, vol.340
, pp. 1580-1583
-
-
Ma, J.1
Bai, L.2
Wang, M.D.3
-
49
-
-
34547604468
-
Noise in gene expression determines cell fate in Bacillus subtilis
-
H. Maamar, A. Raj, and D. Dubnau Noise in gene expression determines cell fate in Bacillus subtilis Science 317 2007 526 529
-
(2007)
Science
, vol.317
, pp. 526-529
-
-
Maamar, H.1
Raj, A.2
Dubnau, D.3
-
50
-
-
0021715525
-
The DNA dependence of the ATPase activity of DNA gyrase
-
A. Maxwell, and M. Gellert The DNA dependence of the ATPase activity of DNA gyrase J. Biol. Chem. 259 1984 14472 14480
-
(1984)
J. Biol. Chem.
, vol.259
, pp. 14472-14480
-
-
Maxwell, A.1
Gellert, M.2
-
51
-
-
48249138167
-
The generation of promoter-mediated transcriptional noise in bacteria
-
N. Mitarai, I.B. Dodd, M.T. Crooks, and K. Sneppen The generation of promoter-mediated transcriptional noise in bacteria PLoS Comput. Biol. 4 2008 e1000109
-
(2008)
PLoS Comput. Biol.
, vol.4
, pp. 1000109
-
-
Mitarai, N.1
Dodd, I.B.2
Crooks, M.T.3
Sneppen, K.4
-
52
-
-
0019542484
-
Contacts between DNA gyrase and its binding site on DNA: Features of symmetry and asymmetry revealed by protection from nucleases
-
A. Morrison, and N.R. Cozzarelli Contacts between DNA gyrase and its binding site on DNA: features of symmetry and asymmetry revealed by protection from nucleases Proc. Natl. Acad. Sci. USA 78 1981 1416 1420
-
(1981)
Proc. Natl. Acad. Sci. USA
, vol.78
, pp. 1416-1420
-
-
Morrison, A.1
Cozzarelli, N.R.2
-
53
-
-
84859641038
-
Using gene expression noise to understand gene regulation
-
B. Munsky, G. Neuert, and A. van Oudenaarden Using gene expression noise to understand gene regulation Science 336 2012 183 187
-
(2012)
Science
, vol.336
, pp. 183-187
-
-
Munsky, B.1
Neuert, G.2
Van Oudenaarden, A.3
-
54
-
-
84860794159
-
Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation
-
T. Muramoto, D. Cannon, M. Gierlinski, A. Corrigan, G.J. Barton, and J.R. Chubb Live imaging of nascent RNA dynamics reveals distinct types of transcriptional pulse regulation Proc. Natl. Acad. Sci. USA 109 2012 7350 7355
-
(2012)
Proc. Natl. Acad. Sci. USA
, vol.109
, pp. 7350-7355
-
-
Muramoto, T.1
Cannon, D.2
Gierlinski, M.3
Corrigan, A.4
Barton, G.J.5
Chubb, J.R.6
-
55
-
-
0036578645
-
Regulation of noise in the expression of a single gene
-
E.M. Ozbudak, M. Thattai, I. Kurtser, A.D. Grossman, and A. van Oudenaarden Regulation of noise in the expression of a single gene Nat. Genet. 31 2002 69 73
-
(2002)
Nat. Genet.
, vol.31
, pp. 69-73
-
-
Ozbudak, E.M.1
Thattai, M.2
Kurtser, I.3
Grossman, A.D.4
Van Oudenaarden, A.5
-
56
-
-
38349185928
-
Effects of molecular memory and bursting on fluctuations in gene expression
-
J.M. Pedraza, and J. Paulsson Effects of molecular memory and bursting on fluctuations in gene expression Science 319 2008 339 343
-
(2008)
Science
, vol.319
, pp. 339-343
-
-
Pedraza, J.M.1
Paulsson, J.2
-
57
-
-
11344266685
-
Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli
-
B.J. Peter, J. Arsuaga, A.M. Breier, A.B. Khodursky, P.O. Brown, and N.R. Cozzarelli Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli Genome Biol. 5 2004 R87
-
(2004)
Genome Biol.
