Biophysics of DNA

Preface 1. DNA structures 2. Conformational transitions 3. Equilibrium large-scale conformational properties of DNA 4. DNA dynamics 5. DNA-protein interaction 6. Circular DNA Index.

[1]  M. Fixman,et al.  Diffusion‐controlled intrachain reactions of polymers. I Theory , 1974 .

[2]  P. Gennes Scaling Concepts in Polymer Physics , 1979 .

[3]  D. Crothers,et al.  Conformation of a bulge‐containing oligomer from a hot‐spot sequence by NMR and energy minimization , 1989, Biopolymers.

[4]  O. Krichevsky,et al.  Fluorescence correlation spectroscopy: the technique and its applications , 2002 .

[5]  J. Schellman,et al.  Compact form of DNA induced by spermidine , 1976, Nature.

[6]  N. Seeman,et al.  Double-stranded DNA homology produces a physical signature , 2010, Proceedings of the National Academy of Sciences.

[7]  Alexander Vologodskii,et al.  Strong bending of the DNA double helix , 2013, Nucleic acids research.

[8]  Evan T. Geller,et al.  Patterns and rates of exonic de novo mutations in autism spectrum disorders , 2012, Nature.

[9]  Jie Yan,et al.  Localized single-stranded bubble mechanism for cyclization of short double helix DNA. , 2004, Physical review letters.

[10]  D. Turner,et al.  Laser temperature-jump study of stacking in adenylic acid polymers. , 1979, Biochemistry.

[11]  K. Downing,et al.  Cryoelectron microscopy of λ phage DNA condensates in vitreous ice: The fine structure of DNA toroids , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[12]  A. Podtelezhnikov,et al.  Large-scale effects of transcriptional DNA supercoiling in vivo. , 1999, Journal of molecular biology.

[13]  M. Vologodskaia,et al.  Contribution of the intrinsic curvature to measured DNA persistence length. , 2002, Journal of molecular biology.

[14]  V. Anshelevich,et al.  Torsional and bending rigidity of the double helix from data on small DNA rings. , 1985, Journal of biomolecular structure & dynamics.

[15]  Leroy F. Liu,et al.  Transcription generates positively and negatively supercoiled domains in the template , 1988, Cell.

[16]  H. Eisenberg,et al.  Studies of the temperature-dependent conformation and phase separation of polyriboadenylic acid solutions at neutral pH. , 1967, Journal of molecular biology.

[17]  K. Breslauer,et al.  Influence of loop residues on the relative stabilities of DNA hairpin structures. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[18]  H. Berman,et al.  Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes. , 1995, Biophysical journal.

[19]  K. Drlica,et al.  Control of bacterial DNA supercoiling , 1992, Molecular microbiology.

[20]  P. Hsieh,et al.  The kinetics of spontaneous DNA branch migration. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[21]  D. Patel,et al.  Structure, dynamics, and energetics of deoxyguanosine . thymidine wobble base pair formation in the self-complementary d(CGTGAATTCGCG) duplex in solution. , 1982, Biochemistry.

[22]  P. Rothemund Folding DNA to create nanoscale shapes and patterns , 2006, Nature.

[23]  Grosberg AYu,et al.  On the toroidal condensed state of closed circular DNA. , 1985 .

[24]  M. Maestre,et al.  Circular dichroism spectra of oriented and unoriented deoxyribonucleic acid films--a preliminary study. , 1970, Journal of molecular biology.

[25]  L. J. Peck,et al.  Flipping of cloned d(pCpG)n.d(pCpG)n DNA sequences from right- to left-handed helical structure by salt, Co(III), or negative supercoiling. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[26]  J. Elf,et al.  Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell , 2007, Science.

[27]  D. Stigter A comparison of Manning's polyelectrolyte theory with the cylindrical Gouy model , 1978 .

[28]  A. S. Benight,et al.  Thermodynamic stability of the 5′ dangling‐ended DNA hairpins formed from sequences 5′‐(XY)2GGATAC(T)4GTATCC‐3′, where X, Y = A,T,G,C , 1990, Biopolymers.

[29]  A. Lane,et al.  Comparison of the thermodynamic stabilities and solution conformations of DNA.RNA hybrids containing purine-rich and pyrimidine-rich strands with DNA and RNA duplexes. , 1996, Biochemistry.

