-
1
-
-
0023711743
-
Transcription termination in Escherichia coli. Measurement of the rate of enzyme release from Rho-independent terminators
-
doi: 10.1016/0022-2836(88)90457-3
-
Arndt KM, Chamberlin MJ. 1988. Transcription termination in Escherichia coli. Measurement of the rate of enzyme release from Rho-independent terminators. Journal of Molecular Biology 202:271-285. doi: 10.1016/0022-2836(88)90457-3.
-
(1988)
Journal of Molecular Biology
, vol.202
, pp. 271-285
-
-
Arndt, K.M.1
Chamberlin, M.J.2
-
2
-
-
33745041963
-
Single-molecule analysis of RNA polymerase transcription
-
doi: 10.1146/annurev.biophys.35.010406.150153
-
Bai L, Santangelo T, Wang M. 2006. Single-molecule analysis of RNA polymerase transcription. Annual Review of Biophysics and Biomolecular Structure 35:343-360. doi: 10.1146/annurev.biophys.35.010406.150153.
-
(2006)
Annual Review of Biophysics and Biomolecular Structure
, vol.35
, pp. 343-360
-
-
Bai, L.1
Santangelo, T.2
Wang, M.3
-
3
-
-
4444313551
-
tRNA dynamics on the ribosome during translation
-
doi: 10.1073/pnas.0403884101
-
Blanchard SC, Kim HD, Gonzalez RL Jnr, Puglisi JD, Chu S. 2004. tRNA dynamics on the ribosome during translation. Proceedings of the National Academy of Sciences of the United States of America 101:12893-12898. doi: 10.1073/pnas.0403884101.
-
(2004)
Proceedings of the National Academy of Sciences of the United States of America
, vol.101
, pp. 12893-12898
-
-
Blanchard, S.C.1
Kim, H.D.2
Gonzalez Jr., R.L.3
Puglisi, J.D.4
Chu, S.5
-
4
-
-
0028027513
-
Characterization of a set of T7 RNA polymerase active site mutants
-
Bonner G, Lafer EM, Sousa R. 1994. Characterization of a set of T7 RNA polymerase active site mutants. Journal of Biological Chemistry 269:25120-25128.
-
(1994)
Journal of Biological Chemistry
, vol.269
, pp. 25120-25128
-
-
Bonner, G.1
Lafer, E.M.2
Sousa, R.3
-
5
-
-
84864770299
-
Opening and closing of the bacterial RNA polymerase clamp
-
doi: 10.1126/science.1218716
-
Chakraborty A, Wang D, Ebright YW, Korlann Y, Kortkhonjia E, Kim T, Chowdhury S, Wigneshweraraj S, Irschik H, Jansen R, Nixon BT, Knight J, Weiss S, Ebright RH. 2012. Opening and closing of the bacterial RNA polymerase clamp. Science 337:591-595. doi: 10.1126/science.1218716.
-
(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
Nixon, B.T.11
Knight, J.12
Weiss, S.13
Ebright, R.H.14
-
6
-
-
0028881098
-
The biophysics of DNA hybridization with immobilized oligonucleotide probes
-
doi: 10.1016/S0006-3495(95)80095-0
-
Chan V, Graves DJ, McKenzie SE. 1995. The biophysics of DNA hybridization with immobilized oligonucleotide probes. Biophysical Journal 69:2243-2255. doi: 10.1016/S0006-3495(95)80095-0.
-
(1995)
Biophysical Journal
, vol.69
, pp. 2243-2255
-
-
Chan, V.1
Graves, D.J.2
McKenzie, S.E.3
-
7
-
-
84862666457
-
A movie of RNA polymerase ii transcription
-
doi: 10.1016/j.cell.2012.06.006
-
Cheung ACM, Cramer P. 2012. A movie of RNA polymerase ii transcription. Cell 149:1431-1437. doi: 10.1016/j.cell.2012.06.006.
-
(2012)
Cell
, vol.149
, pp. 1431-1437
-
-
Cheung, A.C.M.1
Cramer, P.2
-
8
-
-
0031779081
-
RNA polymerase-promoter interactions: The comings and goings of RNA Polymerase
-
DeHaseth PL, Zupancic ML, Record MT. 1998. RNA polymerase-promoter interactions: the comings and goings of RNA Polymerase. Journal of Bacteriology 180:3019-3025.