, vol.5
, pp. 87
-
-
Peter, B.J.1
Arsuaga, J.2
Breier, A.M.3
Khodursky, A.B.4
Brown, P.O.5
Cozzarelli, N.R.6
-
58
-
-
3142774839
-
Topological domain structure of the Escherichia coli chromosome
-
L. Postow, C.D. Hardy, J. Arsuaga, and N.R. Cozzarelli Topological domain structure of the Escherichia coli chromosome Genes Dev. 18 2004 1766 1779
-
(2004)
Genes Dev.
, vol.18
, pp. 1766-1779
-
-
Postow, L.1
Hardy, C.D.2
Arsuaga, J.3
Cozzarelli, N.R.4
-
59
-
-
33748994704
-
Stochastic mRNA synthesis in mammalian cells
-
A. Raj, C.S. Peskin, D. Tranchina, D.Y. Vargas, and S. Tyagi Stochastic mRNA synthesis in mammalian cells PLoS Biol. 4 2006 e309
-
(2006)
PLoS Biol.
, vol.4
, pp. 309
-
-
Raj, A.1
Peskin, C.S.2
Tranchina, D.3
Vargas, D.Y.4
Tyagi, S.5
-
60
-
-
77249114260
-
Variability in gene expression underlies incomplete penetrance
-
A. Raj, S.A. Rifkin, E. Andersen, and A. van Oudenaarden Variability in gene expression underlies incomplete penetrance Nature 463 2010 913 918
-
(2010)
Nature
, vol.463
, pp. 913-918
-
-
Raj, A.1
Rifkin, S.A.2
Andersen, E.3
Van Oudenaarden, A.4
-
61
-
-
2942718723
-
Control of stochasticity in eukaryotic gene expression
-
J.M. Raser, and E.K. O'Shea Control of stochasticity in eukaryotic gene expression Science 304 2004 1811 1814
-
(2004)
Science
, vol.304
, pp. 1811-1814
-
-
Raser, J.M.1
O'Shea, E.K.2
-
62
-
-
0023097389
-
Structure of the DNA gyrase-DNA complex as revealed by transient electric dichroism
-
D.C. Rau, M. Gellert, F. Thoma, and A. Maxwell Structure of the DNA gyrase-DNA complex as revealed by transient electric dichroism J. Mol. Biol. 193 1987 555 569
-
(1987)
J. Mol. Biol.
, vol.193
, pp. 555-569
-
-
Rau, D.C.1
Gellert, M.2
Thoma, F.3
Maxwell, A.4
-
64
-
-
1842788676
-
Promoter unwinding and promoter clearance by RNA polymerase: Detection by single-molecule DNA nanomanipulation
-
A. Revyakin, R.H. Ebright, and T.R. Strick Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation Proc. Natl. Acad. Sci. USA 101 2004 4776 4780
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 4776-4780
-
-
Revyakin, A.1
Ebright, R.H.2
Strick, T.R.3
-
65
-
-
84864746514
-
Transcription initiation by human RNA polymerase II visualized at single-molecule resolution
-
A. Revyakin, Z. Zhang, R.A. Coleman, Y. Li, C. Inouye, J.K. Lucas, S.R. Park, S. Chu, and R. Tjian Transcription initiation by human RNA polymerase II visualized at single-molecule resolution Genes Dev. 26 2012 1691 1702
-
(2012)
Genes Dev.
, vol.26
, pp. 1691-1702
-
-
Revyakin, A.1
Zhang, Z.2
Coleman, R.A.3
Li, Y.4
Inouye, C.5
Lucas, J.K.6
Park, S.R.7
Chu, S.8
Tjian, R.9
-
66
-
-
84866147787
-
Rates of gyrase supercoiling and transcription elongation control supercoil density in a bacterial chromosome
-
N. Rovinskiy, A.A. Agbleke, O. Chesnokova, Z. Pang, and N.P. Higgins Rates of gyrase supercoiling and transcription elongation control supercoil density in a bacterial chromosome PLoS Genet. 8 2012 e1002845
-
(2012)
PLoS Genet.
