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Volumn 6, Issue 2, 2009, Pages

First-principles calculation of DNA looping in tethered particle experiments

Author keywords

[No Author keywords available]

Indexed keywords

CURVED DNA; DNA BINDING PROTEIN; LAC REPRESSOR PROTEIN; PROTEIN; TETRAMER; UNCLASSIFIED DRUG; BACTERIAL DNA; ESCHERICHIA COLI PROTEIN; REPRESSOR PROTEIN;

EID: 68349150612     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/6/2/025001     Document Type: Article
Times cited : (56)

References (122)
  • 3
    • 0031961672 scopus 로고    scopus 로고
    • Lactose repressor protein: Functional properties and structure
    • Matthews K S and Nichols J C 1998 Lactose repressor protein: functional properties and structure Prog. Nucl. Acid Res. Mol. Biol. 58 127-64
    • (1998) Prog. Nucl. Acid Res. Mol. Biol. , vol.58 , pp. 127-164
    • Matthews, K.S.1    Nichols, J.C.2
  • 4
    • 20444411150 scopus 로고    scopus 로고
    • The lac repressor
    • Lewis M 2005 The lac repressor C. R. Biologies 328 521-48
    • (2005) C. R. Biologies , vol.328 , Issue.6 , pp. 521-548
    • Lewis, M.1
  • 6
    • 0021188333 scopus 로고
    • An operator at -280 base pairs that is required for repression of araBAD operon promoter: Addition of DNA helical turns between the operator and promoter cyclically hinders repression
    • Dunn T M, Hahn S, Ogden S and Schleif R F 1984 An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression Proc. Natl Acad. Sci. USA 81 5017-20
    • (1984) Proc. Natl Acad. Sci. USA , vol.81 , Issue.16 , pp. 5017-5020
    • Dunn, T.M.1    Hahn, S.2    Ogden, S.3    Schleif, R.F.4
  • 7
    • 0022529619 scopus 로고
    • Upstream operators enhance repression of the lac promoter
    • Mossing M C and Record M T 1986 Upstream operators enhance repression of the lac promoter Science 233 889-92
    • (1986) Science , vol.233 , Issue.4766 , pp. 889-892
    • Mossing, M.C.1    Record, M.T.2
  • 9
    • 0023665179 scopus 로고
    • Influence of sequence and distance between two operators on interaction with the lac repressor
    • Hsieh W T, Whitson P A, Matthews K S and Wells R D 1987 Influence of sequence and distance between two operators on interaction with the lac repressor J. Biol. Chem. 262 14583-91
    • (1987) J. Biol. Chem. , vol.262 , pp. 14583-14591
    • Hsieh, W.T.1    Whitson, P.A.2    Matthews, K.S.3    Wells, R.D.4
  • 10
    • 0024811753 scopus 로고
    • Multipartite genetic control elements: Communication by DNA loop
    • Adhya S 1989 Multipartite genetic control elements: communication by DNA loop Ann. Rev. Genet. 23 227-50
    • (1989) Ann. Rev. Genet. , vol.23 , Issue.1 , pp. 227-250
    • Adhya, S.1
  • 11
    • 0033545416 scopus 로고    scopus 로고
    • Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances
    • Revet B, von Wilcken-Bergmann B, Bessert H, Barker A and Müller-Hill B 1999 Four dimers of lambda repressor bound to two suitably spaced pairs of lambda operators form octamers and DNA loops over large distances Curr. Biol. 9 151-4
    • (1999) Curr. Biol. , vol.9 , Issue.3 , pp. 151-154
    • Revet, B.1    Von Wilcken-Bergmann, B.2    Bessert, H.3    Barker, A.4    Müller-Hill, B.5
  • 12
    • 0042622638 scopus 로고    scopus 로고
    • DNA looping and physical constraints on transcription regulation
    • Vilar J M G and Leibler S 2003 DNA looping and physical constraints on transcription regulation J. Mol. Biol. 331 981-9
    • (2003) J. Mol. Biol. , vol.331 , Issue.5 , pp. 981-989
    • Vilar, J.M.G.1    Leibler, S.2
  • 13
    • 0029975889 scopus 로고    scopus 로고
    • Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator
    • Muller J, Oehler S and Muller-Hill B 1996 Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator J. Mol. Biol. 257 21-9
    • (1996) J. Mol. Biol. , vol.257 , Issue.1 , pp. 21-29
    • Muller, J.1    Oehler, S.2    Muller-Hill, B.3
  • 14
    • 0028956979 scopus 로고
    • Measurement of lactose repressor-mediated loop formation and breakdown in single DNA-molecules
    • Finzi L and Gelles J 1995 Measurement of lactose repressor-mediated loop formation and breakdown in single DNA-molecules Science 267 378-80
    • (1995) Science , vol.267 , Issue.5196 , pp. 378-380
    • Finzi, L.1    Gelles, J.2
  • 16
    • 33746207766 scopus 로고    scopus 로고