-
(1998)
Journal of Bacteriology
, vol.180
, pp. 3019-3025
-
-
DeHaseth, P.L.1
Zupancic, M.L.2
Record, M.T.3
-
9
-
-
18744407040
-
Stretching single stranded DNA, a model polyelectrolyte
-
doi: 10.1103/PhysRevLett.89.248102
-
Dessinges M-N, Maier B, Zhang Y, Peliti M, Bensimon D, Croquette V. 2002. Stretching single stranded DNA, a model polyelectrolyte. Physical Review Letters 89:248102. doi: 10.1103/PhysRevLett.89.248102.
-
(2002)
Physical Review Letters
, vol.89
, pp. 248102
-
-
Dessinges, M.-N.1
Maier, B.2
Zhang, Y.3
Peliti, M.4
Bensimon, D.5
Croquette, V.6
-
10
-
-
0038756088
-
Cooperation between RNA polymerase molecules in transcription elongation
-
doi: 10.1126/science.1083219
-
Epshtein V, Nudler E. 2003. Cooperation between RNA polymerase molecules in transcription elongation. Science 300:801-805. doi: 10.1126/science.1083219.
-
(2003)
Science
, vol.300
, pp. 801-805
-
-
Epshtein, V.1
Nudler, E.2
-
11
-
-
33746743013
-
Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence
-
doi: 10.1529/biophysj.106.084004
-
Friedman LJ, Chung J, Gelles J. 2006. Viewing dynamic assembly of molecular complexes by multi-wavelength single-molecule fluorescence. Biophysical Journal 91:1023-1031. doi: 10.1529/biophysj.106.084004.
-
(2006)
Biophysical Journal
, vol.91
, pp. 1023-1031
-
-
Friedman, L.J.1
Chung, J.2
Gelles, J.3
-
12
-
-
84857311371
-
Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation
-
doi: 10.1016/j.cell.2012.01.018
-
Friedman LJ, Gelles J. 2012. Mechanism of transcription initiation at an activator-dependent promoter defined by single-molecule observation. Cell 148:679-689. doi: 10.1016/j.cell.2012.01.018.
-
(2012)
Cell
, vol.148
, pp. 679-689
-
-
Friedman, L.J.1
Gelles, J.2
-
14
-
-
34147206187
-
Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner
-
doi: 10.1038/nature05701
-
Galburt EA, Grill SW, Wiedmann A, Lubkowska L, Choy J, Nogales E, Kashlev M, Bustamante C. 2007. Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner. Nature 446:820-823. doi: 10.1038/nature05701.
-
(2007)
Nature
, vol.446
, pp. 820-823
-
-
Galburt, E.A.1
Grill, S.W.2
Wiedmann, A.3
Lubkowska, L.4
Choy, J.5
Nogales, E.6
Kashlev, M.7
Bustamante, C.8
-
15
-
-
33746207804
-
Secondary structure effects on DNA hybridization kinetics: A solution versus surface comparison
-
doi: 10.1093/nar/gkl422
-
Gao Y, Wolf LK, Georgiadis RM. 2006. Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison. Nucleic Acids Research 34:3370-3377. doi: 10.1093/nar/gkl422.
-
(2006)
Nucleic Acids Research
, vol.34
, pp. 3370-3377
-
-
Gao, Y.1
Wolf, L.K.2
Georgiadis, R.M.3
-
16
-
-
0016219032
-
Characterization of T7-specific ribonucleic acid polymerase: IV. Resolution of the major in vitro transcripts by gel electrophoresis
-
Golomb M, Chamberlin M. 1974. Characterization of T7-specific ribonucleic acid polymerase: IV. Resolution of the major in vitro transcripts by gel electrophoresis. Journal of Biological Chemistry 249:2858-2863.