, vol.8
, pp. 1002845
-
-
Rovinskiy, N.1
Agbleke, A.A.2
Chesnokova, O.3
Pang, Z.4
Higgins, N.P.5
-
67
-
-
35748946018
-
Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains
-
R. Samul, and F. Leng Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains J. Mol. Biol. 374 2007 925 935
-
(2007)
J. Mol. Biol.
, vol.374
, pp. 925-935
-
-
Samul, R.1
Leng, F.2
-
68
-
-
10044287423
-
A single-molecule technique to study sequence-dependent transcription pausing
-
A. Shundrovsky, T.J. Santangelo, J.W. Roberts, and M.D. Wang A single-molecule technique to study sequence-dependent transcription pausing Biophys. J. 87 2004 3945 3953
-
(2004)
Biophys. J.
, vol.87
, pp. 3945-3953
-
-
Shundrovsky, A.1
Santangelo, T.J.2
Roberts, J.W.3
Wang, M.D.4
-
69
-
-
77951604611
-
Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression
-
A. Singh, B. Razooky, C.D. Cox, M.L. Simpson, and L.S. Weinberger Transcriptional bursting from the HIV-1 promoter is a significant source of stochastic noise in HIV-1 gene expression Biophys. J. 98 2010 L32 L34
-
(2010)
Biophys. J.
, vol.98
-
-
Singh, A.1
Razooky, B.2
Cox, C.D.3
Simpson, M.L.4
Weinberger, L.S.5
-
70
-
-
0942298127
-
Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle
-
G.M. Skinner, C.G. Baumann, D.M. Quinn, J.E. Molloy, and J.G. Hoggett Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle J. Biol. Chem. 279 2004 3239 3244
-
(2004)
J. Biol. Chem.
, vol.279
, pp. 3239-3244
-
-
Skinner, G.M.1
Baumann, C.G.2
Quinn, D.M.3
Molloy, J.E.4
Hoggett, J.G.5
-
71
-
-
0018384079
-
DNA gyrase on the bacterial chromosome: DNA cleavage induced by oxolinic acid
-
M. Snyder, and K. Drlica DNA gyrase on the bacterial chromosome: DNA cleavage induced by oxolinic acid J. Mol. Biol. 131 1979 287 302
-
(1979)
J. Mol. Biol.
, vol.131
, pp. 287-302
-
-
Snyder, M.1
Drlica, K.2
-
72
-
-
79957608918
-
General properties of transcriptional time series in Escherichia coli
-
L.H. So, A. Ghosh, C. Zong, L.A. Sepúlveda, R. Segev, and I. Golding General properties of transcriptional time series in Escherichia coli Nat. Genet. 43 2011 554 560
-
(2011)
Nat. Genet.
, vol.43
, pp. 554-560
-
-
So, L.H.1
Ghosh, A.2
Zong, C.3
Sepúlveda, L.A.4
Segev, R.5
Golding, I.6
-
73
-
-
79955381895
-
Mammalian genes are transcribed with widely different bursting kinetics
-
D.M. Suter, N. Molina, D. Gatfield, K. Schneider, U. Schibler, and F. Naef Mammalian genes are transcribed with widely different bursting kinetics Science 332 2011 472 474
-
(2011)
Science
, vol.332
, pp. 472-474
-
-
Suter, D.M.1
Molina, N.2
Gatfield, D.3
Schneider, K.4
Schibler, U.5
Naef, F.6
-
74
-
-
76049130687
-
Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase
-
G.Q. Tang, R. Roy, R.P. Bandwar, T. Ha, and S.S. Patel Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase Proc. Natl. Acad. Sci. USA 106 2009 22175 22180
-
(2009)
Proc. Natl. Acad. Sci. USA
, vol.106
, pp. 22175-22180
-
-
Tang, G.Q.1
Roy, R.2
Bandwar, R.P.3
Ha, T.4
Patel, S.S.5
-
75
-
-
77955102352
-
Quantifying E coli proteome and transcriptome with single-molecule sensitivity in single cells
-
Y. Taniguchi, P.J. Choi, G.W. Li, H. Chen, M. Babu, J. Hearn, A. Emili, and X.S. Xie Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells Science 329 2010 533 538
-
(2010)
Science
, vol.329
, pp. 533-538
-
-
Taniguchi, Y.1
Choi, P.J.2
Li, G.W.3
Chen, H.4
Babu, M.5
Hearn, J.6
Emili, A.7
Xie, X.S.8
-
76
-
-
0026542543
-
The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template
-
B. ten Heggeler-Bordier, W. Wahli, M. Adrian, A. Stasiak, and J. Dubochet The apical localization of transcribing RNA polymerases on supercoiled DNA prevents their rotation around the template EMBO J. 11 1992 667 672
-
(1992)
EMBO J.