    • Lac repressor hinge flexibility and DNA looping: Single molecule kinetics by tethered particle motion
    • Vanzi F, Broggio C, Sacconi L and Pavone F S 2006 Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion Nucl. Acids Res. 34 3409-20
    • (2006) Nucl. Acids Res. , vol.34 , Issue.12 , pp. 3409-3420
    • Vanzi, F.1    Broggio, C.2    Sacconi, L.3    Pavone, F.S.4
  • 18
    • 35248840949 scopus 로고    scopus 로고
    • Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments
    • Beausang J F and Nelson P C 2007 Diffusive hidden Markov model characterization of DNA looping dynamics in tethered particle experiments Phys. Biol. 4 205-19
    • (2007) Phys. Biol. , vol.4 , Issue.3 , pp. 205-219
    • Beausang, J.F.1    Nelson, P.C.2
  • 19
    • 0020612485 scopus 로고
    • Dependence of DNA helix flexibility on base composition
    • Hogan M, LeGrange J and Austin B 1983 Dependence of DNA helix flexibility on base composition Nature 304 752-4
    • (1983) Nature , vol.304 , Issue.5928 , pp. 752-754
    • Hogan, M.1    Legrange, J.2    Austin, B.3
  • 21
    • 33644676435 scopus 로고    scopus 로고
    • Volume-exclusion effects in tethered-particle experiments: Bead size matters
    • Segall D E, Nelson P C and Phillips R 2006 Volume-exclusion effects in tethered-particle experiments: bead size matters Phys. Rev. Lett. 96 088306
    • (2006) Phys. Rev. Lett. , vol.96 , Issue.8 , pp. 088306
    • Segall, D.E.1    Nelson, P.C.2    Phillips, R.3
  • 22
    • 35448944463 scopus 로고    scopus 로고
    • Colloidal particle motion as a diagnostic of DNA conformational transitions
    • Nelson P C 2007 Colloidal particle motion as a diagnostic of DNA conformational transitions Curr. Opin. Colloid Interface Sci. 12 307-13
    • (2007) Curr. Opin. Colloid Interface Sci. , vol.12 , Issue.6 , pp. 307-313
    • Nelson, P.C.1
  • 24
    • 54749084305 scopus 로고    scopus 로고
    • Interconvertible lactose repressor-DNA looped complexes revealed by single-molecule experiments
    • Wong O K, Guthold M, Erie D A and Gelles J 2008 Interconvertible lactose repressor-DNA looped complexes revealed by single-molecule experiments PLoS Biol. 6 e232-1-4
    • (2008) PLoS Biol. , vol.6 , Issue.9 , pp. 232
    • Wong, O.K.1    Guthold, M.2    Erie, D.A.3    Gelles, J.4
  • 25
    • 43349099320 scopus 로고    scopus 로고
    • Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping
    • Normanno D, Vanzi F and Pavone F S 2008 Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping Nucl. Acids Res. 36 2505-13
    • (2008) Nucl. Acids Res. , vol.36 , Issue.8 , pp. 2505-2513
    • Normanno, D.1    Vanzi, F.2    Pavone, F.S.3
  • 27
    • 19544379865 scopus 로고    scopus 로고
    • Localized single-stranded bubble mechanism for cyclization of short double helix DNA
    • Yan J and Marko J F 2004 Localized single-stranded bubble mechanism for cyclization of short double helix DNA Phys. Rev. Lett. 93 108108
    • (2004) Phys. Rev. Lett. , vol.93 , Issue.10 , pp. 108108
    • Yan, J.1    Marko, J.F.2
  • 28
    • 41349084347 scopus 로고    scopus 로고
    • Exact theory of kinkable elastic polymers
    • Wiggins P A, Nelson P C and Phillips R 2005 Exact theory of kinkable elastic polymers Phys. Rev. E 71 021909
    • (2005) Phys. Rev. , vol.71 , Issue.2 , pp. 021909
    • Wiggins, P.A.1    Nelson, P.C.2    Phillips, R.3
  • 29
    • 0001191247 scopus 로고
    • DNA flexibility studied by covalent closure of short fragments into circles
    • Shore D, Langowski J and Baldwin R L 1981 DNA flexibility studied by covalent closure of short fragments into circles Proc. Natl Acad. Sci. USA 170 4833-7
    • (1981) Proc. Natl Acad. Sci. USA , vol.78 , Issue.8 , pp. 4833-4837
    • Shore, D.1    Langowski, J.2    Baldwin, R.L.3
  • 30
    • 0021022977 scopus 로고
    • Energetics of DNA twisting: I. Relation between twist and cyclization probability
    • Shore D and Baldwin R L 1983 Energetics of DNA twisting: I. Relation between twist and cyclization probability J. Mol. Biol. 170 957-81
    • (1983) J. Mol. Biol. , vol.170 , Issue.4 , pp. 957-981
    • Shore, D.1    Baldwin, R.L.2
  • 31
    • 0026766290 scopus 로고
    • Protein-induced bending and DNA cyclization
    • Kahn J D and Crothers D M 1992 Protein-induced bending and DNA cyclization Proc. Natl Acad. Sci. USA 89 6343-7
    • (1992) Proc. Natl Acad. Sci. USA , vol.89 , Issue.14 , pp. 6343-6347