-
(1974)
Journal of Biological Chemistry
, vol.249
, pp. 2858-2863
-
-
Golomb, M.1
Chamberlin, M.2
-
17
-
-
0036111913
-
Magnetic tweezers: Micromanipulation and force measurement at the molecular level
-
doi: 10.1016/S0006-3495(02)75672-5
-
Gosse C, Croquette V. 2002. Magnetic tweezers: micromanipulation and force measurement at the molecular level. Biophysical Journal 82:3314-3329. doi: 10.1016/S0006-3495(02)75672-5.
-
(2002)
Biophysical Journal
, vol.82
, pp. 3314-3329
-
-
Gosse, C.1
Croquette, V.2
-
18
-
-
48449095385
-
The Vienna RNA websuite
-
doi: 10.1093/nar/gkn188
-
Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL. 2008. The Vienna RNA websuite. Nucleic Acids Research 36:W70-W74. doi: 10.1093/nar/gkn188.
-
(2008)
Nucleic Acids Research
, vol.36
-
-
Gruber, A.R.1
Lorenz, R.2
Bernhart, S.H.3
Neuböck, R.4
Hofacker, I.L.5
-
19
-
-
80051967505
-
Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells
-
doi: 10.1016/j.cell.2011.07.026
-
Gupta PB, Fillmore CM, Jiang G, Shapira SD, Tao K, Kuperwasser C, Lander ES. 2011. Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell 146:633-644. doi: 10.1016/j.cell.2011.07.026.
-
(2011)
Cell
, vol.146
, pp. 633-644
-
-
Gupta, P.B.1
Fillmore, C.M.2
Jiang, G.3
Shapira, S.D.4
Tao, K.5
Kuperwasser, C.6
Lander, E.S.7
-
20
-
-
70349185347
-
Transcription dynamics
-
doi: 10.1016/j.molcel.2009.09.005
-
Hager GL, McNally JG, Misteli T. 2009. Transcription dynamics. Molecular Cell 35:741-753. doi: 10.1016/j.molcel.2009.09.005.
-
(2009)
Molecular Cell
, vol.35
, pp. 741-753
-
-
Hager, G.L.1
McNally, J.G.2
Misteli, T.3
-
21
-
-
67650762824
-
Super resolution fluorescence microscopy
-
doi: 10.1146/annurev.biochem.77.061906.092014
-
Huang B, Bates M, Zhuang X. 2010. Super resolution fluorescence microscopy. Annual Review of Biochemistry 78:993-1016. doi: 10.1146/annurev.biochem.77.061906.092014.
-
(2010)
Annual Review of Biochemistry
, vol.78
, pp. 993-1016
-
-
Huang, B.1
Bates, M.2
Zhuang, X.3
-
22
-
-
0034721946
-
T7 RNA polymerase elongation complex structure and movement
-
doi: 10.1006/jmbi.2000.4150
-
Huang J, Sousa R. 2000. T7 RNA polymerase elongation complex structure and movement. Journal of Molecular Biology 303:347-358. doi: 10.1006/jmbi.2000.4150.
-
(2000)
Journal of Molecular Biology
, vol.303
, pp. 347-358
-
-
Huang, J.1
Sousa, R.2
-
23
-
-
0028950288
-
RNA polymerase II ternary complexes may become arrested after transcribing to within 10 bases of the end of linear templates
-
doi: 10.1074/jbc.270.5.2290
-
Izban MG, Samkurashvili I, Luse DS. 1995. RNA polymerase II ternary complexes may become arrested after transcribing to within 10 bases of the end of linear templates. Journal of Biological Chemistry 270:2290-2297. doi: 10.1074/jbc.270.5.2290.
-
(1995)
Journal of Biological Chemistry
, vol.270
, pp. 2290-2297
-
-
Izban, M.G.1
Samkurashvili, I.2
Luse, D.S.3
-
24
-
-
0037134940
-
Intramolecular dimers: A new strategy to fluorescence quenching in dual-labeled oligonucleotide probes
-
doi: 10.1021/ja025678o
-
Johansson MK, Fidder H, Dick D, Cook RM. 2002. Intramolecular dimers: a new strategy to fluorescence quenching in dual-labeled oligonucleotide probes. Journal of the American Chemical Society 124:6950-6956. doi: 10.1021/ja025678o.
