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Volumn 8, Issue 10, 2013, Pages

Poly(dA:dT)-Rich DNAs Are Highly Flexible in the Context of DNA Looping

Author keywords

[No Author keywords available]

Indexed keywords

DNA; LAC REPRESSOR; LIGASE; POLY(DEOXYADENYLATE DEOXYTHYMIDYLATE);

EID: 84885396500     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0075799     Document Type: Article
Times cited : (38)

References (77)
  • 1
    • 68349125112 scopus 로고    scopus 로고
    • What controls nucleosome positions?
    • Segal E, Widom J, (2009) What controls nucleosome positions? Trends Genet 25: 335-343.
    • (2009) Trends Genet , vol.25 , pp. 335-343
    • Segal, E.1    Widom, J.2
  • 2
    • 76949093375 scopus 로고    scopus 로고
    • Nucleosome positioning: How is it established, and why does it matter?
    • Radman-Livaja M, Rando OJ, (2010) Nucleosome positioning: How is it established, and why does it matter? Dev Biol 339: 258-266.
    • (2010) Dev Biol , vol.339 , pp. 258-266
    • Radman-Livaja, M.1    Rando, O.J.2
  • 3
    • 84860466555 scopus 로고    scopus 로고
    • Nucleosome positioning: bringing order to the eukaryotic genome
    • Iyer V, (2012) Nucleosome positioning: bringing order to the eukaryotic genome. Trends Cell Biol 22: 250-256.
    • (2012) Trends Cell Biol , vol.22 , pp. 250-256
    • Iyer, V.1
  • 4
    • 84965098202 scopus 로고    scopus 로고
    • Genome DNA sequence variation, evolution and function in bacteria and archea
    • Nishida H, (2012) Genome DNA sequence variation, evolution and function in bacteria and archea. Curr Issues Mol Biol 15: 19-24.
    • (2012) Curr Issues Mol Biol , vol.15 , pp. 19-24
    • Nishida, H.1
  • 5
    • 0033527737 scopus 로고    scopus 로고
    • Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence
    • Widlund HR, Kuduvalli PN, Bengtsson M, Cao H, Tullius TD, et al. (1999) Nucleosome structural features and intrinsic properties of the TATAAACGCC repeat sequence. J Biol Chem 274: 31847-31852.
    • (1999) J Biol Chem , vol.274 , pp. 31847-31852
    • Widlund, H.R.1    Kuduvalli, P.N.2    Bengtsson, M.3    Cao, H.4    Tullius, T.D.5
  • 6
    • 0034610179 scopus 로고    scopus 로고
    • Global structure and mechanical properties of a 10-bp nucleosome positioning motif
    • Roychoudhury M, Sitlani A, Lapham J, Crothers DM, (2000) Global structure and mechanical properties of a 10-bp nucleosome positioning motif. Proc Natl Acad Sci USA 97: 13608-13613.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 13608-13613
    • Roychoudhury, M.1    Sitlani, A.2    Lapham, J.3    Crothers, D.M.4
  • 7
    • 0035704707 scopus 로고    scopus 로고
    • Role of DNA sequence in nucleosome stability and dynamics
    • Widom J, (2001) Role of DNA sequence in nucleosome stability and dynamics. Quart Rev Biophys 34: 1-56.
    • (2001) Quart Rev Biophys , vol.34 , pp. 1-56
    • Widom, J.1
  • 8
    • 2342518189 scopus 로고    scopus 로고
    • Spontaneous sharp bending of double-stranded DNA
    • Cloutier TE, Widom J, (2004) Spontaneous sharp bending of double-stranded DNA. Molec Cell 14: 355-362.
    • (2004) Molec Cell , vol.14 , pp. 355-362
    • Cloutier, T.E.1    Widom, J.2
  • 9
    • 0020612485 scopus 로고
    • Dependence of DNA helix flexibility on base composition
    • Hogan M, LeGrange J, Austin B, (1983) Dependence of DNA helix flexibility on base composition. Nature 304: 752-754.
    • (1983) Nature , vol.304 , pp. 752-754
    • Hogan, M.1    LeGrange, J.2    Austin, B.3
  • 10
    • 77957240284 scopus 로고    scopus 로고
    • DNA curvature and flexibility in vitro and in vivo
    • Peters JP, Maher LJ, (2010) DNA curvature and flexibility in vitro and in vivo. Quart Rev Biophys 43: 22-63.