, vol.11
, pp. 667-672
-
-
Ten Heggeler-Bordier, B.1
Wahli, W.2
Adrian, M.3
Stasiak, A.4
Dubochet, J.5
-
77
-
-
2942555282
-
Stochastic gene expression in fluctuating environments
-
M. Thattai, and A. van Oudenaarden Stochastic gene expression in fluctuating environments Genetics 167 2004 523 530
-
(2004)
Genetics
, vol.167
, pp. 523-530
-
-
Thattai, M.1
Van Oudenaarden, A.2
-
78
-
-
0024968110
-
Transcription-driven supercoiling of DNA: Direct biochemical evidence from in vitro studies
-
Y.P. Tsao, H.Y. Wu, and L.F. Liu Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies Cell 56 1989 111 118
-
(1989)
Cell
, vol.56
, pp. 111-118
-
-
Tsao, Y.P.1
Wu, H.Y.2
Liu, L.F.3
-
79
-
-
80052643394
-
Chromosome organization by a nucleoid-associated protein in live bacteria
-
W. Wang, G.W. Li, C. Chen, X.S. Xie, and X. Zhuang Chromosome organization by a nucleoid-associated protein in live bacteria Science 333 2011 1445 1449
-
(2011)
Science
, vol.333
, pp. 1445-1449
-
-
Wang, W.1
Li, G.W.2
Chen, C.3
Xie, X.S.4
Zhuang, X.5
-
80
-
-
84873323216
-
Structural basis of transcriptional pausing in bacteria
-
A. Weixlbaumer, K. Leon, R. Landick, and S.A. Darst Structural basis of transcriptional pausing in bacteria Cell 152 2013 431 441
-
(2013)
Cell
, vol.152
, pp. 431-441
-
-
Weixlbaumer, A.1
Leon, K.2
Landick, R.3
Darst, S.A.4
-
81
-
-
0028034698
-
The complex of DNA gyrase and quinolone drugs with DNA forms a barrier to transcription by RNA polymerase
-
C.J. Willmott, S.E. Critchlow, I.C. Eperon, and A. Maxwell The complex of DNA gyrase and quinolone drugs with DNA forms a barrier to transcription by RNA polymerase J. Mol. Biol. 242 1994 351 363
-
(1994)
J. Mol. Biol.
, vol.242
, pp. 351-363
-
-
Willmott, C.J.1
Critchlow, S.E.2
Eperon, I.C.3
Maxwell, A.4
-
82
-
-
14744282987
-
Diversity in times of adversity: Probabilistic strategies in microbial survival games
-
D.M. Wolf, V.V. Vazirani, and A.P. Arkin Diversity in times of adversity: probabilistic strategies in microbial survival games J. Theor. Biol. 234 2005 227 253
-
(2005)
