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For: Finzi L, Gelles J. Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science 1995;267:378-80. [PMID: 7824935 DOI: 10.1126/science.7824935] [Citation(s) in RCA: 177] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Number Cited by Other Article(s)
51
Manzo C, Zurla C, Dunlap DD, Finzi L. The effect of nonspecific binding of lambda repressor on DNA looping dynamics. Biophys J 2012;103:1753-61. [PMID: 23083719 DOI: 10.1016/j.bpj.2012.09.006] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Revised: 08/31/2012] [Accepted: 09/05/2012] [Indexed: 12/11/2022]  Open
52
Kinetics and thermodynamics of phenotype: unwinding and rewinding the nucleosome. J Mol Biol 2012;423:687-701. [PMID: 22944905 DOI: 10.1016/j.jmb.2012.08.021] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/23/2012] [Accepted: 08/24/2012] [Indexed: 02/01/2023]
53
Johnson S, Lindén M, Phillips R. Sequence dependence of transcription factor-mediated DNA looping. Nucleic Acids Res 2012;40:7728-38. [PMID: 22718983 PMCID: PMC3439888 DOI: 10.1093/nar/gks473] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]  Open
54
Laurens N, Rusling DA, Pernstich C, Brouwer I, Halford SE, Wuite GJL. DNA looping by FokI: the impact of twisting and bending rigidity on protein-induced looping dynamics. Nucleic Acids Res 2012;40:4988-97. [PMID: 22373924 PMCID: PMC3367208 DOI: 10.1093/nar/gks184] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
55
Rusling DA, Laurens N, Pernstich C, Wuite GJL, Halford SE. DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations. Nucleic Acids Res 2012;40:4977-87. [PMID: 22362745 PMCID: PMC3367207 DOI: 10.1093/nar/gks183] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
56
Ha T, Kozlov AG, Lohman TM. Single-molecule views of protein movement on single-stranded DNA. Annu Rev Biophys 2012;41:295-319. [PMID: 22404684 DOI: 10.1146/annurev-biophys-042910-155351] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
57
Shin J, Sung W. Effects of static and temporally fluctuating tensions on semiflexible polymer looping. J Chem Phys 2012;136:045101. [DOI: 10.1063/1.3673439] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
58
Probing DNA topology using tethered particle motion. Methods Mol Biol 2012;783:295-313. [PMID: 21909895 DOI: 10.1007/978-1-61779-282-3_16] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
59
Lam PM, Neumann RM. Role of chain entropy in an analytic model of protein binding in single-DNA stretching experiments. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;84:032901. [PMID: 22060437 DOI: 10.1103/physreve.84.032901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Indexed: 05/31/2023]
60
Lam PM, Zhen Y. Discrete persistent-chain model for protein binding on DNA. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;83:041912. [PMID: 21599206 DOI: 10.1103/physreve.83.041912] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2010] [Revised: 01/30/2011] [Indexed: 05/30/2023]
61
Lindner M, Nir G, Medalion S, Dietrich HRC, Rabin Y, Garini Y. Force-free measurements of the conformations of DNA molecules tethered to a wall. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011;83:011916. [PMID: 21405722 DOI: 10.1103/physreve.83.011916] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 12/12/2010] [Indexed: 05/30/2023]
62
Schlingman DJ, Mack AH, Mochrie SGJ, Regan L. A new method for the covalent attachment of DNA to a surface for single-molecule studies. Colloids Surf B Biointerfaces 2010;83:91-5. [PMID: 21130613 DOI: 10.1016/j.colsurfb.2010.11.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Revised: 09/27/2010] [Accepted: 11/01/2010] [Indexed: 11/19/2022]
63
Liebesny P, Goyal S, Dunlap D, Family F, Finzi L. Determination of the number of proteins bound non-specifically to DNA. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2010;22:414104. [PMID: 21386587 PMCID: PMC3653182 DOI: 10.1088/0953-8984/22/41/414104] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
64
Manghi M, Tardin C, Baglio J, Rousseau P, Salomé L, Destainville N. Probing DNA conformational changes with high temporal resolution by tethered particle motion. Phys Biol 2010;7:046003. [PMID: 20952812 DOI: 10.1088/1478-3975/7/4/046003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
65
Milstein JN, Chen YF, Meiners JC. Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments. Biopolymers 2010;95:144-50. [PMID: 20882535 DOI: 10.1002/bip.21547] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2010] [Revised: 09/21/2010] [Accepted: 09/21/2010] [Indexed: 11/05/2022]
66
Chu JF, Chang TC, Li HW. Single-molecule TPM studies on the conversion of human telomeric DNA. Biophys J 2010;98:1608-16. [PMID: 20409481 DOI: 10.1016/j.bpj.2009.12.4328] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 12/22/2009] [Accepted: 12/28/2009] [Indexed: 12/18/2022]  Open