-
(2002)
Journal of the American Chemical Society
, vol.124
, pp. 6950-6956
-
-
Johansson, M.K.1
Fidder, H.2
Dick, D.3
Cook, R.M.4
-
25
-
-
33751212468
-
Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
-
doi: 10.1126/science.1131399
-
Kapanidis AN, Margeat E, Ho SO, Kortkhonjia E, Weiss S, Ebright RH. 2006. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 314:1144-1147. doi: 10.1126/science.1131399.
-
(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
-
26
-
-
35949011257
-
Easily calculable measure for the complexity of spatiotemporal patterns
-
doi: 10.1103/PhysRevA.36.842
-
Kaspar F, Schuster H. 1987. Easily calculable measure for the complexity of spatiotemporal patterns. Physical Review A 36:842-848. doi: 10.1103/PhysRevA.36.842.
-
(1987)
Physical Review A
, vol.36
, pp. 842-848
-
-
Kaspar, F.1
Schuster, H.2
-
27
-
-
0037065663
-
Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets
-
doi: 10.1021/ja0041324
-
Kuhn H, Demidov VV, Coull JM, Fiandaca MJ, Gildea BD, Frank-Kamenetskii MD. 2002. Hybridization of DNA and PNA molecular beacons to single-stranded and double-stranded DNA targets. Journal of the American Chemical Society 124:1097-1103. doi: 10.1021/ja0041324.
-
(2002)
Journal of the American Chemical Society
, vol.124
, pp. 1097-1103
-
-
Kuhn, H.1
Demidov, V.V.2
Coull, J.M.3
Fiandaca, M.J.4
Gildea, B.D.5
Frank-Kamenetskii, M.D.6
-
28
-
-
0035823868
-
Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins
-
doi: 10.1021/ja016310e
-
Kushon SA, Jordan JP, Seifert JL, Nielsen H, Nielsen PE, Armitage BA. 2001. Effect of secondary structure on the thermodynamics and kinetics of PNA hybridization to DNA hairpins. Journal of the American Chemical Society 123:10805-10813. doi: 10.1021/ja016310e.
-
(2001)
Journal of the American Chemical Society
, vol.123
, pp. 10805-10813
-
-
Kushon, S.A.1
Jordan, J.P.2
Seifert, J.L.3
Nielsen, H.4
Nielsen, P.E.5
Armitage, B.A.6
-
29
-
-
0026621339
-
Implication of RNA structure on antisense oligonucleotide hybridization kinetics
-
doi: 10.1021/bi00163a013
-
Lima WF, Monia BP, Ecker DJ, Freier SM. 1992. Implication of RNA structure on antisense oligonucleotide hybridization kinetics. Biochemistry 31:12055-12061. doi: 10.1021/bi00163a013.
-
(1992)
Biochemistry
, vol.31
, pp. 12055-12061
-
-
Lima, W.F.1
Monia, B.P.2
Ecker, D.J.3
Freier, S.M.4
-
30
-
-
84859424298
-
Transcription goes digital
-
doi: 10.1038/embor.2012.31
-
Lionnet T, Singer RH. 2012. Transcription goes digital. EMBO Reports 13:313-321. doi: 10.1038/embor.2012.31.
-
(2012)
EMBO Reports
, vol.13
, pp. 313-321
-
-
Lionnet, T.1
Singer, R.H.2
-
31
-
-
84879682825
-
Transcription under torsion
-
doi: 10.1126/science.1235441
-
Ma J, Bai L, Wang M. 2013. Transcription under torsion. Science 340:1580-1583. doi: 10.1126/science.1235441.
-
(2013)
Science
, vol.340
, pp. 1580-1583
-
-
Ma, J.1
Bai, L.2
Wang, M.3
-
32
-
-
0036835759
-
Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes
-
Marras SAE, Kramer FR, Tyagi S. 2002. Efficiencies of fluorescence resonance energy transfer and contact-mediated quenching in oligonucleotide probes. Nucleic Acids Research 30:e122.