[30]  A T Ansevin,et al.  High‐resolution thermal denaturation of DNA. I. Theoretical and practical considerations for the resolution of thermal subtransitions , 1976, Biopolymers.

[31]  Núria Forns,et al.  Single-molecule derivation of salt dependent base-pair free energies in DNA , 2010, Proceedings of the National Academy of Sciences.

[32]  S. Mirkin,et al.  Formation of (dA-dT)n cruciforms in Escherichia coli cells under different environmental conditions , 1991, Journal of bacteriology.

[33]  A. Vologodskii DNA Extension under the Action of an External Force , 1994 .

[34]  The statistics of superhelicity. , 1978, Journal of molecular biology.

[35]  Gerald S. Manning,et al.  Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions I. Colligative Properties , 1969 .

[36]  D. Reichman,et al.  Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6. , 2007, Molecular cell.

[37]  Richard Lavery,et al.  Kinking occurs during molecular dynamics simulations of small DNA minicircles. , 2006, Structure.

[38]  L. J. Peck,et al.  DNA supercoiling and its effects on DNA structure and function. , 1983, Cold Spring Harbor symposia on quantitative biology.

[39]  M. Suzuki,et al.  Stereochemical basis of DNA bending by transcription factors. , 1995, Nucleic acids research.

[40]  James C. Wang,et al.  E. coli and M. luteus DNA topoisomerase I can catalyze catenation or decatenation of double-stranded DNA rings , 1980, Cell.

[41]  J. SantaLucia,et al.  Nearest-neighbor thermodynamics of internal A.C mismatches in DNA: sequence dependence and pH effects. , 1998, Biochemistry.

[42]  B R Amirikyan,et al.  Allowance for heterogeneous stacking in the DNA helix-coil transition theory. , 1984, Journal of biomolecular structure & dynamics.

[43]  M. Guéron,et al.  Characterization of base-pair opening in deoxynucleotide duplexes using catalyzed exchange of the imino proton. , 1988, Journal of Molecular Biology.

[44]  Richard Lavery,et al.  Base pair opening within B-DNA: free energy pathways for GC and AT pairs from umbrella sampling simulations. , 2003, Nucleic acids research.

[45]  S. Benkovic,et al.  Real-time observation of bacteriophage T4 gp41 helicase reveals an unwinding mechanism , 2007, Proceedings of the National Academy of Sciences.

[46]  D. Stigter,et al.  Interactions of highly charged colloidal cylinders with applications to double‐stranded DNA , 1977 .

[47]  Y. Lyubchenko,et al.  Direct comparison of theoretical and experimental melting profiles for RFII ΦX174 DNA , 1978, Nature.

[48]  V. Zhurkin,et al.  Sequence-dependent B<-->A transition in DNA evaluated with dimeric and trimeric scales. , 2001, Biophysical journal.

[49]  J. Michael Schurr The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations. , 1979, Biophysical chemistry.

[50]  T. Odijk Polyelectrolytes near the rod limit , 1977 .

[51]  Irreducible representation for nucleotide sequence physical properties and self-consistency of nearest-neighbor dimer sets. , 2007, Biophysical journal.

[52]  D. W. Gruenwedel Salt effects on the denaturation of DNA. 3. A calorimetric investigation of the transition enthalpy of calf thymus DNA in Na2SO4 solutions of varying ionic strength. , 1974, Biochimica et biophysica acta.

[53]  N. Seeman Nanomaterials based on DNA. , 2010, Annual review of biochemistry.

[54]  D. Porschke,et al.  Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix. , 1974, Biophysical chemistry.

[55]  A. Vologodskii Simulation of Equilibrium and Dynamic Properties of Large DNA Molecules , 2006 .

[56]  T. Ha,et al.  Probing single-stranded DNA conformational flexibility using fluorescence spectroscopy. , 2004, Biophysical journal.

[57]  D. Patel,et al.  Conformational transitions in thymidine bulge-containing deoxytridecanucleotide duplexes. Role of flanking sequence and temperature in modulating the equilibrium between looped out and stacked thymidine bulge states. , 1990, The Journal of biological chemistry.

[58]  J. Michael Schurr,et al.  Structure of viral φ29 DNA condensed by simple triamines: A light‐scattering and electron‐microscopy study , 1981, Biopolymers.

[59]  W. Hunter,et al.  Structure of an adenine˙cytosine base pair in DNA and its implications for mismatch repair , 1986, Nature.