    • (2010) Quart Rev Biophys , vol.43 , pp. 22-63
    • Peters, J.P.1    Maher, L.J.2
  • 11
    • 79958038927 scopus 로고    scopus 로고
    • Working the kinks out of nucleosomal DNA
    • Olson WK, Zhurkin VB, (2011) Working the kinks out of nucleosomal DNA. Curr Opin Struct Biol 21: 348-357.
    • (2011) Curr Opin Struct Biol , vol.21 , pp. 348-357
    • Olson, W.K.1    Zhurkin, V.B.2
  • 12
    • 3042572330 scopus 로고    scopus 로고
    • Implications of the dependence of the elastic properties of DNA on nucleotide sequence
    • Olson WK, Swigon D, Coleman BD, (2004) Implications of the dependence of the elastic properties of DNA on nucleotide sequence. Phil Trans R Soc Lond A 362: 1403-1422.
    • (2004) Phil Trans R Soc Lond A , vol.362 , pp. 1403-1422
    • Olson, W.K.1    Swigon, D.2    Coleman, B.D.3
  • 13
    • 68149108057 scopus 로고    scopus 로고
    • Using DNA mechanics to predict in vitro nucleosome positions and formation energies
    • Morozov AV, Fortney K, Gaykalov DA, Studitsky VM, Widom J, et al. (2009) Using DNA mechanics to predict in vitro nucleosome positions and formation energies. Nucleic Acids Res 37: 4704-4722.
    • (2009) Nucleic Acids Res , vol.37 , pp. 4704-4722
    • Morozov, A.V.1    Fortney, K.2    Gaykalov, D.A.3    Studitsky, V.M.4    Widom, J.5
  • 14
    • 66149110385 scopus 로고    scopus 로고
    • DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences
    • Balasubramanian S, Xu F, Olson WK, (2009) DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. Biophys J 96: 2245-2260.
    • (2009) Biophys J , vol.96 , pp. 2245-2260
    • Balasubramanian, S.1    Xu, F.2    Olson, W.K.3
  • 15
    • 77957255973 scopus 로고    scopus 로고
    • Sequence dependence of DNA bending rigidity
    • Geggier S, Vologodskii A, (2010) Sequence dependence of DNA bending rigidity. Proc Natl Acad Sci USA 107: 15421-15426.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 15421-15426
    • Geggier, S.1    Vologodskii, A.2
  • 17
    • 75149135277 scopus 로고    scopus 로고
    • G+C content dominates intrinsic nucleosome occupancy
    • Tillo D, Hughes TR, (2009) G+C content dominates intrinsic nucleosome occupancy. BMC Bioinformatics 10: 442.
    • (2009) BMC Bioinformatics , vol.10 , pp. 442
    • Tillo, D.1    Hughes, T.R.2
  • 18
    • 69949132191 scopus 로고    scopus 로고
    • Chromatin organization marks exon-intron structure
    • Schwartz S, Meshorer E, Ast G, (2009) Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 16: 990-995.
    • (2009) Nat Struct Mol Biol , vol.16 , pp. 990-995
    • Schwartz, S.1    Meshorer, E.2    Ast, G.3
  • 20
    • 0029026719 scopus 로고
    • Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure
    • Iyer V, Struhl K, (1995) Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J 14: 2570-2579.
    • (1995) EMBO J , vol.14 , pp. 2570-2579
    • Iyer, V.1    Struhl, K.2
  • 21
    • 60349115060 scopus 로고    scopus 로고
    • Poly(dA:dT) tracts: major determinants of nucleosome organization
    • Segal E, Widom J, (2009) Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol 19: 65-71.
    • (2009) Curr Opin Struct Biol , vol.19 , pp. 65-71
    • Segal, E.1    Widom, J.2
  • 22
    • 57149119464 scopus 로고    scopus 로고
    • Distinct modes of regulation by chromatin encoded through nucleosome positioning signals
    • Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, et al. (2008) Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLOS Comput Biol 4: e1000216.
    • (2008) PLOS Comput Biol , vol.4
    • Field, Y.1    Kaplan, N.2    Fondufe-Mittendorf, Y.3    Moore, I.K.4    Sharon, E.5
  • 23
    • 22744432660 scopus 로고    scopus 로고
    • Genome-scale identification of nucleosome positions in S. cerevisiae
    • Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, et al. (2005) Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 627-630.