J. Theor. Biol.
, vol.234
, pp. 227-253
-
-
Wolf, D.M.1
Vazirani, V.V.2
Arkin, A.P.3
-
83
-
-
0024279845
-
Transcription generates positively and negatively supercoiled domains in the template
-
H.Y. Wu, S.H. Shyy, J.C. Wang, and L.F. Liu Transcription generates positively and negatively supercoiled domains in the template Cell 53 1988 433 440
-
(1988)
Cell
, vol.53
, pp. 433-440
-
-
Wu, H.Y.1
Shyy, S.H.2
Wang, J.C.3
Liu, L.F.4
-
84
-
-
84898743524
-
Single-molecule tracking of the transcription cycle by sub-second RNA detection
-
Z. Zhang, A. Revyakin, J.B. Grimm, L.D. Lavis, and R. Tjian Single-molecule tracking of the transcription cycle by sub-second RNA detection eLife 3 2014 e01775
-
(2014)
ELife
, vol.3
, pp. 01775
-
-
Zhang, Z.1
Revyakin, A.2
Grimm, J.B.3
Lavis, L.D.4
Tjian, R.5
-
85
-
-
78649838304
-
Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene
-
C. Zong, L.H. So, L.A. Sepúlveda, S.O. Skinner, and I. Golding Lysogen stability is determined by the frequency of activity bursts from the fate-determining gene Mol. Syst. Biol. 6 2010 440
-
(2010)
Mol. Syst. Biol.
, vol.6
, pp. 440
-
-
Zong, C.1
So, L.H.2
Sepúlveda, L.A.3
Skinner, S.O.4
Golding, I.5
-
86
-
-
41449108157
-
An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments
-
C.E. Aitken, R.A. Marshall, and J.D. Puglisi An oxygen scavenging system for improvement of dye stability in single-molecule fluorescence experiments Biophys. J. 94 2008 1826 1835
-
(2008)
Biophys. J.
, vol.94
, pp. 1826-1835
-
-
Aitken, C.E.1
Marshall, R.A.2
Puglisi, J.D.3
-
87
-
-
84877294439
-
Measurement and modeling of intrinsic transcription terminators
-
G. Cambray, J.C. Guimaraes, V.K. Mutalik, C. Lam, Q.A. Mai, T. Thimmaiah, J.M. Carothers, A.P. Arkin, and D. Endy Measurement and modeling of intrinsic transcription terminators Nucleic Acids Res. 41 2013 5139 5148
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 5139-5148
-
-
Cambray, G.1
Guimaraes, J.C.2
Mutalik, V.K.3
Lam, C.4
Mai, Q.A.5
Thimmaiah, T.6
Carothers, J.M.7
Arkin, A.P.8
Endy, D.9
-
88
-
-
0034612342
-
One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products
-
K.A. Datsenko, and B.L. Wanner One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products Proc. Natl. Acad. Sci. USA 97 2000 6640 6645
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 6640-6645
-
-
Datsenko, K.A.1
Wanner, B.L.2
-
89
-
-
34250173432
-
Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA
-
S. Kim, P.C. Blainey, C.M. Schroeder, and X.S. Xie Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA Nat. Methods 4 2007 397 399
-
(2007)
Nat. Methods
, vol.4
, pp. 397-399
-
-
Kim, S.1
Blainey, P.C.2
Schroeder, C.M.3
Xie, X.S.4
-
90
-
-
84873647198
-
Probing allostery through DNA
-
S. Kim, E. Broströmer, D. Xing, J. Jin, S. Chong, H. Ge, S. Wang, C. Gu, L. Yang, and Y.Q. Gao et al. Probing allostery through DNA Science 339 2013 816 819
-
(2013)
Science
, vol.339
, pp. 816-819
-
-
Kim, S.1
Broströmer, E.2
Xing, D.3
Jin, J.4
Chong, S.5
Ge, H.6
Wang, S.7
Gu, C.8
Yang, L.9
Gao, Y.Q.10
-
91
-
-
0025020967
-
Cell volume increase in Escherichia coli after shifts to richer media
-
H.E. Kubitschek Cell volume increase in Escherichia coli after shifts to richer media J. Bacteriol. 172 1990 94 101
-
(1990)
