Sequence dependence of DNA bending rigidity
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[1] Homer Jacobson,et al. Intramolecular Reaction in Polycondensations. I. The Theory of Linear Systems , 1950 .
[2] Ignacio Tinoco,et al. A new approach to the study of sequence‐dependent properties of polynucleotides , 1970 .
[3] J. Schellman,et al. Flexibility of DNA , 1974, Biopolymers.
[4] V. Zhurkin,et al. Anisotropic flexibility of DNA and the nucleosomal structure. , 1979, Nucleic acids research.
[5] J. Wang,et al. Helical repeat of DNA in solution. , 1979, Proceedings of the National Academy of Sciences of the United States of America.
[6] C. Gaillard,et al. Helical periodicity of DNA, Poly(dA) . poly(dT) and poly(dA-dT). poly(dA-dT) in solution. , 2005, European journal of biochemistry.
[7] L. J. Peck,et al. Sequence dependence of the helical repeat of DNA in solution , 1981, Nature.
[8] R. L. Baldwin,et al. DNA flexibility studied by covalent closure of short fragments into circles. , 1981, Proceedings of the National Academy of Sciences of the United States of America.
[9] M. Frank-Kamenetskii,et al. Premelting of superhelical DNA: an expression for superhelical energy , 1981, FEBS letters.
[10] Harrison H. Barrett,et al. 2 – Theory of Linear Systems , 1981 .
[11] D M Crothers,et al. Bent helical structure in kinetoplast DNA. , 1982, Proceedings of the National Academy of Sciences of the United States of America.
[12] John E. Dennis,et al. Numerical methods for unconstrained optimization and nonlinear equations , 1983, Prentice Hall series in computational mathematics.
[13] R. L. Baldwin,et al. Energetics of DNA twisting. I. Relation between twist and cyclization probability. , 1983, Journal of molecular biology.
[14] Jiro Shimada,et al. Ring-closure probabilities for twisted wormlike chains: application to DNA , 1984 .
[15] B R Amirikyan,et al. Allowance for heterogeneous stacking in the DNA helix-coil transition theory. , 1984, Journal of biomolecular structure & dynamics.
[16] D. Crothers,et al. Ring closure probabilities for DNA fragments by Monte Carlo simulation. , 1986, Journal of molecular biology.
[17] Paul J. Hagerman,et al. Sequence-directed curvature of DNA , 1986, Nature.
[18] Hen-Ming Wu,et al. DNA bending at adenine · thymine tracts , 1986, Nature.
[19] Y. Zivanovic,et al. Helical repeat of DNA in solution. The V curve method. , 1987, Nucleic acids research.
[20] A. Lipanov,et al. Poly(dA)\ṁpoly(dT) is a B-type double helix with a distinctively narrow minor groove , 1987, Nature.
[21] P. Hagerman. Flexibility of DNA. , 1988, Annual review of biophysics and biophysical chemistry.
[22] V V Anshelevich,et al. Variance of writhe for wormlike DNA rings with excluded volume. , 1989, Journal of biomolecular structure & dynamics.
[23] P. Hagerman,et al. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. II. NaCl-dependence of DNA flexibility and helical repeat. , 1990, Journal of molecular biology.
[24] P. Hagerman,et al. Application of the method of phage T4 DNA ligase-catalyzed ring-closure to the study of DNA structure. I. Computational analysis. , 1990, Journal of molecular biology.
[25] A S Benight,et al. How many numbers are required to specify sequence‐dependent properties of polynucleotides? , 1992, Biopolymers.
[26] D. Crothers,et al. DNA bending, flexibility, and helical repeat by cyclization kinetics. , 1992, Methods in enzymology.
[27] I. Brukner,et al. Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. , 1994, Journal of molecular biology.
[28] S. Harvey,et al. Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. , 1995, Biophysical chemistry.
[29] Alexander Bolshoy,et al. CC dinucleotides contribute to the bending of DNA in chromatin , 1995, Nature Structural Biology.
[30] J. SantaLucia,et al. Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.
[31] C. R. Calladine,et al. Conformational characteristics of DNA: empirical classifications and a hypothesis for the conformational behaviour of dinucleotide steps , 1997, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.
[32] V. Zhurkin,et al. DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[33] Stretching a heteropolymer , 1998 .
[34] J. Widom,et al. New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning. , 1998, Journal of molecular biology.
[35] J. Widom,et al. Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences. , 1999, Journal of molecular biology.
[36] G. Bocchinfuso,et al. A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability. , 2000, Biophysical journal.
[37] A. Podtelezhnikov,et al. Multimerization-cyclization of DNA fragments as a method of conformational analysis. , 2000, Biophysical journal.
[38] Solution structure of an A-tract DNA bend. , 2001, Journal of molecular biology.
[39] D. Bhattacharyya,et al. Structural basis of DNA flexibility. , 2001, Indian journal of biochemistry & biophysics.
[40] J. Widom,et al. Role of DNA sequence in nucleosome stability and dynamics , 2001, Quarterly Reviews of Biophysics.
[41] M. Vologodskaia,et al. Contribution of the intrinsic curvature to measured DNA persistence length. , 2002, Journal of molecular biology.
[42] B. Robinson,et al. Sequence-dependent dynamics of duplex DNA: the applicability of a dinucleotide model. , 2002, Biophysical journal.
[43] D. Crothers,et al. Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization. , 2003, Biophysical journal.
[44] T. Richmond,et al. The structure of DNA in the nucleosome core , 2003, Nature.
[45] M. Frank-Kamenetskii,et al. Stacked-unstacked equilibrium at the nick site of DNA. , 2004, Journal of molecular biology.
[46] Alexander Vologodskii,et al. Gapped DNA and cyclization of short DNA fragments. , 2005, Biophysical journal.
[47] Nahum Shiffeldrim,et al. Cyclization of short DNA fragments and bending fluctuations of the double helix. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[48] J. Kahn,et al. Bacterial repression loops require enhanced DNA flexibility. , 2005, Journal of molecular biology.
[49] F. Lankaš. Sequence-Dependent Harmonic Deformability of Nucleic Acids Inferred from Atomistic Molecular Dynamics , 2006 .
[50] A. Vologodskii. Simulation of Equilibrium and Dynamic Properties of Large DNA Molecules , 2006 .
[51] M. Frank-Kamenetskii,et al. Base-stacking and base-pairing contributions into thermal stability of the DNA double helix , 2006, Nucleic acids research.
[52] David Swigon,et al. Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[53] Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets. , 2007, Biophysical journal.
[54] Martin Buck,et al. IHF-binding sites inhibit DNA loop formation and transcription initiation , 2009, Nucleic acids research.
[55] W. Olson,et al. DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. , 2009, Biophysical journal.