    • Kahn, J.D.1    Crothers, D.M.2
  • 32
    • 14844342574 scopus 로고    scopus 로고
    • DNA twisting flexibility and the formation of sharply looped protein-DNA complexes
    • Cloutier T E and Widom J 2005 DNA twisting flexibility and the formation of sharply looped protein-DNA complexes Proc. Natl Acad. Sci. USA 102 3634-50
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , Issue.10 , pp. 3645-3650
    • Cloutier, T.E.1    Widom, J.2
  • 35
    • 15744393452 scopus 로고    scopus 로고
    • DNA looping in gene regulation: From the assembly of macromolecular complexes to the control of transcriptional noise
    • Vilar J M and Saiz L 2005 DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise Curr. Opin. Genet. Dev. 15 136-44
    • (2005) Curr. Opin. Genet. Dev. , vol.15 , Issue.2 , pp. 136-144
    • Vilar, J.M.1    Saiz, L.2
  • 36
    • 19444387811 scopus 로고    scopus 로고
    • Bacterial repression loops require enhanced DNA flexibility
    • Becker N A, Kahn J D and Maher L J 2005 Bacterial repression loops require enhanced DNA flexibility J. Mol. Biol. 349 716-30
    • (2005) J. Mol. Biol. , vol.349 , Issue.4 , pp. 716-730
    • Becker, N.A.1    Kahn, J.D.2    Maher, L.J.3
  • 37
    • 26844548864 scopus 로고    scopus 로고
    • Bacterial repression loops require enhanced DNA flexibility
    • erratum
    • Becker N A, Kahn J D and Maher L J 2005 Bacterial repression loops require enhanced DNA flexibility J. Mol. Biol. 353 924-6 (erratum)
    • (2005) J. Mol. Biol. , vol.353 , Issue.4 , pp. 924-926
    • Becker, N.A.1    Kahn, J.D.2    Maher, L.J.3
  • 38
    • 0027510369 scopus 로고
    • In vivo thermodynamic analysis of repression with and without looping in lac constructs-estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo
    • Law S M, Bellomy G R, Schlax P J and Record M T 1993 In vivo thermodynamic analysis of repression with and without looping in lac constructs-estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo J. Mol. Biol. 230 161-73
    • (1993) J. Mol. Biol. , vol.230 , Issue.1 , pp. 161-173
    • Law, S.M.1    Bellomy, G.R.2    Schlax, P.J.3    Record, M.T.4
  • 39
    • 34547642985 scopus 로고    scopus 로고
    • Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli
    • Becker N A, Kahn J D and Maher L J III 2007 Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli Nucl. Acids Res. 35 3988-4000
    • (2007) Nucl. Acids Res. , vol.35 , Issue.12 , pp. 3988-4000
    • Becker, N.A.1    Kahn, J.D.2    Maher, L.J.3
  • 42
    • 29144433945 scopus 로고    scopus 로고
    • Inferring the in vivo looping properties of DNA
    • Saiz L, Rubi J M and Vilar J M 2005 Inferring the in vivo looping properties of DNA Proc. Natl Acad. Sci. USA 49 17642-5
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , Issue.49 , pp. 17642-17645
    • Saiz, L.1    Rubi, J.M.2    Vilar, J.M.3
  • 43
    • 34547852967 scopus 로고    scopus 로고
    • Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping
    • Zhang Y, McEwen A E, Crothers D M and Levene S D 2006 Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping PLoS ONE 1 e136-1-13
    • (2006) PLoS ONE , vol.1 , Issue.1 , pp. 136
    • Zhang, Y.1    McEwen, A.E.2    Crothers, D.M.3    Levene, S.D.4
  • 45
    • 0025867008 scopus 로고
    • Transcription by single molecules of RNA-polymerase observed by light-microscopy
    • Schafer D A, Gelles J, Sheetz M P and Landick R 1991 Transcription by single molecules of RNA-polymerase observed by light-microscopy Nature 352 444-8
    • (1991) Nature , vol.352 , Issue.6334 , pp. 444-448
    • Schafer, D.A.1    Gelles, J.2    Sheetz, M.P.3    Landick, R.4
  • 46
    • 33645322437 scopus 로고    scopus 로고
    • Novel tethered particle motion analysis of cI protein-mediated DNA looping in the regulation of bacteriophage lambda
    • Zurla C, Franzini A, Galli G, Dunlap D D, Lewis D E A, Adhya S and Finzi L 2006 Novel tethered particle motion analysis of cI protein-mediated DNA looping in the regulation of bacteriophage lambda J. Phys.: Condens. Matter 18 S225-34
    • (2006) J. Phys.: Condens. Matter , vol.18 , Issue.14
    • Zurla, C.1    Franzini, A.2    Galli, G.3    Dunlap, D.D.4    Lewis, D.E.A.5    Adhya, S.6    Finzi, L.7
  • 47
    • 31544452261 scopus 로고    scopus 로고
    • Real-time observation of DNA looping dynamics of type IIE restriction enzymes NaeI and NarI
