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For: Loverdo C, Bénichou O, Voituriez R, Biebricher A, Bonnet I, Desbiolles P. Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins. Phys Rev Lett 2009;102:188101. [PMID: 19518914 DOI: 10.1103/physrevlett.102.188101] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2008] [Indexed: 05/27/2023]
Number Cited by Other Article(s)
51
Kolomeisky AB, Veksler A. How to accelerate protein search on DNA: location and dissociation. J Chem Phys 2012;136:125101. [PMID: 22462896 DOI: 10.1063/1.3697763] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
52
Meyer B, Bénichou O, Kafri Y, Voituriez R. Geometry-induced bursting dynamics in gene expression. Biophys J 2012;102:2186-91. [PMID: 22824283 PMCID: PMC3341560 DOI: 10.1016/j.bpj.2012.03.060] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 03/21/2012] [Accepted: 03/26/2012] [Indexed: 11/17/2022]  Open
53
Normanno D, Dahan M, Darzacq X. Intra-nuclear mobility and target search mechanisms of transcription factors: a single-molecule perspective on gene expression. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012;1819:482-93. [PMID: 22342464 DOI: 10.1016/j.bbagrm.2012.02.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Revised: 01/26/2012] [Accepted: 02/03/2012] [Indexed: 12/26/2022]
54
Haeusler AR, Goodson KA, Lillian TD, Wang X, Goyal S, Perkins NC, Kahn JD. FRET studies of a landscape of Lac repressor-mediated DNA loops. Nucleic Acids Res 2012;40:4432-45. [PMID: 22307389 PMCID: PMC3378866 DOI: 10.1093/nar/gks019] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]  Open
55
Sheinman M, Bénichou O, Kafri Y, Voituriez R. Classes of fast and specific search mechanisms for proteins on DNA. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2012;75:026601. [PMID: 22790348 DOI: 10.1088/0034-4885/75/2/026601] [Citation(s) in RCA: 77] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
56
Towards a molecular view of transcriptional control. Curr Opin Struct Biol 2012;22:160-7. [PMID: 22296921 DOI: 10.1016/j.sbi.2012.01.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Revised: 01/06/2012] [Accepted: 01/09/2012] [Indexed: 11/21/2022]
57
Vuzman D, Levy Y. Intrinsically disordered regions as affinity tuners in protein–DNA interactions. ACTA ACUST UNITED AC 2012;8:47-57. [DOI: 10.1039/c1mb05273j] [Citation(s) in RCA: 154] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
58
Eliazar I. Langevin dynamics, entropic crowding, and stochastic cloaking. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;84:061132. [PMID: 22304065 DOI: 10.1103/physreve.84.061132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2011] [Indexed: 05/31/2023]
59
Mayo ML, Perkins EJ, Ghosh P. First-passage time analysis of a one-dimensional diffusion-reaction model: application to protein transport along DNA. BMC Bioinformatics 2011;12 Suppl 10:S18. [PMID: 22165905 PMCID: PMC3236840 DOI: 10.1186/1471-2105-12-s10-s18] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
60
Sanchez H, Suzuki Y, Yokokawa M, Takeyasu K, Wyman C. Protein-DNA interactions in high speed AFM: single molecule diffusion analysis of human RAD54. Integr Biol (Camb) 2011;3:1127-34. [PMID: 21986699 DOI: 10.1039/c1ib00039j] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
61
Chechkin AV, Zaid IM, Lomholt MA, Sokolov IM, Metzler R. Effective surface motion on a reactive cylinder of particles that perform intermittent bulk diffusion. J Chem Phys 2011;134:204116. [PMID: 21639433 DOI: 10.1063/1.3593198] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
62
Tafvizi A, Mirny LA, van Oijen AM. Dancing on DNA: kinetic aspects of search processes on DNA. Chemphyschem 2011;12:1481-9. [PMID: 21560221 DOI: 10.1002/cphc.201100112] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2011] [Indexed: 11/12/2022]
63
Meyer B, Chevalier C, Voituriez R, Bénichou O. Universality classes of first-passage-time distribution in confined media. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;83:051116. [PMID: 21728499 DOI: 10.1103/physreve.83.051116] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2010] [Indexed: 05/31/2023]
64
Bonnet I, Desbiolles P. The diffusion constant of a labeled protein sliding along DNA. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2011;34:25. [PMID: 21400049 DOI: 10.1140/epje/i2011-11025-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2010] [Accepted: 02/11/2011] [Indexed: 05/30/2023]
65
DeSantis MC, Li JL, Wang YM. Protein sliding and hopping kinetics on DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;83:021907. [PMID: 21405863 PMCID: PMC3683889 DOI: 10.1103/physreve.83.021907] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Indexed: 05/16/2023]
66
Bénichou O, Chevalier C, Meyer B, Voituriez R. Facilitated diffusion of proteins on chromatin. PHYSICAL REVIEW LETTERS 2011;106:038102. [PMID: 21405302 DOI: 10.1103/physrevlett.106.038102] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2010] [Indexed: 05/30/2023]
67
Paillusson F, Dahirel V, Jardat M, Victor JM, Barbi M. Effective interaction between charged nanoparticles and DNA. Phys Chem Chem Phys 2011;13:12603-13. [DOI: 10.1039/c1cp20324j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
68
Vuzman D, Polonsky M, Levy Y. Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker. Biophys J 2010;99:1202-11. [PMID: 20713004 DOI: 10.1016/j.bpj.2010.06.007] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2010] [Revised: 05/30/2010] [Accepted: 06/02/2010] [Indexed: 10/19/2022]  Open
69
Kolomeisky AB. Physics of protein-DNA interactions: mechanisms of facilitated target search. Phys Chem Chem Phys 2010;13:2088-95. [PMID: 21113556 DOI: 10.1039/c0cp01966f] [Citation(s) in RCA: 139] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
70
DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail. Proc Natl Acad Sci U S A 2010;107:21004-9. [PMID: 21078959 DOI: 10.1073/pnas.1011775107] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
71
Tejedor V, Bénichou O, Voituriez R, Jungmann R, Simmel F, Selhuber-Unkel C, Oddershede LB, Metzler R. Quantitative analysis of single particle trajectories: mean maximal excursion method. Biophys J 2010;98:1364-72. [PMID: 20371337 DOI: 10.1016/j.bpj.2009.12.4282] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Revised: 11/19/2009] [Accepted: 12/02/2009] [Indexed: 11/26/2022]  Open
72
de la Rosa MAD, Koslover EF, Mulligan PJ, Spakowitz AJ. Dynamic strategies for target-site search by DNA-binding proteins. Biophys J 2010;98:2943-53. [PMID: 20550907 DOI: 10.1016/j.bpj.2010.02.055] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 02/01/2010] [Accepted: 02/12/2010] [Indexed: 10/19/2022]  Open
73
Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails. J Mol Biol 2009;396:674-84. [PMID: 19958775 DOI: 10.1016/j.jmb.2009.11.056] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 11/23/2009] [Accepted: 11/24/2009] [Indexed: 11/22/2022]
74
Bénichou O, Kafri Y, Sheinman M, Voituriez R. Searching fast for a target on DNA without falling to traps. PHYSICAL REVIEW LETTERS 2009;103:138102. [PMID: 19905543 DOI: 10.1103/physrevlett.103.138102] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Indexed: 05/28/2023]
75
Loverdo C, Bénichou O, Moreau M, Voituriez R. Robustness of optimal intermittent search strategies in one, two, and three dimensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009;80:031146. [PMID: 19905101 DOI: 10.1103/physreve.80.031146] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2009] [Indexed: 05/28/2023]
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