[60]  G. Felsenfeld,et al.  Conformation of polyribouridylic acid in solution. , 1970, Journal of molecular biology.

[61]  W. Bauer,et al.  The interaction of closed circular DNA with intercalative dyes. I. The superhelix density of SV40 DNA in the presence and absence of dye. , 1970, Journal of molecular biology.

[62]  T Schlick,et al.  Internal motion of supercoiled DNA: brownian dynamics simulations of site juxtaposition. , 1998, Journal of molecular biology.

[63]  J. Wang,et al.  Knotting of a DNA chain during ring closure. , 1993, Science.

[64]  Hen-Ming Wu,et al.  The locus of sequence-directed and protein-induced DNA bending , 1984, Nature.

[65]  V. Ivanov,et al.  Three-state diagram for DNA. , 1985, Journal of biomolecular structure & dynamics.

[66]  Kurt Binder,et al.  Monte Carlo Simulations in Statistical Physics , 2009, Encyclopedia of Complexity and Systems Science.

[67]  D. Pettijohn,et al.  Supercoils in prokaryotic DNA restrained in vivo. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[68]  James C. Wang Untangling the Double Helix: DNA Entanglement and the Action of the DNA Topoisomerases , 2009 .

[69]  V. Ivanov,et al.  The B to A transition of DNA in solution. , 1974, Journal of molecular biology.

[70]  P. Dervan,et al.  Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. , 1991, Science.

[71]  D. Crothers,et al.  Structural model for an oligonucleotide containing a bulged guanosine by NMR and energy minimization. , 1988, Biochemistry.

[72]  Giuseppe Chirico,et al.  Kinetics of DNA supercoiling studied by Brownian dynamics simulation , 1994 .

[73]  R. Sinden,et al.  Measurement of unrestrained negative supercoiling and topological domain size in living human cells. , 1997, Biochemistry.

[74]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[75]  D. Lilley,et al.  Structures of helical junctions in nucleic acids , 2000, Quarterly Reviews of Biophysics.

[76]  A. Rich,et al.  A computer aided thermodynamic approach for predicting the formation of Z‐DNA in naturally occurring sequences. , 1986, The EMBO journal.

[77]  S. Halford,et al.  Enzyme-mediated DNA looping. , 2004, Annual review of biophysics and biomolecular structure.

[78]  David Stoddart,et al.  Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore , 2009, Proceedings of the National Academy of Sciences.

[79]  S. Mirkin,et al.  Structure of (dG)n.(dC)n under superhelical stress and acid pH. , 1987, Journal of biomolecular structure & dynamics.

[80]  D. Turner,et al.  Solvent effects on the dynamics of (dG‐dC)3 , 1983, Biopolymers.

[81]  Stuart A. Allison,et al.  Brownian dynamics simulation of wormlike chains. Fluorescence depolarization and depolarized light scattering , 1986 .

[82]  C. Benham,et al.  Torsional stress and local denaturation in supercoiled DNA. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[83]  Michael D. Stone,et al.  Structural transitions and elasticity from torque measurements on DNA , 2003, Nature.

[84]  H. M. Sobell,et al.  Visualization of drug--nucleic acid interactions at atomic resolution. VI. Structure of two drug--dinucleoside monophosphate crystalline complexes, ellipticine--5-iodocytidylyy (3'-5') guanosine and 3,5,6,8-tetramethyl-N-methyl phenanthrolinium--5-iodocytidylyl (3'-5') guanosine. , 1979, Journal of molecular biology.

[85]  Alexander Vologodskii,et al.  Kinking the double helix by bending deformation , 2007, Nucleic acids research.

[86]  B. Zimm,et al.  Monte Carlo approach to the analysis of the rotational diffusion of wormlike chains , 1981 .

[87]  D M Crothers,et al.  Intrinsically bent DNA. , 1990, The Journal of biological chemistry.

[88]  J. Michael Schurr,et al.  Torsion dynamics and depolarization of fluorescence of linear macromolecules: II. Fluorescence polarization anisotropy measurements on a clean viral φ29 DNA , 1980 .

[89]  J. Griffith,et al.  Curved helix segments can uniquely orient the topology of supertwisted DNA , 1988, Cell.

[90]  F. Crick,et al.  The structure of DNA. , 1953, Cold Spring Harbor symposia on quantitative biology.

[91]  Hen-Ming Wu,et al.  DNA bending at adenine · thymine tracts , 1986, Nature.