-
(2002)
Nucleic Acids Research
, vol.30
-
-
Marras, S.A.E.1
Kramer, F.R.2
Tyagi, S.3
-
33
-
-
0023198428
-
Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters
-
doi: 10.1021/bi00384a006
-
Martin CT, Coleman JE. 1987. Kinetic analysis of T7 RNA polymerase-promoter interactions with small synthetic promoters. Biochemistry 26:2690-2696. doi: 10.1021/bi00384a006.
-
(1987)
Biochemistry
, vol.26
, pp. 2690-2696
-
-
Martin, C.T.1
Coleman, J.E.2
-
34
-
-
0027155574
-
Kinetic analysis of T7 RNA polymerase transcription initiation from promoters containing single-stranded regions
-
doi: 10.1021/bi00067a017
-
Maslak M, Martin CT. 1993. Kinetic analysis of T7 RNA polymerase transcription initiation from promoters containing single-stranded regions. Biochemistry 32:4281-4285. doi: 10.1021/bi00067a017.
-
(1993)
Biochemistry
, vol.32
, pp. 4281-4285
-
-
Maslak, M.1
Martin, C.T.2
-
35
-
-
0023651444
-
Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates
-
doi: 10.1093/nar/15.21.8783
-
Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC. 1987. Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Research 15:8783-8798. doi: 10.1093/nar/15.21.8783.
-
(1987)
Nucleic Acids Research
, vol.15
, pp. 8783-8798
-
-
Milligan, J.F.1
Groebe, D.R.2
Witherell, G.W.3
Uhlenbeck, O.C.4
-
36
-
-
0027572577
-
Cyanine dye labeling reagents: Sulfoindocyanine succinimidyl esters
-
doi: 10.1021/bc00020a001
-
Mujumdar RB, Ernst LA, Mujumdar SR, Lewis SJ, Waggoner AS. 1993. Cyanine dye labeling reagents: sulfoindocyanine succinimidyl esters. Bioconjugate Chemistry 4:105-111. doi: 10.1021/bc00020a001.
-
(1993)
Bioconjugate Chemistry
, vol.4
, pp. 105-111
-
-
Mujumdar, R.B.1
Ernst, L.A.2
Mujumdar, S.R.3
Lewis, S.J.4
Waggoner, A.S.5
-
37
-
-
0037308665
-
Bacterial RNA polymerases: The wholo story
-
doi: 10.1016/S0959-440X(02)00005-2
-
Murakami KS, Darst SA. 2003. Bacterial RNA polymerases: the wholo story. Current Opinion in Structural Biology 13:31-39. doi: 10.1016/S0959-440X(02)00005-2.
-
(2003)
Current Opinion in Structural Biology
, vol.13
, pp. 31-39
-
-
Murakami, K.S.1
Darst, S.A.2
-
38
-
-
0345047725
-
Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking
-
doi: 10.1016/S0092-8674(03)00845-6
-
Neuman KC, Abbondanzieri EA, Landick R, Gelles J, Block SM. 2003. Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell 115:437-447. doi: 10.1016/S0092-8674(03)00845-6.
-
(2003)
Cell
, vol.115
, pp. 437-447
-
-
Neuman, K.C.1
Abbondanzieri, E.A.2
Landick, R.3
Gelles, J.4
Block, S.M.5
-
39
-
-
0027325195
-
Differentiation and proliferation of hematopoietic stem cells
-
Ogawa K. 1993. Differentiation and proliferation of hematopoietic stem cells. Blood 81:2844-2853.
-
(1993)
Blood
, vol.81
, pp. 2844-2853
-
-
Ogawa, K.1
-
40
-
-
3242892432
-
Complexity: An internet resource for analysis of DNA sequence complexity
-
doi: 10.1093/nar/gkh466
-
Orlov YL, Potapov VN. 2004. Complexity: an internet resource for analysis of DNA sequence complexity. Nucleic Acids Research 32:W628-W633. doi: 10.1093/nar/gkh466.
-
(2004)
Nucleic Acids Research
, vol.32
-
-
Orlov, Y.L.1
Potapov, V.N.2
-
41
-
-
84878781230
-
Copper-catalyzed azide-alkyne click chemistry for bioconjugation
-
doi: 10.1002/9780470559277.ch110148
-
Presolski SI, Hong VP, Finn MG. 2011. Copper-catalyzed azide-alkyne click chemistry for bioconjugation. Current Protocols in Chemical Biology 3:153-162. doi: 10.1002/9780470559277.ch110148.