67
Finzi L, Dunlap DD. Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription. J Biol Chem 2010;285:18973-8. [PMID: 20382734 PMCID: PMC2885173 DOI: 10.1074/jbc.r109.062612] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
68
Towards building a chromosome segregation machine. Nature 2010;463:446-56. [PMID: 20110988 DOI: 10.1038/nature08912] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
69
Chen YF, Milstein JN, Meiners JC. Femtonewton entropic forces can control the formation of protein-mediated DNA loops. PHYSICAL REVIEW LETTERS 2010;104:048301. [PMID: 20366742 DOI: 10.1103/physrevlett.104.048301] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Indexed: 05/29/2023]
70
Manzo C, Finzi L. Quantitative analysis of DNA-looping kinetics from tethered particle motion experiments. Methods Enzymol 2010;475:199-220. [PMID: 20627159 PMCID: PMC3653189 DOI: 10.1016/s0076-6879(10)75009-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
71
Tetramer opening in LacI-mediated DNA looping. Proc Natl Acad Sci U S A 2009;106:16627-32. [PMID: 19805348 DOI: 10.1073/pnas.0904617106] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
72
Destainville N, Manghi M, Palmeri J. Microscopic mechanism for experimentally observed anomalous elasticity of DNA in two dimensions. Biophys J 2009;96:4464-9. [PMID: 19486670 DOI: 10.1016/j.bpj.2009.03.035] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Revised: 02/26/2009] [Accepted: 03/10/2009] [Indexed: 11/27/2022]  Open
73
Chen YF, Blab GA, Meiners JC. Stretching submicron biomolecules with constant-force axial optical tweezers. Biophys J 2009;96:4701-8. [PMID: 19486692 DOI: 10.1016/j.bpj.2009.03.009] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2008] [Revised: 12/04/2008] [Accepted: 03/06/2009] [Indexed: 11/27/2022]  Open
74
Chen YF, Wilson DP, Raghunathan K, Meiners JC. Entropic boundary effects on the elasticity of short DNA molecules. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009;80:020903. [PMID: 19792069 DOI: 10.1103/physreve.80.020903] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2009] [Indexed: 05/28/2023]
75
Wu D, Ghosh K, Inamdar M, Lee HJ, Fraser S, Dill K, Phillips R. Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes. PHYSICAL REVIEW LETTERS 2009;103:050603. [PMID: 19792475 PMCID: PMC3273425 DOI: 10.1103/physrevlett.103.050603] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2008] [Indexed: 05/17/2023]
76
Laurens N, Bellamy SRW, Harms AF, Kovacheva YS, Halford SE, Wuite GJL. Dissecting protein-induced DNA looping dynamics in real time. Nucleic Acids Res 2009;37:5454-64. [PMID: 19586932 PMCID: PMC2760800 DOI: 10.1093/nar/gkp570] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
77
Calibration of Tethered Particle Motion Experiments. ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-1-4419-0670-0_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
78
Towles KB, Beausang JF, Garcia HG, Phillips R, Nelson PC. First-principles calculation of DNA looping in tethered particle experiments. Phys Biol 2009;6:025001. [PMID: 19571369 PMCID: PMC3298194 DOI: 10.1088/1478-3975/6/2/025001] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
79
Concentration and length dependence of DNA looping in transcriptional regulation. PLoS One 2009;4:e5621. [PMID: 19479049 PMCID: PMC2682762 DOI: 10.1371/journal.pone.0005621] [Citation(s) in RCA: 77] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2009] [Accepted: 04/06/2009] [Indexed: 11/19/2022]  Open
80
Zurla C, Manzo C, Dunlap D, Lewis DEA, Adhya S, Finzi L. Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor. Nucleic Acids Res 2009;37:2789-95. [PMID: 19276206 PMCID: PMC2685085 DOI: 10.1093/nar/gkp134] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]  Open
81
Manghi M, Palmeri J, Destainville N. Coupling between denaturation and chain conformations in DNA: stretching, bending, torsion and finite size effects. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009;21:034104. [PMID: 21817249 DOI: 10.1088/0953-8984/21/3/034104] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
82
Wong OK, Guthold M, Erie DA, Gelles J. Interconvertible lac repressor-DNA loops revealed by single-molecule experiments. PLoS Biol 2008;6:e232. [PMID: 18828671 PMCID: PMC2553838 DOI: 10.1371/journal.pbio.0060232] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2008] [Accepted: 08/13/2008] [Indexed: 11/18/2022]  Open
83
Lee JW, Hwang I, Jeon WS, Ko YH, Sakamoto S, Yamaguchi K, Kim K. Synthetic Molecular Machine Based on Reversible End-to-Interior and End-to-End Loop Formation Triggered by Electrochemical Stimuli. Chem Asian J 2008;3:1277-83. [DOI: 10.1002/asia.200800054] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
84