    • van den Broek B, Vanzi F, Normanno D, Pavone F S and Wuite G J L 2006 Real-time observation of DNA looping dynamics of type IIE restriction enzymes NaeI and NarI Nucl. Acids Res. 34 167-74
    • (2006) Nucl. Acids Res. , vol.34 , Issue.1 , pp. 167-174
    • Van Den Broek, B.1    Vanzi, F.2    Normanno, D.3    Pavone, F.S.4    Wuite, G.J.L.5
  • 49
    • 33845793417 scopus 로고    scopus 로고
    • Effect of supercoiling on formation of protein-mediated DNA loops
    • Purohit P K and Nelson P C 2006 Effect of supercoiling on formation of protein-mediated DNA loops Phys. Rev. E 74 061907
    • (2006) Phys. Rev. , vol.74 , Issue.6 , pp. 061907
    • Purohit, P.K.1    Nelson, P.C.2
  • 50
    • 33947614580 scopus 로고    scopus 로고
    • Effect of supercoiling on formation of protein-mediated DNA loops
    • erratum
    • Purohit P K and Nelson P C 2007 Effect of supercoiling on formation of protein-mediated DNA loops Phys. Rev. E 75 039903 (erratum)
    • (2007) Phys. Rev. , vol.75 , Issue.3 , pp. 039903
    • Purohit, P.K.1    Nelson, P.C.2
  • 54
    • 0032937079 scopus 로고    scopus 로고
    • Estimating the persistence length of a worm-like chain molecule from force-extension measurements
    • Bouchiat C, Wang M D, Allemand J F, Strick T, Block S M and Croquette V 1999 Estimating the persistence length of a worm-like chain molecule from force-extension measurements Biophys. J. 76 409-13
    • (1999) Biophys. J. , vol.76 , Issue.1 , pp. 409-413
    • Bouchiat, C.1    Wang, M.D.2    Allemand, J.F.3    Strick, T.4    Block, S.M.5    Croquette, V.6
  • 55
    • 0028375446 scopus 로고
    • Bending and twisting elasticity of DNA
    • Marko J F and Siggia E D 1994 Bending and twisting elasticity of DNA Macromolecules 27 981-8
    • (1994) Macromolecules , vol.27 , Issue.4 , pp. 981-988
    • Marko, J.F.1    Siggia, E.D.2
  • 56
    • 1542382023 scopus 로고    scopus 로고
    • Bending and twisting elasticity of DNA
    • erratum
    • Marko J F and Siggia E D 1996 Bending and twisting elasticity of DNA Macromolecules 29 4820 (erratum)
    • (1996) Macromolecules , vol.29 , Issue.13 , pp. 4820
    • Marko, J.F.1    Siggia, E.D.2
  • 58
    • 0032497194 scopus 로고    scopus 로고
    • Entropic elasticity of twist-storing polymers
    • Moroz J D and Nelson P 1998 Entropic elasticity of twist-storing polymers Macromolecules 31 6333-47
    • (1998) Macromolecules , vol.31 , Issue.18 , pp. 6333-6347
    • Moroz, J.D.1    Nelson, P.2
  • 59
    • 0032530555 scopus 로고    scopus 로고
    • DNA sequence-dependent deformability deduced from protein-DNA crystal complexes
    • the covariance matrices are available at
    • Olson W K, Gorin A A, Lu X-J, Hock L M and Zhurkin V B 1998 DNA sequence-dependent deformability deduced from protein-DNA crystal complexes Proc. Natl Acad. Sci. USA 95 11163-8 (the covariance matrices are available at http://rutchem.rutgers.edu/∼olson/cov-matrix.html)
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , Issue.19 , pp. 11163-11168
    • Olson, W.K.1    Gorin, A.A.2    Lu, X.-J.3    Hock, L.M.4    Zhurkin, V.B.5
  • 64
    • 37349067907 scopus 로고    scopus 로고
    • Elasticity of short DNA molecules: Theory and experiment for contour lengths of 0.6-7 νm
    • Seol Y, Li J, Nelson P C, Perkins T T and Betterton M D 2007 Elasticity of short DNA molecules: theory and experiment for contour lengths of 0.6-7 νm Biophys. J. 93 4360-73
    • (2007) Biophys. J. , vol.93 , Issue.12 , pp. 4360-4373
    • Seol, Y.1    Li, J.2    Nelson, P.C.3    Perkins, T.T.4    Betterton, M.D.5
  • 65
    • 84856396192 scopus 로고    scopus 로고
    • Entropic elasticity of double-strand DNA subject to simple spatial constraints
    • article P03019-1-28
    • Bouchiat C 2006 Entropic elasticity of double-strand DNA subject to simple spatial constraints J. Stat. Mech. Theor. Exp. (article P03019-1-28)
    • (2006) J. Stat. Mech. Theor. Exp.
    • Bouchiat, C.1
  • 66
    • 34548688948 scopus 로고    scopus 로고
    • Spatial constraint corrections to the elasticity of double stranded DNA measured with magnetic tweezers
    • article P06001-1-22
    • Bouchiat C 2007 Spatial constraint corrections to the elasticity of double stranded DNA measured with magnetic tweezers J. Stat. Mech. Theor. Exp. (article P06001-1-22)
    • (2007) J. Stat. Mech. Theor. Exp.