    • (2005) Science , vol.309 , pp. 627-630
    • Yuan, G.C.1    Liu, Y.J.2    Dion, M.F.3    Slack, M.D.4    Wu, L.F.5
  • 24
    • 0018372296 scopus 로고
    • Nucleosome cores reconstituted from poly(dA-dT) and the octamer of histones
    • Rhodes D, (1979) Nucleosome cores reconstituted from poly(dA-dT) and the octamer of histones. Nucleic Acids Res 6: 1805-1816.
    • (1979) Nucleic Acids Res , vol.6 , pp. 1805-1816
    • Rhodes, D.1
  • 25
    • 0019867238 scopus 로고
    • Nucleosomes will not form on double-stranded RNA or over poly(dA)·poly(dT) tracts in recombinant DNA
    • Kunkel G, Martinson H, (1981) Nucleosomes will not form on double-stranded RNA or over poly(dA)·poly(dT) tracts in recombinant DNA. Nucleic Acids Res 9: 6869-6888.
    • (1981) Nucleic Acids Res , vol.9 , pp. 6869-6888
    • Kunkel, G.1    Martinson, H.2
  • 26
    • 0020338583 scopus 로고
    • Nucleosome reconstitution on plasmid-insertedpoly(dA)·poly(dT)
    • Prunell A, (1982) Nucleosome reconstitution on plasmid-insertedpoly(dA)·poly(dT). EMBO J 1: 173-179.
    • (1982) EMBO J , vol.1 , pp. 173-179
    • Prunell, A.1
  • 27
    • 0025144957 scopus 로고
    • Effects of DNA sequence and histone-histone interactions on nucleosome placement
    • Shrader TE, Crothers DM, (1990) Effects of DNA sequence and histone-histone interactions on nucleosome placement. J Mol Biol 216: 69-84.
    • (1990) J Mol Biol , vol.216 , pp. 69-84
    • Shrader, T.E.1    Crothers, D.M.2
  • 28
    • 0034999881 scopus 로고    scopus 로고
    • Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites
    • Anderson JD, Widom J, (2001) Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol Cell Biol 21: 3830-3839.
    • (2001) Mol Cell Biol , vol.21 , pp. 3830-3839
    • Anderson, J.D.1    Widom, J.2
  • 29
    • 0011031885 scopus 로고
    • Naturally occurring poly(dA:dT) sequences are upstream promoter elements for constitutive transcription in yeast
    • Struhl K, (1985) Naturally occurring poly(dA:dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci USA 82: 8419-8423.
    • (1985) Proc Natl Acad Sci USA , vol.82 , pp. 8419-8423
    • Struhl, K.1
  • 30
    • 84862984796 scopus 로고    scopus 로고
    • Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast
    • Raveh-Sadka T, Levo M, Shabi U, Shany B, Keren L, Lotan-Pompan M, et al. (2012) Manipulating nucleosome disfavoring sequences allows fine-tune regulation of gene expression in yeast. Nat Genet 44: 743-750.
    • (2012) Nat Genet , vol.44 , pp. 743-750
    • Raveh-Sadka, T.1    Levo, M.2    Shabi, U.3    Shany, B.4    Keren, L.5    Lotan-Pompan, M.6
  • 31
    • 67649710352 scopus 로고    scopus 로고
    • The unique structure of A-tracts and intrinsic DNA bending
    • Haran TE, Mohanty U, (2009) The unique structure of A-tracts and intrinsic DNA bending. Quart Rev Biophys 42: 41-81.
    • (2009) Quart Rev Biophys , vol.42 , pp. 41-81
    • Haran, T.E.1    Mohanty, U.2
  • 32
    • 0023513912 scopus 로고
    • The structure of an oligo(dA)·oligo(dT) tract and its biological implications
    • Nelson HCM, Finch JT, Luisi BF, Klug A, (1987) The structure of an oligo(dA)·oligo(dT) tract and its biological implications. Nature 330: 221-226.
    • (1987) Nature , vol.330 , pp. 221-226
    • Nelson, H.C.M.1    Finch, J.T.2    Luisi, B.F.3    Klug, A.4
  • 33
    • 0034310723 scopus 로고    scopus 로고
    • Poly(dA·dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo
    • Sutter B, Schnappauf G, Thoma F, (2000) Poly(dA·dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucleic Acids Res 28: 4083-4089.