[92]  David Bensimon,et al.  Single-molecule analysis of DNA uncoiling by a type II topoisomerase , 2000, Nature.

[93]  S. Cockroft,et al.  Real-time monitoring of DNA polymerase function and stepwise single-nucleotide DNA strand translocation through a protein nanopore. , 2010, Angewandte Chemie.

[94]  Alexander Vologodskii,et al.  Brownian dynamics simulation of knot diffusion along a stretched DNA molecule. , 2006, Biophysical journal.

[95]  J. Michael Schurr,et al.  Rotational dynamics of DNA from 10−10 to 10−5 seconds: Comparison of theory with optical experiments , 1985, Biopolymers.

[96]  Y. Blagoi,et al.  Magnesium ion effect on the helix‐coil transition of DNA , 1978, Biopolymers.

[97]  J. Schellman,et al.  Flexibility of DNA , 1974, Biopolymers.

[98]  M. Gellert,et al.  DNA gyrase and DNA supercoiling. , 1979, Cold Spring Harbor symposia on quantitative biology.

[99]  N. Cozzarelli,et al.  Formation and resolution of DNA catenanes by DNA gyrase , 1980, Cell.

[100]  V. Ivanov,et al.  CC/GG contacts facilitate the B to A transition of DNA in solution. , 1986, Journal of biomolecular structure & dynamics.

[101]  A. Peterlin Light Scattering by very Stiff Chain Molecules , 1953, Nature.

[102]  I. Tinoco,et al.  Comparison of the kinetics of ribo-, deoxyribo- and hybrid oligonucleotide double-strand formation by temperature-jump kinetics , 1982 .

[103]  V. Katritch,et al.  The effect of intrinsic curvature on conformational properties of circular DNA. , 1997, Biophysical journal.

[104]  Tamar Schlick,et al.  A Combined Wormlike-Chain and Bead Model for Dynamic Simulations of Long Linear DNA , 1997 .

[105]  J. Marko,et al.  How do site-specific DNA-binding proteins find their targets? , 2004, Nucleic acids research.

[106]  A. Vologodskii,et al.  Temperature dependence of DNA persistence length , 2010, Nucleic acids research.

[107]  R. Watson,et al.  The twisted circular form of polyoma viral DNA. , 1965, Proceedings of the National Academy of Sciences of the United States of America.

[108]  R. Warner,et al.  Kinetics of branch migration in double-stranded DNA. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[109]  E. Guth,et al.  Zur innermolekularen, Statistik, insbesondere bei Kettenmolekiilen I , 1934 .

[110]  N. Cozzarelli,et al.  Biochemical topology: applications to DNA recombination and replication. , 1986, Science.

[111]  J. Wang,et al.  Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling. , 1984, Journal of molecular biology.

[112]  Bruno H. Zimm,et al.  Internal condensation of a single DNA molecule , 1979 .

[113]  J. Wang,et al.  Thermodynamic and kinetic studies on the interconversion between the linear and circular forms of phage lambda DNA. , 1966, Journal of molecular biology.

[114]  Annaleen Vermeulen,et al.  Determining DNA Global Structure and DNA Bending by Application of NMR Residual Dipolar Couplings , 2000 .

[115]  R. Wells,et al.  B-Z DNA junctions contain few, if any, nonpaired bases at physiological superhelical densities. , 1985, Journal of Biological Chemistry.

[116]  Michelle D. Wang,et al.  Single-Molecule Studies Reveal Dynamics of DNA Unwinding by the Ring-Shaped T7 Helicase , 2007, Cell.

[117]  A. Vologodskii Bridged DNA Circles: A New Model System To Study DNA Topology , 2012 .

[118]  W. Olson,et al.  DNA sequence-directed organization of chromatin: structure-based computational analysis of nucleosome-binding sequences. , 2009, Biophysical journal.

[119]  M. Muir Physical Chemistry , 1888, Nature.

[120]  R. L. Baldwin,et al.  Energetics of DNA twisting. I. Relation between twist and cyclization probability. , 1983, Journal of molecular biology.

[121]  M. Guéron,et al.  A single mode of DNA base-pair opening drives imino proton exchange , 1987, Nature.

[122]  R. Burgess,et al.  Nonspecific interactions of Escherichia coli RNA polymerase with native and denatured DNA: differences in the binding behavior of core and holoenzyme. , 1978, Biochemistry.