    • Bouchiat, C.1
  • 67
    • 33749243974 scopus 로고    scopus 로고
    • Sequence-dependent effects in the cyclization of short DNA
    • Czapla L, Swigon D and Olson W K 2006 Sequence-dependent effects in the cyclization of short DNA J. Chem. Theor. Comput. 2 685-95
    • (2006) J. Chem. Theor. Comput. , vol.2 , Issue.3 , pp. 685-695
    • Czapla, L.1    Swigon, D.2    Olson, W.K.3
  • 68
    • 33846129071 scopus 로고    scopus 로고
    • Entropic elasticity of DNA with a permanent kink
    • Li J Y, Nelson P C and Betterton M D 2006 Entropic elasticity of DNA with a permanent kink Macromolecules 39 8816-21
    • (2006) Macromolecules , vol.39 , Issue.25 , pp. 8816-8821
    • Li, J.Y.1    Nelson, P.C.2    Betterton, M.D.3
  • 70
    • 0030564945 scopus 로고    scopus 로고
    • Cooperative and anticooperative effects in binding of the first and second plasmid Osym operators to a LacI tetramer: Evidence for contributions of non-operator DNA binding by wrapping and looping
    • Levandoski M M, Tsodikov O V, Frank D E, Melcher S E, Saecker R M and Record M T 1996 Cooperative and anticooperative effects in binding of the first and second plasmid Osym operators to a LacI tetramer: evidence for contributions of non-operator DNA binding by wrapping and looping J. Mol. Biol. 260 697-717
    • (1996) J. Mol. Biol. , vol.260 , Issue.5 , pp. 697-717
    • Levandoski, M.M.1    Tsodikov, O.V.2    Frank, D.E.3    Melcher, S.E.4    Saecker, R.M.5    Record, M.T.6
  • 71
    • 0033580635 scopus 로고    scopus 로고
    • Thermodynamic analysis of unfolding and dissociation in lactose repressor protein
    • Barry J K and Matthews K S 1999 Thermodynamic analysis of unfolding and dissociation in lactose repressor protein Biochemistry 38 6520-8
    • (1999) Biochemistry , vol.38 , Issue.20 , pp. 6520-6528
    • Barry, J.K.1    Matthews, K.S.2
  • 73
    • 0025343547 scopus 로고
    • The 3 operators of the lac operon cooperate in repression
    • Oehler S, Eismann E R, Krämer H and Muller-Hill B 1990 The 3 operators of the lac operon cooperate in repression EMBO J. 9 973-9
    • (1990) EMBO J. , vol.9 , pp. 973-979
    • Oehler, S.1    Eismann, E.R.2    Krämer, H.3    Muller-Hill, B.4
  • 74
    • 0035850794 scopus 로고    scopus 로고
    • Structure of a variant of lac repressor with increased thermostability and decreased affinity for operator
    • Bell C E, Barry J, Matthews K S and Lewis M 2001 Structure of a variant of lac repressor with increased thermostability and decreased affinity for operator J. Mol. Biol. 313 99-109
    • (2001) J. Mol. Biol. , vol.313 , Issue.1 , pp. 99-109
    • Bell, C.E.1    Barry, J.2    Matthews, K.S.3    Lewis, M.4
  • 75
    • 0035812627 scopus 로고    scopus 로고
    • Crystallographic analysis of lac repressor bound to natural operator O1
    • Bell C E and Lewis M 2001 Crystallographic analysis of lac repressor bound to natural operator O1 J. Mol. Biol. 312 921-6
    • (2001) J. Mol. Biol. , vol.312 , Issue.5 , pp. 921-926
    • Bell, C.E.1    Lewis, M.2
  • 77
    • 33745595880 scopus 로고    scopus 로고
    • Modeling the Lac repressor-operator assembly: The influence of DNA looping on Lac repressor conformation
    • Swigon D, Coleman B D and Olson W K 2006 Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation Proc. Natl Acad. Sci. USA 103 9879-84
    • (2006) Proc. Natl Acad. Sci. USA , vol.103 , Issue.26 , pp. 9879-9884
    • Swigon, D.1    Coleman, B.D.2    Olson, W.K.3
  • 78
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations: I. the theory of linear systems
    • Jacobson H and Stockmayer W H 1950 Intramolecular reaction in polycondensations: I. The theory of linear systems J. Chem. Phys. 18 1600-6
    • (1950) J. Chem. Phys. , vol.18 , Issue.12 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.H.2
  • 79
    • 0000323202 scopus 로고
    • Macrocyclization equilibria: II. Poly(dimethylsiloxane)
    • Flory P J, Suter U W and Mutter M 1976 Macrocyclization equilibria: II. Poly(dimethylsiloxane) J. Am. Chem. Soc. 98 5733-9
    • (1976) J. Am. Chem. Soc. , vol.98 , Issue.19 , pp. 5733-5739
    • Flory, P.J.1    Suter, U.W.2    Mutter, M.3
  • 80
    • 0020403941 scopus 로고
    • Loop formation in polynucleotide chains: I. Theory of hairpin loop closure
    • Marky N L and Olson W K 1982 Loop formation in polynucleotide chains: I. Theory of hairpin loop closure Biopolymers 21 2329-44