    • (2000) Nucleic Acids Res , vol.28 , pp. 4083-4089
    • Sutter, B.1    Schnappauf, G.2    Thoma, F.3
  • 34
    • 84865546608 scopus 로고    scopus 로고
    • Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization
    • Vafabakhsh R, Ha T, (2012) Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization. Science 337: 1097-1101.
    • (2012) Science , vol.337 , pp. 1097-1101
    • Vafabakhsh, R.1    Ha, T.2
  • 35
    • 84870573112 scopus 로고    scopus 로고
    • Sequence dependence of transcription factor-mediated DNA looping
    • Johnson S, Lindén M, Phillips R, (2012) Sequence dependence of transcription factor-mediated DNA looping. Nucleic Acids Res 40: 7728-7738.
    • (2012) Nucleic Acids Res , vol.40 , pp. 7728-7738
    • Johnson, S.1    Lindén, M.2    Phillips, R.3
  • 37
    • 0033585029 scopus 로고    scopus 로고
    • Designed hyperstable Lac repressor·DNA loop topologies suggest alternative loop geometries
    • Mehta RA, Kahn JD, (1999) Designed hyperstable Lac repressor·DNA loop topologies suggest alternative loop geometries. J Mol Biol 294: 67-77.
    • (1999) J Mol Biol , vol.294 , pp. 67-77
    • Mehta, R.A.1    Kahn, J.D.2
  • 38
    • 0037306915 scopus 로고    scopus 로고
    • Fluorescence resonance energy transfer over 130 basepairs in hyperstable Lac repressor-DNA loops
    • Edelman LM, Cheong R, Kahn JD, (2003) Fluorescence resonance energy transfer over 130 basepairs in hyperstable Lac repressor-DNA loops. Biophys J 84: 1131-1145.
    • (2003) Biophys J , vol.84 , pp. 1131-1145
    • Edelman, L.M.1    Cheong, R.2    Kahn, J.D.3
  • 39
    • 25844459690 scopus 로고    scopus 로고
    • Single-molecule spectroscopic determination of lac repressor-DNA loop conformation
    • Morgan MA, Okamoto K, Kahn J, English DS, (2005) Single-molecule spectroscopic determination of lac repressor-DNA loop conformation. Biophys J 89: 2588-2596.
    • (2005) Biophys J , vol.89 , pp. 2588-2596
    • Morgan, M.A.1    Okamoto, K.2    Kahn, J.3    English, D.S.4
  • 41
    • 0032881569 scopus 로고    scopus 로고
    • A- and T-tract-mediated intrinsic curvature in native DNA between the binding site of upstream activator NtrC and the nifLA promoter of Klebsiella pneumoniae facilitates transcription
    • Cheema AK, Choudhury NR, Das HK, (1999) A- and T-tract-mediated intrinsic curvature in native DNA between the binding site of upstream activator NtrC and the nifLA promoter of Klebsiella pneumoniae facilitates transcription. J Bacteriol 181: 5296-5302.
    • (1999) J Bacteriol , vol.181 , pp. 5296-5302
    • Cheema, A.K.1    Choudhury, N.R.2    Das, H.K.3
  • 42
    • 0034697997 scopus 로고    scopus 로고
    • The effect of the DNA conformation on the rate of NtrC activated transcription of Escherichia coli RNA Polymerase·σ54 holoenzyme
    • Schulz A, Langowski J, Rippe K, (2004) The effect of the DNA conformation on the rate of NtrC activated transcription of Escherichia coli RNA Polymerase·σ54 holoenzyme. J Mol Biol 300: 709-725.
    • (2004) J Mol Biol , vol.300 , pp. 709-725
    • Schulz, A.1    Langowski, J.2    Rippe, K.3
  • 43
    • 0025753820 scopus 로고
    • Transcription activation at a distance by phage Φ 29 protein p4. Effect of bent and non-bent intervening sequences
    • Serrano M, Barthelemy I, Salas M, (1991) Transcription activation at a distance by phage Φ 29 protein p4. Effect of bent and non-bent intervening sequences. J Mol Biol 219: 403-414.