J. Bacteriol.
, vol.172
, pp. 94-101
-
-
Kubitschek, H.E.1
-
92
-
-
0036138908
-
A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications
-
T. Nagai, K. Ibata, E.S. Park, M. Kubota, K. Mikoshiba, and A. Miyawaki A variant of yellow fluorescent protein with fast and efficient maturation for cell-biological applications Nat. Biotechnol. 20 2002 87 90
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 87-90
-
-
Nagai, T.1
Ibata, K.2
Park, E.S.3
Kubota, M.4
Mikoshiba, K.5
Miyawaki, A.6
-
93
-
-
0025517653
-
A DNA gyrase-binding site at the center of the bacteriophage Mu genome is required for efficient replicative transposition
-
M.L. Pato, M.M. Howe, and N.P. Higgins A DNA gyrase-binding site at the center of the bacteriophage Mu genome is required for efficient replicative transposition Proc. Natl. Acad. Sci. USA 87 1990 8716 8720
-
(1990)
Proc. Natl. Acad. Sci. USA
, vol.87
, pp. 8716-8720
-
-
Pato, M.L.1
Howe, M.M.2
Higgins, N.P.3
-
94
-
-
23644449865
-
Single-molecule DNA nanomanipulation: Improved resolution through use of shorter DNA fragments
-
A. Revyakin, R.H. Ebright, and T.R. Strick Single-molecule DNA nanomanipulation: improved resolution through use of shorter DNA fragments Nat. Methods 2 2005 127 138
-
(2005)
Nat. Methods
, vol.2
, pp. 127-138
-
-
Revyakin, A.1
Ebright, R.H.2
Strick, T.R.3
-
95
-
-
44449084022
-
Hydrodynamic Flow-stretching Assay for Single-Molecule Studies of Nucleic Acid-Protein Interactions
-
P.R. Selvin, T. Ha, Cold Spring Harbor Laboratory Press Cold Spring Harbor
-
C.M. Schroeder, P.C. Blainey, S. Kim, and X.S. Xie Hydrodynamic Flow-stretching Assay for Single-Molecule Studies of Nucleic Acid-Protein Interactions P.R. Selvin, T. Ha, Single-Molecule Techniques: A Laboratory Manual 2008 Cold Spring Harbor Laboratory Press Cold Spring Harbor 461 492
-
(2008)
Single-Molecule Techniques: A Laboratory Manual
, pp. 461-492
-
-
Schroeder, C.M.1
Blainey, P.C.2
Kim, S.3
Xie, X.S.4
-
96
-
-
79951795015
-
A perturbation analysis of rate theory of self-regulating genes and signaling networks
-
P.Z. Shi, and H. Qian A perturbation analysis of rate theory of self-regulating genes and signaling networks J. Chem. Phys. 134 2011 065104
-
(2011)
J. Chem. Phys.
, vol.134
, pp. 065104
-
-
Shi, P.Z.1
Qian, H.2
-
97
-
-
0024338495
-
Terminator-distal sequences determine the in vitro efficiency of the early terminators of bacteriophages T3 and T7
-
A. Telesnitsky, and M.J. Chamberlin Terminator-distal sequences determine the in vitro efficiency of the early terminators of bacteriophages T3 and T7 Biochemistry 28 1989 5210 5218
-
(1989)
Biochemistry
, vol.28
, pp. 5210-5218
-
-
Telesnitsky, A.1
Chamberlin, M.J.2
-
98
-
-
84860347144
-
Quantification of dye-mediated photodamage during single-molecule DNA imaging
-
M.A. Tycon, C.F. Dial, K. Faison, W. Melvin, and C.J. Fecko Quantification of dye-mediated photodamage during single-molecule DNA imaging Anal. Biochem. 426 2012 13 21
-
(2012)
Anal. Biochem.
, vol.426
, pp. 13-21
-
-
Tycon, M.A.1
Dial, C.F.2
Faison, K.3
Melvin, W.4
Fecko, C.J.5
|