    • (1982) Biopolymers , vol.21 , Issue.12 , pp. 2329-2344
    • Marky, N.L.1    Olson, W.K.2
  • 81
    • 0000545475 scopus 로고
    • Ring-closure probabilities for twisted wormlike chains-applications to DNA
    • Shimada J and Yamakawa H 1984 Ring-closure probabilities for twisted wormlike chains-applications to DNA Macromolecules 17 689-98
    • (1984) Macromolecules , vol.17 , Issue.4 , pp. 689-698
    • Shimada, J.1    Yamakawa, H.2
  • 82
    • 0022413269 scopus 로고
    • Analysis of the ring-closure probabilities of isotropic wormlike chains: Application to duplex DNA
    • Hagerman P J 1985 Analysis of the ring-closure probabilities of isotropic wormlike chains: application to duplex DNA Biopolymers 24 1881-97
    • (1985) Biopolymers , vol.24 , Issue.10 , pp. 1881-1897
    • Hagerman, P.J.1
  • 83
    • 0023042215 scopus 로고
    • Ring closure probabilities for DNA fragments by Monte Carlo simulation
    • Levene S D and Crothers D M 1986 Ring closure probabilities for DNA fragments by Monte Carlo simulation J. Mol. Biol. 189 61-72
    • (1986) J. Mol. Biol. , vol.189 , Issue.1 , pp. 61-72
    • Levene, S.D.1    Crothers, D.M.2
  • 84
    • 0031880930 scopus 로고    scopus 로고
    • Looping dynamics of linear DNA molecules and the effect of DNA curvature: A study by Brownian dynamics simulation
    • Merlitz H, Rippe K, Klenin K V and Langowski J 1998 Looping dynamics of linear DNA molecules and the effect of DNA curvature: a study by Brownian dynamics simulation Biophys. J. 74 773-9
    • (1998) Biophys. J. , vol.74 , Issue.2 , pp. 773-779
    • Merlitz, H.1    Rippe, K.2    Klenin, K.V.3    Langowski, J.4
  • 85
    • 0033539595 scopus 로고    scopus 로고
    • Equilibrium distributions of topological states in circular DNA: Interplay of supercoiling and knotting
    • Podtelezhnikov A A, Cozzarelli N R and Vologodskii A V 1999 Equilibrium distributions of topological states in circular DNA: interplay of supercoiling and knotting Proc. Natl Acad. Sci. USA 96 12974-9
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , Issue.23 , pp. 12974-12979
    • Podtelezhnikov, A.A.1    Cozzarelli, N.R.2    Vologodskii, A.V.3
  • 86
    • 0033729723 scopus 로고    scopus 로고
    • Multimerization-cyclization of DNA fragments as a method of conformational analysis
    • Podtelezhnikov A A, Mao C D, Seeman N C and Vologodskii A 2000 Multimerization-cyclization of DNA fragments as a method of conformational analysis Biophys. J. 79 2692-704
    • (2000) Biophys. J. , vol.79 , Issue.5 , pp. 2692-2704
    • Podtelezhnikov, A.A.1    Mao, C.D.2    Seeman, N.C.3    Vologodskii, A.4
  • 87
    • 0037215722 scopus 로고    scopus 로고
    • Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization
    • Zhang Y L and Crothers D M 2003 Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization Biophys. J. 84 136-53
    • (2003) Biophys. J. , vol.84 , Issue.1 , pp. 136-153
    • Zhang, Y.L.1    Crothers, D.M.2
  • 88
    • 7544230445 scopus 로고    scopus 로고
    • Effect of spontaneous curvature and sequence disorder on cyclization of fluctuating filaments
    • Rappaport S and Rabin Y 2004 Effect of spontaneous curvature and sequence disorder on cyclization of fluctuating filaments Macromolecules 37 7847-9
    • (2004) Macromolecules , vol.37 , Issue.21 , pp. 7847-7849
    • Rappaport, S.1    Rabin, Y.2
  • 89
    • 3943108162 scopus 로고    scopus 로고
    • Exact results for a semiflexible polymer chain in an aligning field
    • Spakowitz A J and Wang Z G 2004 Exact results for a semiflexible polymer chain in an aligning field Macromolecules 37 5814-23
    • (2004) Macromolecules , vol.37 , Issue.15 , pp. 5814-5823
    • Spakowitz, A.J.1    Wang, Z.G.2
  • 90
    • 28844465153 scopus 로고    scopus 로고
    • End-to-end distance vector distribution with fixed end orientations for the wormlike chain model
    • Spakowitz A J and Wang Z G 2005 End-to-end distance vector distribution with fixed end orientations for the wormlike chain model Phys. Rev. E 72 041802
    • (2005) Phys. Rev. , vol.72 , Issue.4 , pp. 041802
    • Spakowitz, A.J.1    Wang, Z.G.2
  • 91
    • 18244404581 scopus 로고    scopus 로고
    • Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules
    • Ranjith P, Sunil Kumar P B and Menon G I 2005 Distribution functions, loop formation probabilities, and force-extension relations in a model for short double-stranded DNA molecules Phys. Rev. Lett. 94 138102