-
(2011)
Current Protocols in Chemical Biology
, vol.3
, pp. 153-162
-
-
Presolski, S.I.1
Hong, V.P.2
Finn, M.G.3
-
42
-
-
67650319009
-
Single-molecule approaches to stochastic gene expression
-
doi: 10.1146/annurev.biophys.37.032807.125928
-
Raj A, Van Oudenaarden A. 2009. Single-molecule approaches to stochastic gene expression. Annual Review of Biophysics 38:255-270. doi: 10.1146/annurev.biophys.37.032807.125928.
-
(2009)
Annual Review of Biophysics
, vol.38
, pp. 255-270
-
-
Raj, A.1
Van Oudenaarden, A.2
-
44
-
-
33751218319
-
Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching
-
doi: 10.1126/science.1131398
-
Revyakin A, Liu C, Ebright RH, Strick TR. 2006. Abortive initiation and productive initiation by RNA polymerase involve DNA scrunching. Science 314:1139-1143. doi: 10.1126/science.1131398.
-
(2006)
Science
, vol.314
, pp. 1139-1143
-
-
Revyakin, A.1
Liu, C.2
Ebright, R.H.3
Strick, T.R.4
-
45
-
-
84864746514
-
Transcription initiation by human RNA polymerase II visualized at single-molecule resolution
-
doi: 10.1101/gad.194936.112
-
Revyakin A, Zhang Z, Coleman RA, Li Y, Inouye C, Lucas JK, Park SR, Chu S, Tjian R. 2012. Transcription initiation by human RNA polymerase II visualized at single-molecule resolution. Genes & Development 26:1691-1702. doi: 10.1101/gad.194936.112.
-
(2012)
Genes & Development
, 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
-
46
-
-
84874113188
-
The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: Implications for transcription start-site selection
-
doi: 10.1016/j.jmb.2012.12.015
-
Robb NC, Cordes T, Hwang LC, Gryte K, Duchi D, Craggs TD, Santoso Y, Weiss S, Ebright RH, Kapanidis AN. 2013. The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection. Journal of Molecular Biology 425:875-885. doi: 10.1016/j.jmb.2012.12.015.
-
(2013)
Journal of Molecular Biology
, vol.425
, pp. 875-885
-
-
Robb, N.C.1
Cordes, T.2
Hwang, L.C.3
Gryte, K.4
Duchi, D.5
Craggs, T.D.6
Santoso, Y.7
Weiss, S.8
Ebright, R.H.9
Kapanidis, A.N.10
-
47
-
-
33645028600
-
Folding DNA to create nanoscale shapes and patterns
-
doi: 10.1038/nature04586
-
Rothemund PWK. 2006. Folding DNA to create nanoscale shapes and patterns. Nature 440:297-302. doi: 10.1038/nature04586.
-
(2006)
Nature
, vol.440
, pp. 297-302
-
-
Rothemund, P.W.K.1
-
49
-
-
0346258014
-
Backtracking by single RNA polymerase molecules observed at near-base-pair resolution
-
doi: 10.1038/nature02191
-
Shaevitz JW, Abbondanzieri EA, Landick R, Block SM. 2003. Backtracking by single RNA polymerase molecules observed at near-base-pair resolution. Nature 426:684-687. doi: 10.1038/nature02191.
-
(2003)
Nature
, vol.426
, pp. 684-687
-
-
Shaevitz, J.W.1
Abbondanzieri, E.A.2
Landick, R.3
Block, S.M.4
-
50
-
-
0942298127
-
Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle
-
doi: 10.1074/jbc.M310471200
-
Skinner GM, Baumann CG, Quinn DM, Molloy JE, Hoggett JG. 2004. Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle. Journal of Biological Chemistry 279:3239-3244. doi: 10.1074/jbc.M310471200.
-
(2004)
Journal of Biological Chemistry
, 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
-
51
-
-
0030024985
-
Overstretching B-DNA: The elastic response of individual double-stranded and single-stranded DNA molecules
-
doi: 10.1126/science.271.5250.795
-
Smith SB, Cui Y, Bustamante C. 1996. Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271:795-799. doi: 10.1126/science.271.5250.795.