van Mameren J, Peterman EJG, Wuite GJL. See me, feel me: methods to concurrently visualize and manipulate single DNA molecules and associated proteins. Nucleic Acids Res 2008;36:4381-9. [PMID: 18586820 PMCID: PMC2490750 DOI: 10.1093/nar/gkn412] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
85
Mehraeen S, Sudhanshu B, Koslover EF, Spakowitz AJ. End-to-end distribution for a wormlike chain in arbitrary dimensions. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008;77:061803. [PMID: 18643291 DOI: 10.1103/physreve.77.061803] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 09/12/2007] [Indexed: 05/26/2023]
86
Normanno D, Vanzi F, Pavone FS. Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping. Nucleic Acids Res 2008;36:2505-13. [PMID: 18310101 PMCID: PMC2377426 DOI: 10.1093/nar/gkn071] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2007] [Revised: 01/07/2008] [Accepted: 02/05/2008] [Indexed: 11/12/2022]  Open
87
Visnapuu ML, Duzdevich D, Greene EC. The importance of surfaces in single-molecule bioscience. MOLECULAR BIOSYSTEMS 2008;4:394-403. [PMID: 18414737 PMCID: PMC3033744 DOI: 10.1039/b800444g] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
88
Agrawal NJ, Radhakrishnan R, Purohit PK. Geometry of mediating protein affects the probability of loop formation in DNA. Biophys J 2008;94:3150-8. [PMID: 18192346 PMCID: PMC2275674 DOI: 10.1529/biophysj.107.122986] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 11/30/2007] [Indexed: 11/18/2022]  Open
89
Zhang W, Machón C, Orta A, Phillips N, Roberts CJ, Allen S, Soultanas P. Single-molecule atomic force spectroscopy reveals that DnaD forms scaffolds and enhances duplex melting. J Mol Biol 2008;377:706-14. [PMID: 18291414 PMCID: PMC3033579 DOI: 10.1016/j.jmb.2008.01.067] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Revised: 01/18/2008] [Accepted: 01/22/2008] [Indexed: 11/23/2022]
90
Zhang H, Marko JF. Maxwell relations for single-DNA experiments: Monitoring protein binding and double-helix torque with force-extension measurements. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008;77:031916. [PMID: 18517431 DOI: 10.1103/physreve.77.031916] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2007] [Indexed: 05/26/2023]
91
Catto LE, Bellamy SRW, Retter SE, Halford SE. Dynamics and consequences of DNA looping by the FokI restriction endonuclease. Nucleic Acids Res 2008;36:2073-81. [PMID: 18276642 PMCID: PMC2346600 DOI: 10.1093/nar/gkn051] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]  Open
92
Palmeri J, Manghi M, Destainville N. Thermal denaturation of fluctuating finite DNA chains: the role of bending rigidity in bubble nucleation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2008;77:011913. [PMID: 18351882 DOI: 10.1103/physreve.77.011913] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2007] [Indexed: 05/26/2023]
93
Hugel T, Michaelis J, Hetherington CL, Jardine PJ, Grimes S, Walter JM, Falk W, Anderson DL, Bustamante C. Experimental test of connector rotation during DNA packaging into bacteriophage phi29 capsids. PLoS Biol 2007;5:e59. [PMID: 17311473 PMCID: PMC1800307 DOI: 10.1371/journal.pbio.0050059] [Citation(s) in RCA: 116] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Accepted: 12/26/2006] [Indexed: 12/02/2022]  Open
94
Beausang JF, Nelson PC. Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments. Phys Biol 2007;4:205-19. [PMID: 17928659 DOI: 10.1088/1478-3975/4/3/007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
95
Seol Y, Li J, Nelson PC, Perkins TT, Betterton MD. Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 microm. Biophys J 2007;93:4360-73. [PMID: 17766363 PMCID: PMC2098713 DOI: 10.1529/biophysj.107.112995] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]  Open
96
Nelson PC, Zurla C, Brogioli D, Beausang JF, Finzi L, Dunlap D. Tethered particle motion as a diagnostic of DNA tether length. J Phys Chem B 2007;110:17260-7. [PMID: 16928025 DOI: 10.1021/jp0630673] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
97
Vanzi F, Sacconi L, Pavone FS. Analysis of kinetics in noisy systems: application to single molecule tethered particle motion. Biophys J 2007;93:21-36. [PMID: 17434935 PMCID: PMC1914433 DOI: 10.1529/biophysj.106.094151] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2006] [Accepted: 02/15/2007] [Indexed: 11/18/2022]  Open
98
Guerra RF, Imperadori L, Mantovani R, Dunlap DD, Finzi L. DNA compaction by the nuclear factor-Y. Biophys J 2007;93:176-82. [PMID: 17434933 PMCID: PMC1914443 DOI: 10.1529/biophysj.106.099929] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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Beausang JF, Zurla C, Manzo C, Dunlap D, Finzi L, Nelson PC. DNA looping kinetics analyzed using diffusive hidden Markov model. Biophys J 2007;92:L64-6. [PMID: 17277177 PMCID: PMC1831694 DOI: 10.1529/biophysj.107.104828] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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