    • (2005) Phys. Rev. Lett. , vol.94 , Issue.13 , pp. 138102
    • Ranjith, P.1    Sunil Kumar, P.B.2    Menon, G.I.3
  • 92
    • 27944487890 scopus 로고    scopus 로고
    • Statistics of loop formation along double helix DNAs
    • Yan J, Kawamura R and Marko J F 2005 Statistics of loop formation along double helix DNAs Phys. Rev. E 71 061905
    • (2005) Phys. Rev. , vol.71 , Issue.6 , pp. 061905
    • Yan, J.1    Kawamura, R.2    Marko, J.F.3
  • 93
    • 28844474555 scopus 로고    scopus 로고
    • Protein-mediated DNA loops: Effects of protein bridge size and kinks
    • Douarche N and Cocco S 2005 Protein-mediated DNA loops: effects of protein bridge size and kinks Phys. Rev. E 72 061902
    • (2005) Phys. Rev. , vol.72 , Issue.6 , pp. 061902
    • Douarche, N.1    Cocco, S.2
  • 95
    • 33644791019 scopus 로고    scopus 로고
    • Generalized theory of semiflexible polymers
    • Wiggins P A and Nelson P C 2006 Generalized theory of semiflexible polymers Phys. Rev. E 73 031906
    • (2006) Phys. Rev. , vol.73 , Issue.3 , pp. 031906
    • Wiggins, P.A.1    Nelson, P.C.2
  • 96
    • 33644891042 scopus 로고    scopus 로고
    • Wormlike chain statistics with twist and fixed ends
    • Spakowitz A J 2006 Wormlike chain statistics with twist and fixed ends Europhys. Lett. 73 684-90
    • (2006) Europhys. Lett. , vol.73 , Issue.5 , pp. 684-690
    • Spakowitz, A.J.1
  • 98
    • 0028365289 scopus 로고
    • Quality and position of the three lac operators of E. coli define efficiency of repression
    • Oehler S, Amouyal M, Kolkhof P, von Wilcken-Bergmann B and Muller-Hill B 1994 Quality and position of the three lac operators of E. coli define efficiency of repression EMBO J. 13 3348-55
    • (1994) EMBO J. , vol.13 , pp. 3348-3355
    • Oehler, S.1    Amouyal, M.2    Kolkhof, P.3    Von Wilcken-Bergmann, B.4    Muller-Hill, B.5
  • 99
    • 18744391399 scopus 로고    scopus 로고
    • Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
    • Villa E, Balaeff A and Schulten K 2005 Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation Proc. Natl Acad. Sci. USA 102 6783-8
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , Issue.19 , pp. 6783-6788
    • Villa, E.1    Balaeff, A.2    Schulten, K.3
  • 100
    • 2142855754 scopus 로고
    • DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor
    • Krämer H, Amouyal M, Nordheim A and Müller-Hill B 1988 DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor EMBO J. 7 547-56
    • (1988) EMBO J. , vol.7 , pp. 547-556
    • Krämer, H.1    Amouyal, M.2    Nordheim, A.3    Müller-Hill, B.4
  • 101
    • 55849089592 scopus 로고    scopus 로고
    • Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes
    • Saiz L and Vilar J M G 2007 Multilevel deconstruction of the in vivo behavior of looped DNA-protein complexes PLoS ONE 2 e355-1-7
    • (2007) PLoS ONE , vol.2 , Issue.4 , pp. 355
    • Saiz, L.1    Vilar, J.M.G.2
  • 103
    • 0034227093 scopus 로고    scopus 로고
    • Conformational statistics of stiff macromolecules as solutions to partial differential equations on the rotation and motion groups
    • Chirikjian G S and Wang Y 2000 Conformational statistics of stiff macromolecules as solutions to partial differential equations on the rotation and motion groups Phys. Rev. E 62 880-92
    • (2000) Phys. Rev. , vol.62 , Issue.1 , pp. 880-892
    • Chirikjian, G.S.1    Wang, Y.2
  • 104
    • 44949249758 scopus 로고    scopus 로고
    • End-to-end distribution for a wormlike chain in arbitrary dimensions
    • Mehraeen S, Sudhanshu B, Koslover E F and Spakowitz A J 2008 End-to-end distribution for a wormlike chain in arbitrary dimensions Phys. Rev. E 77 0601803
    • (2008) Phys. Rev. , vol.77 , Issue.6 , pp. 061803
    • Mehraeen, S.1    Sudhanshu, B.2    Koslover, E.F.3    Spakowitz, A.J.4
  • 107
    • 34547659294 scopus 로고    scopus 로고
    • Effects of sequence disorder on DNA looping and cyclization
    • Popov Y O and Tkachenko A V 2007 Effects of sequence disorder on DNA looping and cyclization Phys. Rev. E 76 021901
    • (2007) Phys. Rev. , vol.76 , Issue.2 , pp. 021901
    • Popov, Y.O.1    Tkachenko, A.V.2
  • 108
    • 0000323998 scopus 로고    scopus 로고
    • A continuum rod model of sequence-dependent DNA structure
