TY - JOUR AU - Kratky, O. AU - Porod, G. PY - 1949 DA - 1949// TI - Röntgenuntersuchung gelöster fadenmoleküle JO - Recueil des Travaux Chimiques des Pays-Bas VL - 68 UR - https://doi.org/10.1002/recl.19490681203 DO - 10.1002/recl.19490681203 ID - Kratky1949 ER - TY - JOUR AU - Hagerman, P. J. AU - Zimm, B. H. PY - 1981 DA - 1981// TI - Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains JO - Biopolymers VL - 20 UR - https://doi.org/10.1002/bip.1981.360200709 DO - 10.1002/bip.1981.360200709 ID - Hagerman1981 ER - TY - STD TI - Olson WK, Zhurkin VB. Twenty Years of DNA Bending. In: Sarma & Sarma, editor. Biological Structure and Dynamics Volume 2, The Proceedings of the Ninth Conversation held at The University-SUNY Albany. Adenine Press; 1995. p. 341-4. ID - ref3 ER - TY - JOUR AU - Travers, A. PY - 2013 DA - 2013// TI - Dynamic DNA underpins chromosome dynamics JO - Biophys J VL - 105 UR - https://doi.org/10.1016/j.bpj.2013.10.011 DO - 10.1016/j.bpj.2013.10.011 ID - Travers2013 ER - TY - BOOK AU - Wu, H. -. M. AU - Crothers, D. M. PY - 1984 DA - 1984// TI - The locus of sequence-directed and protein-induced DNA bending ID - Wu1984 ER - TY - JOUR AU - Cloutier, T. AU - Widom, J. PY - 2005 DA - 2005// TI - DNA twisting flexibility and the formation of sharply looped protein–DNA complexes JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0409059102 DO - 10.1073/pnas.0409059102 ID - Cloutier2005 ER - TY - JOUR AU - Wei, J. AU - Czapla, L. AU - Grosner, M. A. AU - Swigon, D. AU - Olson, W. K. PY - 2014 DA - 2014// TI - DNA topology confers sequence specificity to nonspecific architectural proteins JO - Proc Natl Acad Sci U S A VL - 111 UR - https://doi.org/10.1073/pnas.1405016111 DO - 10.1073/pnas.1405016111 ID - Wei2014 ER - TY - JOUR AU - Davis, N. A. AU - Majee, S. S. AU - Kahn, J. D. PY - 1999 DA - 1999// TI - TATA box DNA deformation with and without the TATA box-binding protein JO - J Mol Biol VL - 291 UR - https://doi.org/10.1006/jmbi.1999.2947 DO - 10.1006/jmbi.1999.2947 ID - Davis1999 ER - TY - JOUR AU - Kahn, J. D. AU - Crothers, D. M. PY - 1992 DA - 1992// TI - Protein-induced bending and DNA cyclization JO - Proc Natl Acad Sci U S A VL - 89 UR - https://doi.org/10.1073/pnas.89.14.6343 DO - 10.1073/pnas.89.14.6343 ID - Kahn1992 ER - TY - JOUR AU - Shimada, J. AU - Yamakawa, H. PY - 1984 DA - 1984// TI - Ring-closure probabilities for twisted wormlike chains–application to DNA JO - Macromolecules VL - 17 UR - https://doi.org/10.1021/ma00134a028 DO - 10.1021/ma00134a028 ID - Shimada1984 ER - TY - JOUR AU - Hays, J. B. AU - Magar, M. E. AU - Zimm, B. H. PY - 1969 DA - 1969// TI - Persistence length of DNA JO - Biopolymers VL - 8 UR - https://doi.org/10.1002/bip.1969.360080410 DO - 10.1002/bip.1969.360080410 ID - Hays1969 ER - TY - JOUR AU - Godfrey, J. E. AU - Eisenberg, H. PY - 1976 DA - 1976// TI - The flexibility of low molecular weight double-stranded dna as a function of