    • (1991) J Mol Biol , vol.219 , pp. 403-414
    • Serrano, M.1    Barthelemy, I.2    Salas, M.3
  • 44
    • 4344689731 scopus 로고    scopus 로고
    • Geometric and dynamic requirements for DNA looping, wrapping and unwrapping in the activation of E. coli glnAp2 transcription by NtrC
    • Lilja AE, Jenssen JR, Kahn JD, (2004) Geometric and dynamic requirements for DNA looping, wrapping and unwrapping in the activation of E. coli glnAp2 transcription by NtrC. J Mol Biol 342: 467-478.
    • (2004) J Mol Biol , vol.342 , pp. 467-478
    • Lilja, A.E.1    Jenssen, J.R.2    Kahn, J.D.3
  • 45
    • 0020695571 scopus 로고
    • Structural features of a phased nucleosome core particle
    • Simpson RT, Stafford DW, (1983) Structural features of a phased nucleosome core particle. Proc Natl Acad Sci USA 80: 51-55.
    • (1983) Proc Natl Acad Sci USA , vol.80 , pp. 51-55
    • Simpson, R.T.1    Stafford, D.W.2
  • 46
    • 0039837085 scopus 로고    scopus 로고
    • Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences
    • Thåström A, Lowary PT, Widlund HR, Cao H, Kubista M, et al. (1999) Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. J Mol Biol 288: 213-229.
    • (1999) J Mol Biol , vol.288 , pp. 213-229
    • Thåström, A.1    Lowary, P.T.2    Widlund, H.R.3    Cao, H.4    Kubista, M.5
  • 47
    • 0025867008 scopus 로고
    • Transcription by single molecules of RNA polymerase observed by light microscopy
    • Schafer DA, Gelles J, Sheetz MP, Landick R, (1991) Transcription by single molecules of RNA polymerase observed by light microscopy. Nature 352: 444-448.
    • (1991) Nature , vol.352 , pp. 444-448
    • Schafer, D.A.1    Gelles, J.2    Sheetz, M.P.3    Landick, R.4
  • 48
    • 0028143652 scopus 로고
    • Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule
    • Yin H, Landick R, Gelles J, (1994) Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule. Biophys J 67: 2468-2478.
    • (1994) Biophys J , vol.67 , pp. 2468-2478
    • Yin, H.1    Landick, R.2    Gelles, J.3
  • 49
    • 0028956979 scopus 로고
    • Measurement of Lactose repressor-mediated loop formation and breakdown in single DNA molecules
    • Finzi L, Gelles J, (1995) Measurement of Lactose repressor-mediated loop formation and breakdown in single DNA molecules. Science 267: 378-380.
    • (1995) Science , vol.267 , pp. 378-380
    • Finzi, L.1    Gelles, J.2
  • 50
  • 51
    • 66249118030 scopus 로고    scopus 로고
    • Concentration and length dependence of DNA looping in transcriptional regulation
    • Han L, Garcia HG, Blumberg S, Towles KB, Beausang JF, et al. (2009) Concentration and length dependence of DNA looping in transcriptional regulation. PLOS ONE 4: e5621.
    • (2009) PLOS ONE , vol.4
    • Han, L.1    Garcia, H.G.2    Blumberg, S.3    Towles, K.B.4    Beausang, J.F.5
  • 52
    • 0001191247 scopus 로고
    • DNA flexibility studied by covalent closure of short fragments into circles
    • Shore D, Langowski J, Baldwin RL, (1981) DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci USA 78: 4833-4837.
    • (1981) Proc Natl Acad Sci USA , vol.78 , pp. 4833-4837
    • Shore, D.1    Langowski, J.2    Baldwin, R.L.3
  • 53
    • 0026796061 scopus 로고
    • DNA bending, flexibility, and helical repeat by cyclization kinetics
    • Crothers DM, Drak J, Kahn J, Levene S, (1992) DNA bending, flexibility, and helical repeat by cyclization kinetics. Methods Enzymol 212: 3-29.
    • (1992) Methods Enzymol , vol.212 , pp. 3-29
    • Crothers, D.M.1    Drak, J.2    Kahn, J.3    Levene, S.4
  • 54
    • 0037453011 scopus 로고    scopus 로고
    • High-throughput approach for detection of DNA bending and flexibility based on cyclization
    • Zhang Y, Crothers DM, (2003) High-throughput approach for detection of DNA bending and flexibility based on cyclization. Proc Natl Acad Sci USA 100: 31613166.