-
(1996)
Science
, vol.271
, pp. 795-799
-
-
Smith, S.B.1
Cui, Y.2
Bustamante, C.3
-
52
-
-
0037020232
-
The +2 NTP binding drives open complex formation in T7 RNA polymerase
-
doi: 10.1074/jbc.M201600200
-
Stano NM, Levin MK, Patel SS. 2002. The +2 NTP binding drives open complex formation in T7 RNA polymerase. Journal of Biological Chemistry 277:37292-37300. doi: 10.1074/jbc.M201600200.
-
(2002)
Journal of Biological Chemistry
, vol.277
, pp. 37292-37300
-
-
Stano, N.M.1
Levin, M.K.2
Patel, S.S.3
-
53
-
-
33645896417
-
Rapid binding of T7 RNA polymerase is followed by simultaneous bending and opening of the promoter DNA
-
doi: 10.1021/bi052292s
-
Tang G-Q, Patel SS. 2006. Rapid binding of T7 RNA polymerase is followed by simultaneous bending and opening of the promoter DNA. Biochemistry 45:4947-4956. doi: 10.1021/bi052292s.
-
(2006)
Biochemistry
, vol.45
, pp. 4947-4956
-
-
Tang, G.-Q.1
Patel, S.S.2
-
54
-
-
76049130687
-
Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase
-
doi: 10.1073/pnas.0906979106
-
Tang G-Q, Roy R, Bandwar RP, Ha T, Patel SS. 2009. Real-time observation of the transition from transcription initiation to elongation of the RNA polymerase. Proceedings of the National Academy of Sciences of the United States of America 106:22175-22180. doi: 10.1073/pnas.0906979106.
-
(2009)
Proceedings of the National Academy of Sciences of the United States of America
, vol.106
, pp. 22175-22180
-
-
Tang, G.-Q.1
Roy, R.2
Bandwar, R.P.3
Ha, T.4
Patel, S.S.5
-
55
-
-
51649113736
-
T7 RNA polymerase studied by force measurements varying cofactor concentration
-
doi: 10.1529/biophysj.107.125096
-
Thomen P, Lopez PJ, Bockelmann U, Guillerez J, Dreyfus M, Heslot F. 2008. T7 RNA polymerase studied by force measurements varying cofactor concentration. Biophysical Journal 95:2423-2433. doi: 10.1529/biophysj.107.125096.
-
(2008)
Biophysical Journal
, vol.95
, pp. 2423-2433
-
-
Thomen, P.1
Lopez, P.J.2
Bockelmann, U.3
Guillerez, J.4
Dreyfus, M.5
Heslot, F.6
-
56
-
-
0037440736
-
Hybridization kinetics and thermodynamics of molecular beacons
-
doi: 10.1093/nar/gkg212
-
Tsourkas A, Behlke MA, Rose SD, Bao G. 2003. Hybridization kinetics and thermodynamics of molecular beacons. Nucleic Acids Research 31:1319-1330. doi: 10.1093/nar/gkg212.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 1319-1330
-
-
Tsourkas, A.1
Behlke, M.A.2
Rose, S.D.3
Bao, G.4
-
57
-
-
84873558007
-
The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion
-
doi: 10.1038/nsmb.2472
-
Wang F, Redding S, Finkelstein IJ, Gorman J, Reichman DR, Greene EC. 2012. The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion. Nature Structure Molecular Biology 20:174-181. doi: 10.1038/nsmb.2472.
-
(2012)
Nature Structure Molecular Biology
, vol.20
, pp. 174-181
-
-
Wang, F.1
Redding, S.2
Finkelstein, I.J.3
Gorman, J.4
Reichman, D.R.5
Greene, E.C.6
-
58
-
-
5444267847
-
Computational identification of antisense oligonucleotides that rapidly hybridize to RNA
-
doi: 10.1089/oli.2004.14.167
-
Wang J-Y, Drlica K. 2004. Computational identification of antisense oligonucleotides that rapidly hybridize to RNA. Oligonucleotides 14:167-175. doi: 10.1089/oli.2004.14.167.