length: II. Light scattering measurements and the estimation of persistence lengths from light scattering, sedimentation and viscosity JO - Biophys Chem VL - 5 UR - https://doi.org/10.1016/0301-4622(76)80042-7 DO - 10.1016/0301-4622(76)80042-7 ID - Godfrey1976 ER - TY - JOUR AU - Schleif, R. PY - 1992 DA - 1992// TI - DNA looping JO - Annu Rev Biochem VL - 61 UR - https://doi.org/10.1146/annurev.bi.61.070192.001215 DO - 10.1146/annurev.bi.61.070192.001215 ID - Schleif1992 ER - TY - JOUR AU - Jacobson, H. AU - Stockmayer, W. H. PY - 1950 DA - 1950// TI - Intramolecular reaction in polycondensations. I. The theory of linear systems JO - J Chem Phys VL - 18 UR - https://doi.org/10.1063/1.1747547 DO - 10.1063/1.1747547 ID - Jacobson1950 ER - TY - JOUR AU - Levene, S. D. AU - Giovan, S. M. AU - Hanke, A. AU - Shoura, M. J. PY - 2013 DA - 2013// TI - The thermodynamics of DNA loop formation, from J to Z JO - Biochem Soc Trans VL - 41 UR - https://doi.org/10.1042/BST20120324 DO - 10.1042/BST20120324 ID - Levene2013 ER - TY - JOUR AU - Cloutier, T. E. AU - Widom, J. PY - 2004 DA - 2004// TI - Spontaneous sharp bending of double-stranded DNA JO - Mol Cell VL - 14 UR - https://doi.org/10.1016/S1097-2765(04)00210-2 DO - 10.1016/S1097-2765(04)00210-2 ID - Cloutier2004 ER - TY - JOUR AU - Richmond, T. J. AU - Davey, C. A. PY - 2003 DA - 2003// TI - The structure of DNA in the nucleosome core JO - Nature VL - 423 UR - https://doi.org/10.1038/nature01595 DO - 10.1038/nature01595 ID - Richmond2003 ER - TY - JOUR AU - Li, G. AU - Levitus, M. AU - Bustamante, C. AU - Widom, J. PY - 2005 DA - 2005// TI - Rapid spontaneous accessibility of nucleosomal DNA JO - Nat Struct Mol Biol VL - 12 UR - https://doi.org/10.1038/nsmb869 DO - 10.1038/nsmb869 ID - Li2005 ER - TY - JOUR AU - Du, Q. AU - Smith, C. AU - Shiffeldrim, N. AU - Vologodskaia, M. AU - Vologodskii, A. PY - 2005 DA - 2005// TI - Cyclization of short DNA fragments and bending fluctuations of the double helix JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0500983102 DO - 10.1073/pnas.0500983102 ID - Du2005 ER - TY - JOUR AU - Vafabakhsh, R. AU - Ha, T. PY - 2012 DA - 2012// TI - Extreme bendability of DNA less than 100 base pairs long revealed by single-molecule cyclization JO - Science VL - 337 UR - https://doi.org/10.1126/science.1224139 DO - 10.1126/science.1224139 ID - Vafabakhsh2012 ER - TY - JOUR AU - Shore, D. AU - Langowski, J. AU - Baldwin, R. L. PY - 1981 DA - 1981// TI - DNA flexibility studied by covalent closure of short fragments into circles JO - Proc Natl Acad Sci VL - 78 UR - https://doi.org/10.1073/pnas.78.8.4833 DO - 10.1073/pnas.78.8.4833 ID - Shore1981 ER - TY - JOUR AU - Vologodskii, A. AU - Frank-Kamenetskii, M. D. PY - 2013 DA - 2013// TI - Strong bending of the DNA double helix JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt396 DO - 10.1093/nar/gkt396 ID - Vologodskii2013 ER - TY - JOUR AU - Shore, D. AU - Baldwin, R. L. PY - 1983 DA - 1983// TI - Energetics of DNA twisting: I. Relation between twist and cyclization probability JO - J Mol Biol VL - 170 UR - https://doi.org/10.1016/S0022-2836(83)80198-3 DO - 10.1016/S0022-2836(83)80198-3 ID - Shore1983 ER - TY - JOUR AU - Drak, J. AU - Crothers, D. M. PY - 1991 DA - 1991// TI - Helical repeat and chirality effects on DNA gel electrophoretic mobility JO - Proc Natl Acad Sci VL - 88 UR - https://doi.org/10.1073/pnas.88.8.3074 DO - 10.1073/pnas.88.8.3074 ID - Drak1991 ER - TY - JOUR AU - Livshits, M. PY - 1996 DA - 1996// TI - Calculating the probability for cyclization of a short intrinsically curved and twisted DNA fragment JO - Mol Biol VL - 30 ID - Livshits1996 ER - TY - JOUR AU - Crothers, D. M. AU - Drak, J. AU - Kahn, J. D. AU - Levene, S. D. PY - 1992 DA - 1992// TI - DNA bending, flexibility, and helical repeat by cyclization kinetics JO - Methods Enzymol VL - 212 UR - https://doi.org/10.1016/0076-6879(92)12003-9 DO - 10.1016/0076-6879(92)12003-9 ID - Crothers1992 ER - TY - JOUR AU - Hagerman, P. J. PY - 1990 DA - 1990// TI - Sequence-directed curvature of DNA JO - Annu Rev Biochem VL - 59 UR - https://doi.org/10.1146/annurev.bi.59.070190.003543 DO - 10.1146/annurev.bi.59.070190.003543 ID - Hagerman1990 ER - TY - JOUR AU - Zhurkin, V. AU - Ulyanov, N. AU - Gorin, A. AU - Jernigan, R. PY - 1991 DA - 1991// TI - Static and statistical bending of DNA evaluated by Monte Carlo simulations JO - Proc Natl Acad Sci VL - 88 UR - https://doi.org/10.1073/pnas.88.16.7046 DO - 10.1073/pnas.88.16.7046 ID - Zhurkin1991 ER - TY - JOUR AU - Levene, S. D. AU - Crothers, D. M. PY - 1986 DA - 1986// TI - Ring closure probabilities for DNA fragments by Monte Carlo simulation JO - J Mol Biol VL - 189 UR - https://doi.org/10.1016/0022-2836(86)90381-5 DO - 10.1016/0022-2836(86)90381-5 ID - Levene1986 ER - TY - JOUR AU - Zhang, Y. AU - Crothers, D. M. PY - 2003 DA - 2003// TI - Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization JO - Biophys J VL - 84 UR - https://doi.org/10.1016/S0006-3495(03)74838-3 DO - 10.1016/S0006-3495(03)74838-3 ID - Zhang2003 ER - TY - JOUR AU - Czapla, L. AU - Swigon, D. AU - Olson, W. K. PY - 2006 DA - 2006// TI - Sequence-dependent effects in the cyclization of short DNA JO - J Chem Theory Comput VL - 2 UR - https://doi.org/10.1021/ct060025+ DO - 10.1021/ct060025+ ID - Czapla2006 ER - TY - JOUR AU - Diekmann, S. PY - 1989 DA - 1989// TI - Definitions and nomenclature of nucleic acid structure parameters JO - J Mol Biol VL - 205 UR - https://doi.org/10.1016/0022-2836(89)90324-0 DO - 10.1016/0022-2836(89)90324-0 ID - Diekmann1989 ER - TY - JOUR AU - Rohs, R. AU - West, S. M. AU - Sosinsky, A. AU - Liu, P. AU - Mann, R. S. AU - Honig, B. PY - 2009 DA - 2009// TI - The role of DNA shape in protein–DNA recognition JO - Nature VL - 461 UR - https://doi.org/10.1038/nature08473 DO - 10.1038/nature08473 ID - Rohs2009 ER - TY - JOUR AU - Abe, N. AU - Dror, I. AU - Yang, L. AU - Slattery, M. AU - Zhou, T. AU - Bussemaker, H. J. PY - 2015 DA - 2015// TI - Deconvolving the recognition of DNA shape from sequence JO - Cell VL - 161 UR - https://doi.org/10.1016/j.cell.2015.02.008 DO - 10.1016/j.cell.2015.02.008 ID - Abe2015 ER - TY - JOUR AU - Alexandrov, B. S. AU - Fukuyo, Y. AU - Lange, M. AU - Horikoshi, N. AU - Gelev, V. AU - Rasmussen, K. Ø. PY - 2012 DA - 2012// TI - DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells JO - Nucleic Acids Res VL - 40 UR - https://doi.org/10.1093/nar/gks758 DO - 10.1093/nar/gks758 ID - Alexandrov2012 ER - TY - STD TI - Czapla L, Grosner MA, Swigon D, Olson WK. Interplay of protein and DNA structure revealed in simulations of the lac operon. PLoS One. 2013;8(2):e56548. doi:10.1371/journal.pone.0056548. ID - ref36 ER - TY - JOUR AU - Kahn, J. D. AU - Crothers, D. M. PY - 1998 DA - 1998// TI - Measurement of the DNA bend angle induced by the catabolite activator protein using Monte Carlo simulation of cyclization kinetics JO - J Mol Biol VL - 276 UR - https://doi.org/10.1006/jmbi.1997.1515 DO - 10.1006/jmbi.1997.1515 ID - Kahn1998 ER - TY - JOUR AU - Manning, R. S. AU - Maddocks, J. H. AU - Kahn, J. D. PY - 1996 DA - 1996// TI - A continuum rod model of sequence-dependent DNA structure JO - J Chem Phys VL - 105 UR - https://doi.org/10.1063/1.472373 DO - 10.1063/1.472373 ID - Manning1996 ER - TY - JOUR AU - Satchwell, S. C. AU - Drew, H. R. AU - Travers, A. A. PY - 1986 DA - 1986// TI - Sequence periodicities in chicken nucleosome core DNA JO - J Mol Biol VL - 191 UR - https://doi.org/10.1016/0022-2836(86)90452-3 DO - 10.1016/0022-2836(86)90452-3 ID - Satchwell1986 ER - TY - JOUR AU - Goodsell, D. S. AU - Dickerson, R. E. PY - 1994 DA - 1994// TI - Bending and curvature calculations in B-DNA JO - Nucleic Acids Res VL - 22 UR - https://doi.org/10.1093/nar/22.24.5497 DO - 10.1093/nar/22.24.5497 ID - Goodsell1994 ER - TY - JOUR AU - Heath, P. J. AU - Clendenning, J. B. AU - Fujimoto, B. S. AU - Schurr, M. J. PY - 1996 DA - 1996// TI - Effect of bending strain on the torsion elastic constant of DNA JO - J Mol Biol VL - 260 UR - https://doi.org/10.1006/jmbi.1996.0432 DO - 10.1006/jmbi.1996.0432 ID - Heath1996 ER - TY - JOUR AU - Horowitz, D. S. AU - Wang, J. C. PY - 1984 DA - 1984// TI - Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling JO - J Mol Biol VL - 173 UR - https://doi.org/10.1016/0022-2836(84)90404-2 DO - 10.1016/0022-2836(84)90404-2 ID - Horowitz1984 ER - TY - STD TI - Zhou T, Yang L, Lu Y, Dror I, Machado ACD, Ghane T, et al. DNAshape: a method for the high-throughputprediction of DNA structural features on a genomic scale. Nucl. Acids Res. 2013;41(W1):W56-62. doi:10.1093/nar/gkt437. ID - ref43 ER - TY - JOUR AU - Brukner, I. AU - Sanchez, R. AU - Suck, D. AU - Pongor, S. PY - 1995 DA - 1995// TI - Sequence-dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides JO - EMBO J VL - 14 ID - Brukner1995 ER - TY - JOUR AU - Gabrielian, A. AU - Pongor, S. PY - 1996 DA - 1996// TI - Correlation of intrinsic DNA curvature with DNA property periodicity JO - FEBS Lett VL - 393 UR - https://doi.org/10.1016/0014-5793(96)00855-1 DO - 10.1016/0014-5793(96)00855-1 ID - Gabrielian1996 ER - TY - JOUR AU - Ulyanov, N. B. AU - James, T. L. PY - 1995 DA - 1995// TI - Statistical analysis of DNA duplex structural features JO - Methods Enzymol VL - 261 UR - https://doi.org/10.1016/S0076-6879(95)61006-5 DO - 10.1016/S0076-6879(95)61006-5 ID - Ulyanov1995 ER - TY - JOUR AU - Rachofsky, E. L. AU - Ross, J. AU - Osman, R. PY - 2001 DA - 2001// TI - Conformation and dynamics of normal and damaged DNA JO - Comb Chem High Throughput Screen VL - 4 UR - https://doi.org/10.2174/1386207013330706 DO - 10.2174/1386207013330706 ID - Rachofsky2001 ER - TY - JOUR AU - Olson, W. K. AU - Gorin, A. A. AU - Lu, X. -. J. AU - Hock, L. M. AU - Zhurkin, V. B. PY - 1998 DA - 1998// TI - DNA sequence-dependent deformability deduced from protein–DNA crystal complexes JO - Proc Natl Acad Sci VL - 95 UR - https://doi.org/10.1073/pnas.95.19.11163 DO - 10.1073/pnas.95.19.11163 ID - Olson1998 ER - TY - JOUR AU - Geggier, S. AU - Vologodskii, A. PY - 2010 DA - 2010// TI - Sequence dependence of DNA bending rigidity JO - Proc Natl Acad Sci VL - 107 UR - https://doi.org/10.1073/pnas.1004809107 DO - 10.1073/pnas.1004809107 ID - Geggier2010 ER - TY - JOUR AU - Rosanio, G. AU - Widom, J. AU - Uhlenbeck, O. C. PY - 2015 DA - 2015// TI - In vitro selection of DNAs with an increased propensity to form small circles JO - Biopolymers VL - 103 UR - https://doi.org/10.1002/bip.22608 DO - 10.1002/bip.22608 ID - Rosanio2015 ER - TY - JOUR AU - Le, T. T. AU - Kim, H. D. PY - 2014 DA - 2014// TI - Probing the elastic limit of DNA bending JO - Nucleic Acids Res VL - 42 UR - https://doi.org/10.1093/nar/gku735 DO - 10.1093/nar/gku735 ID - Le2014 ER - TY - JOUR AU - Yan, J. AU - Marko, J. F. PY - 2004 DA - 2004// TI - Localized single-stranded bubble mechanism for cyclization of short double helix DNA JO - Phys Rev Lett VL - 93 UR - https://doi.org/10.1103/PhysRevLett.93.108108 DO - 10.1103/PhysRevLett.93.108108 ID - Yan2004 ER - TY - JOUR AU - Shin, J. AU - Lee, O. -. C. AU - Sung, W. PY - 2015 DA - 2015// TI - How a short double-stranded DNA bends JO - J Chem Phys VL - 142 UR - https://doi.org/10.1063/1.4916379 DO - 10.1063/1.4916379 ID - Shin2015 ER - TY - JOUR AU - Alexandrowicz, Z. PY - 1969 DA - 1969// TI - Monte Carlo of chains with excluded volume: a way to evade sample attrition JO - J Chem Phys VL - 51 UR - https://doi.org/10.1063/1.1672034 DO - 10.1063/1.1672034 ID - Alexandrowicz1969 ER - TY - JOUR AU - Yamakawa, H. AU - Stockmayer, W. PY - 1972 DA - 1972// TI - Statistical mechanics of wormlike chains. II. Excluded volume effects JO - J Chem Phys VL - 57 UR - https://doi.org/10.1063/1.1678675 DO - 10.1063/1.1678675 ID - Yamakawa1972 ER -