    • (2003) Proc Natl Acad Sci USA , vol.100 , pp. 31613166
    • Zhang, Y.1    Crothers, D.M.2
  • 57
    • 79952326786 scopus 로고    scopus 로고
    • Temperature dependence of DNA persistence length
    • Geggier S, Kotlyar A, Vologodskii A, (2011) Temperature dependence of DNA persistence length. Nucleic Acids Res 39: 1419-1426.
    • (2011) Nucleic Acids Res , vol.39 , pp. 1419-1426
    • Geggier, S.1    Kotlyar, A.2    Vologodskii, A.3
  • 58
    • 33845504065 scopus 로고    scopus 로고
    • Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF
    • Kuznetsov SV, Sugimura S, Vivas P, Crothers DM, Ansari A, (2006) Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF. Proc Natl Acad Sci USA 103: 18515-18520.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 18515-18520
    • Kuznetsov, S.V.1    Sugimura, S.2    Vivas, P.3    Crothers, D.M.4    Ansari, A.5
  • 59
    • 0032512794 scopus 로고    scopus 로고
    • New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning
    • Lowary PT, Widom J, (1998) New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. J Mol Biol 276: 19-42.
    • (1998) J Mol Biol , vol.276 , pp. 19-42
    • Lowary, P.T.1    Widom, J.2
  • 60
    • 14844342574 scopus 로고    scopus 로고
    • DNA twisting flexibility and the formation of sharply looped protein- DNA complexes
    • Cloutier TE, Widom J, (2005) DNA twisting flexibility and the formation of sharply looped protein- DNA complexes. Proc Natl Acad Sci USA 102: 3645-3650.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 3645-3650
    • Cloutier, T.E.1    Widom, J.2
  • 61
    • 3843114319 scopus 로고
    • Intramolecular reaction in polycondensations. I. The theory of linear systems
    • Jacobson H, Stockmayer WH, (1950) Intramolecular reaction in polycondensations. I. The theory of linear systems. J Chem Phys 18: 1600-1606.
    • (1950) J Chem Phys , vol.18 , pp. 1600-1606
    • Jacobson, H.1    Stockmayer, W.H.2
  • 62
    • 0000545475 scopus 로고
    • Ring-closure probabilities for twisted wormlike chains. Application to DNA
    • Shimada J, Yamakawa H, (1984) Ring-closure probabilities for twisted wormlike chains. Application to DNA. Macromolecules 17: 689-698.
    • (1984) Macromolecules , vol.17 , pp. 689-698
    • Shimada, J.1    Yamakawa, H.2
  • 63
    • 0021022977 scopus 로고
    • Energetics of DNA twisting. I. Relation between twist and cyclization probability
    • Shore D, Baldwin RL, (1983) Energetics of DNA twisting. I. Relation between twist and cyclization probability. J Mol Biol 170: 957-981.
    • (1983) J Mol Biol , vol.170 , pp. 957-981
    • Shore, D.1    Baldwin, R.L.2
  • 64
    • 0019870039 scopus 로고
    • Sequence dependence of the helical repeat of DNA in solution
    • Peck L, Wang J, (1981) Sequence dependence of the helical repeat of DNA in solution. Nature 292: 375-378.
    • (1981) Nature , vol.292 , pp. 375-378
    • Peck, L.1    Wang, J.2
  • 65
    • 0019602939 scopus 로고
    • Helical periodicity of DNA, poly(dA)·poly(dT) and poly(dA-dT)·poly(dA-dT) in solution
    • Strauss F, Gaillard C, Prunell A, (1981) Helical periodicity of DNA, poly(dA)·poly(dT) and poly(dA-dT)·poly(dA-dT) in solution. Eur J Biochem 118: 215-222.
    • (1981) Eur J Biochem , vol.118 , pp. 215-222
    • Strauss, F.1    Gaillard, C.2    Prunell, A.3
  • 66
    • 54749084305 scopus 로고    scopus 로고
    • Interconvertible Lac repressor-DNA loops revealed by single-molecule experiments
    • Wong OK, Guthold M, Erie DA, Gelles J, (2008) Interconvertible Lac repressor-DNA loops revealed by single-molecule experiments. PLOS Biol 6: e232.
    • (2008) PLOS Biol , vol.6
    • Wong, O.K.1    Guthold, M.2    Erie, D.A.3    Gelles, J.4
  • 67
    • 43349099320 scopus 로고    scopus 로고
    • Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping
    • Normanno D, Vanzi F, Pavone FS, (2008) Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping. Nucleic Acids Res 36: 2505-2513.