-
(2004)
Oligonucleotides
, vol.14
, pp. 167-175
-
-
Wang, J.-Y.1
Drlica, K.2
-
59
-
-
0032582494
-
Force and velocity measured for single molecules of RNA polymerase
-
doi: 10.1126/science.282.5390.902
-
Wang MD, Schnitzer MJ, Yin H, Landick R, Gelles J, Block SM. 1998. Force and velocity measured for single molecules of RNA polymerase. Science 282:902-907. doi: 10.1126/science.282.5390.902.
-
(1998)
Science
, vol.282
, pp. 902-907
-
-
Wang, M.D.1
Schnitzer, M.J.2
Yin, H.3
Landick, R.4
Gelles, J.5
Block, S.M.6
-
60
-
-
0033548686
-
Fluorescence spectroscopy of single biomolecules
-
doi: 10.1126/science.283.5408.1676
-
Weiss S. 1999. Fluorescence spectroscopy of single biomolecules. Science 283:1676-1683. doi: 10.1126/science.283.5408.1676.
-
(1999)
Science
, vol.283
, pp. 1676-1683
-
-
Weiss, S.1
-
61
-
-
0036843471
-
An open-source oligomicroarray standard for human and mouse
-
doi: 10.1038/nbt1102-1082
-
Wright M, Church GM. 2002. An open-source oligomicroarray standard for human and mouse. Nature Biotechnology 20:1082-1083. doi: 10.1038/nbt1102-1082.
-
(2002)
Nature Biotechnology
, vol.20
, pp. 1082-1083
-
-
Wright, M.1
Church, G.M.2
-
62
-
-
67650095196
-
Elite and stochastic models for induced pluripotent stem cell generation
-
doi: 10.1038/nature08180
-
Yamanaka S. 2009. Elite and stochastic models for induced pluripotent stem cell generation. Nature 460:49-52. doi: 10.1038/nature08180.
-
(2009)
Nature
, vol.460
, pp. 49-52
-
-
Yamanaka, S.1
-
63
-
-
33644856670
-
Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides
-
doi: 10.1128/AEM.72.1.733-744.2006
-
Yilmaz LS, Okten HE, Noguera DR. 2006. Making all parts of the 16S rRNA of Escherichia coli accessible in situ to single DNA oligonucleotides. Applied and Environmental Microbiology 72:733-744. doi: 10.1128/AEM.72.1.733-744.2006.
-
(2006)
Applied and Environmental Microbiology
, vol.72
, pp. 733-744
-
-
Yilmaz, L.S.1
Okten, H.E.2
Noguera, D.R.3
-
64
-
-
33747647960
-
Observed instability of T7 RNA polymerase elongation complexes can be dominated by collision-induced "bumping"
-
doi: 10.1074/jbc.M604369200
-
Zhou Y, Martin CT. 2006. Observed instability of T7 RNA polymerase elongation complexes can be dominated by collision-induced "bumping". Journal of Biological Chemistry 281:24441-24448. doi: 10.1074/jbc.M604369200.
-
(2006)
Journal of Biological Chemistry
, vol.281
, pp. 24441-24448
-
-
Zhou, Y.1
Martin, C.T.2
-
65
-
-
27744505584
-
Fluorescence quenching by TEMPO: A sub-30 A single-molecule ruler
-
doi: 10.1529/biophysj.105.071027
-
Zhu P, Clamme J-P, Deniz AA. 2005. Fluorescence quenching by TEMPO: a sub-30 A single-molecule ruler. Biophysical Journal 89:L37-L39. doi: 10.1529/biophysj.105.071027.
-
(2005)
Biophysical Journal
, vol.89
-
-
Zhu, P.1
Clamme, J.-P.2
Deniz, A.A.3
-
67
-
-
0042121256
-
Mfold web server for nucleic acid folding and hybridization prediction
-
doi: 10.1093/nar/gkg595
-
Zuker M. 2003. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Research 31:3406-3415. doi: 10.1093/nar/gkg595.
-
(2003)
Nucleic Acids Research
, vol.31
, pp. 3406-3415
-
-
Zuker, M.1
|