    • Manning R S, Maddocks J H and Kahn J D 1996 A continuum rod model of sequence-dependent DNA structure J. Chem. Phys. 105 5626-46
    • (1996) J. Chem. Phys. , vol.105 , Issue.13 , pp. 5626-5646
    • Manning, R.S.1    Maddocks, J.H.2    Kahn, J.D.3
  • 109
    • 3042572330 scopus 로고    scopus 로고
    • Implications of the dependence of the elastic properties of DNA on nucleotide sequence
    • Olson W K, Swigon D and Coleman B D 2004 Implications of the dependence of the elastic properties of DNA on nucleotide sequence Phil. Trans. R. Soc. Lond. A 362 1403-22
    • (2004) Phil. Trans. R. Soc. Lond. , vol.362 , Issue.1820 , pp. 1403-1422
    • Olson, W.K.1    Swigon, D.2    Coleman, B.D.3
  • 110
    • 44949122468 scopus 로고    scopus 로고
    • Sequence-dependent effects on the properties of semiflexible biopolymers
    • Zhou Z C and Joos B 2008 Sequence-dependent effects on the properties of semiflexible biopolymers Phys. Rev. E 77 061906
    • (2008) Phys. Rev. , vol.77 , Issue.6 , pp. 061906
    • Zhou, Z.C.1    Joos, B.2
  • 111
    • 0030058275 scopus 로고    scopus 로고
    • Effect of supercoiling on the juxtaposition and relative orientation of DNA sites
    • Vologodskii A and Cozzarelli N R 1996 Effect of supercoiling on the juxtaposition and relative orientation of DNA sites Biophys. J. 70 2548-56
    • (1996) Biophys. J. , vol.70 , Issue.6 , pp. 2548-2556
    • Vologodskii, A.1    Cozzarelli, N.R.2
  • 112
    • 0034126370 scopus 로고    scopus 로고
    • Monte Carlo implementation of supercoiled double-stranded DNA
    • Zhang Y, Zhou H and Ou-Yang Z-C 2000 Monte Carlo implementation of supercoiled double-stranded DNA Biophys. J. 78 1979-87
    • (2000) Biophys. J. , vol.78 , Issue.4 , pp. 1979-1987
    • Zhang, Y.1    Zhou, H.2    Ou-Yang, Z.-C.3
  • 114
    • 17944383822 scopus 로고    scopus 로고
    • Elastic rod model of a DNA loop in the lac operon
    • Balaeff A, Mahadevan L and Schulten K 1999 Elastic rod model of a DNA loop in the lac operon Phys. Rev. Lett. 83 4900-3
    • (1999) Phys. Rev. Lett. , vol.83 , Issue.23 , pp. 4900-4903
    • Balaeff, A.1    Mahadevan, L.2    Schulten, K.3
  • 117
    • 33645086141 scopus 로고    scopus 로고
    • Modeling DNA loops using the theory of elasticity
    • Balaeff A, Mahadevan L and Schulten K 2006 Modeling DNA loops using the theory of elasticity Phys. Rev. E 73 031919
    • (2006) Phys. Rev. , vol.73 , Issue.3 , pp. 031919
    • Balaeff, A.1    Mahadevan, L.2    Schulten, K.3
  • 118
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • Cloutier T E and Widom J 2004 Spontaneous sharp bending of double-stranded DNA Mol. Cell 14 355-62
    • (2004) Mol. Cell , vol.14 , Issue.3 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 119
    • 0033585029 scopus 로고    scopus 로고
    • Designed hyperstable Lac repressor: DNA loop topologies suggest alternative loop geometries
    • Mehta R A and Kahn J D 1999 Designed hyperstable Lac repressor: DNA loop topologies suggest alternative loop geometries J. Mol. Biol. 294 67-77
    • (1999) J. Mol. Biol. , vol.294 , Issue.1 , pp. 67-77
    • Mehta, R.A.1    Kahn, J.D.2
  • 120
    • 25844459690 scopus 로고    scopus 로고
    • Single-molecule spectroscopic determination of Lac repressor-DNA loop conformation
    • Morgan M A, Okamoto K, Kahn J D and English D S 2005 Single-molecule spectroscopic determination of Lac repressor-DNA loop conformation Biophys. J. 89 2588-96
    • (2005) Biophys. J. , vol.89 , Issue.4 , pp. 2588-2596
    • Morgan, M.A.1    Okamoto, K.2    Kahn, J.D.3    English, D.S.4
  • 121
    • 0037306915 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer over ∼130 basepairs in hyperstable lac repressor-DNA loops
    • Edelman L M, Cheong R and Kahn J D 2003 Fluorescence resonance energy transfer over ∼130 basepairs in hyperstable lac repressor-DNA loops Biophys. J. 84 1131-45
    • (2003) Biophys. J. , vol.84 , Issue.2 , pp. 1131-1145
    • Edelman, L.M.1    Cheong, R.2    Kahn, J.D.3
  • 122
    • 43149113705 scopus 로고    scopus 로고
    • Geometry of mediating protein affects the probability of loop formation in DNA
    • Agrawal N J, Radhakrishnan R and Purohit P K 2008 Geometry of mediating protein affects the probability of loop formation in DNA Biophys. J. 94 3150-8
    • (2008) Biophys. J. , vol.94 , Issue.8 , pp. 3150-3158
    • Agrawal, N.J.1    Radhakrishnan, R.2    Purohit, P.K.3


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