    • (2008) Nucleic Acids Res , vol.36 , pp. 2505-2513
    • Normanno, D.1    Vanzi, F.2    Pavone, F.S.3
  • 69
    • 68349150612 scopus 로고    scopus 로고
    • First-principles calculation of DNA looping in tethered particle experiments
    • Towles KB, Beausang JF, Garcia HG, Phillips R, Nelson PC, (2009) First-principles calculation of DNA looping in tethered particle experiments. Phys Biol 6: 025001.
    • (2009) Phys Biol , vol.6 , pp. 025001
    • Towles, K.B.1    Beausang, J.F.2    Garcia, H.G.3    Phillips, R.4    Nelson, P.C.5
  • 70
    • 0029938053 scopus 로고    scopus 로고
    • Crystal structure of the lactose operon repressor and its complexes with DNA and inducer
    • Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, et al. (1996) Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. Science 271: 1247-1254.
    • (1996) Science , vol.271 , pp. 1247-1254
    • Lewis, M.1    Chang, G.2    Horton, N.C.3    Kercher, M.A.4    Pace, H.C.5
  • 71
    • 18744391399 scopus 로고    scopus 로고
    • Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation
    • Villa E, Balaeff A, Schulten K, (2005) Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation. Proc Natl Acad Sci USA 102: 6783-6788.
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 6783-6788
    • Villa, E.1    Balaeff, A.2    Schulten, K.3
  • 72
    • 33745595880 scopus 로고    scopus 로고
    • Modeling the Lac repressor-operator assembly: the inuence of DNA looping on Lac repressor conformation
    • Swigon D, Coleman BD, Olson WK, (2006) Modeling the Lac repressor-operator assembly: the inuence of DNA looping on Lac repressor conformation. Proc Natl Acad Sci USA 103: 9879-9884.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 9879-9884
    • Swigon, D.1    Coleman, B.D.2    Olson, W.K.3
  • 73
    • 34547852967 scopus 로고    scopus 로고
    • Analysis of in vivo LacRmediated gene repression based on the mechanics of DNA looping
    • Zhang Y, McEwen AE, Crothers DM, Levene SD, Fraser P, (2006) Analysis of in vivo LacRmediated gene repression based on the mechanics of DNA looping. PLOS ONE 1: e136.
    • (2006) PLOS ONE , vol.1
    • Zhang, Y.1    McEwen, A.E.2    Crothers, D.M.3    Levene, S.D.4    Fraser, P.5
  • 74
    • 84867644247 scopus 로고    scopus 로고
    • The effect of nonspecific binding of lambda repressor on DNA looping dynamics
    • Manzo C, Zurla C, Dunlap D, Finzi L, (2012) The effect of nonspecific binding of lambda repressor on DNA looping dynamics. Biophys J 103: 1753-1761.
    • (2012) Biophys J , vol.103 , pp. 1753-1761
    • Manzo, C.1    Zurla, C.2    Dunlap, D.3    Finzi, L.4
  • 75
    • 70350686719 scopus 로고    scopus 로고
    • The role of DNA shape in protein-DNA recognition
    • Rohs R, West S, Sosinsky A, Liu P, Mann R, et al. (2009) The role of DNA shape in protein-DNA recognition. Nature 461: 1248-1253.
    • (2009) Nature , vol.461 , pp. 1248-1253
    • Rohs, R.1    West, S.2    Sosinsky, A.3    Liu, P.4    Mann, R.5
  • 76
    • 0034967389 scopus 로고    scopus 로고
    • Evidence for two mechanisms of palindrome-stimulated deletion in Escherichia coli: single-strand annealing and replication slipped mispairing
    • Bzymek M, Lovett ST, (2001) Evidence for two mechanisms of palindrome-stimulated deletion in Escherichia coli: single-strand annealing and replication slipped mispairing. Genetics 158: 527-540.
    • (2001) Genetics , vol.158 , pp. 527-540
    • Bzymek, M.1    Lovett, S.T.2
  • 77
    • 33847164986 scopus 로고    scopus 로고
    • Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity
    • Garcia H, Grayson P, Han L, Inamdar M, Kondev J, et al. (2007) Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Biopolymers 85: 115-130.
    • (2007) Biopolymers , vol.85 , pp. 115-130
    • Garcia, H.1    Grayson, P.2    Han, L.3    Inamdar, M.4    Kondev, J.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.