[123]  A. Maxwell,et al.  A model for the mechanism of strand passage by DNA gyrase. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[124]  S. Wölfl,et al.  Transcription of the human corticotropin-releasing hormone gene in NPLC cells is correlated with Z-DNA formation. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[125]  C. Bustamante,et al.  Tension induces a base-paired overstretched DNA conformation , 2012, Proceedings of the National Academy of Sciences.

[126]  M Frank-Kamenetskii,et al.  Conformational and thermodynamic properties of supercoiled DNA. , 1992, Journal of molecular biology.

[127]  J. Šponer,et al.  Refinement of the AMBER Force Field for Nucleic Acids: Improving the Description of α/γ Conformers , 2007 .

[128]  R. L. Baldwin,et al.  Energetics of DNA twisting. II. Topoisomer analysis. , 1983, Journal of molecular biology.

[129]  H. Weintraub,et al.  An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin , 1982, Cell.

[130]  Ignacio Tinoco,et al.  A new approach to the study of sequence‐dependent properties of polynucleotides , 1970 .

[131]  Y. Lyubchenko,et al.  Equilibrium melting of plasmid ColE1 DNA: electron-microscopic visualization. , 1980, Nucleic acids research.

[132]  A. Hochschild 3 Protein-Protein Interactions and DNA Loop Formation , 1990 .

[133]  P. V. von Hippel,et al.  Alteration of the relative stability of dA-dT and dG-dC base pairs in DNA. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[134]  J. Vinograd,et al.  Sedimentation velocity behavior of closed circular SV40 DNA as a function of superhelix density, ionic strength, counterion and temperature. , 1971, Journal of molecular biology.

[135]  R. Pecora,et al.  Brownian dynamics simulations of wormlike chains: dynamic light scattering from a 2311 base pair DNA fragment , 1990 .

[136]  D. Lilley,et al.  Facile cruciform formation by an (A-T)34 sequence from a Xenopus globin gene. , 1985, Journal of molecular biology.

[137]  Yusaku Tagashira,et al.  Stabilities of nearest‐neighbor doublets in double‐helical DNA determined by fitting calculated melting profiles to observed profiles , 1981 .

[138]  D. Lilley,et al.  The structure of branched DNA species , 1993, Quarterly Reviews of Biophysics.

[139]  R. Kaptein,et al.  Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes , 2004, Science.

[140]  Dynamics of small loops in DNA molecules , 2000 .

[141]  N R Cozzarelli,et al.  Effect of supercoiling on the juxtaposition and relative orientation of DNA sites. , 1996, Biophysical journal.

[142]  R. Mann,et al.  Origins of specificity in protein-DNA recognition. , 2010, Annual review of biochemistry.

[143]  K. Klenin,et al.  Effect of excluded volume on topological properties of circular DNA. , 1988, Journal of biomolecular structure & dynamics.

[144]  Ioulia Rouzina,et al.  Thermodynamics of DNA interactions from single molecule stretching experiments. , 2002, Accounts of chemical research.

[145]  E. Lund,et al.  Human U1 RNA genes contain an unusually sensitive nuclease S1 cleavage site within the conserved 3' flanking region. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[146]  L. J. Peck,et al.  Energetics of B-to-Z transition in DNA. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[147]  J. Wang The degree of unwinding of the DNA helix by ethidium. I. Titration of twisted PM2 DNA molecules in alkaline cesium chloride density gradients. , 1974, Journal of molecular biology.

[148]  D. Stock,et al.  Crystal structure of reverse gyrase: insights into the positive supercoiling of DNA , 2002, The EMBO journal.

[149]  K. Svoboda,et al.  Biological applications of optical forces. , 1994, Annual review of biophysics and biomolecular structure.

[150]  Jie Yan,et al.  Transition dynamics and selection of the distinct S-DNA and strand unpeeling modes of double helix overstretching , 2010, Nucleic acids research.

[151]  D. Patel,et al.  Deoxyguanosine-deoxyadenosine pairing in the d(C-G-A-G-A-A-T-T-C-G-C-G) duplex: conformation and dynamics at and adjacent to the dG X dA mismatch site. , 1984, Biochemistry.

[152]  J. Mccammon,et al.  Dynamics of Proteins and Nucleic Acids , 2018 .

[153]  E. Freese,et al.  THE RATE OF DNA STRAND SEPARATION. , 1963, Biochemistry.

[154]  D. Lilley,et al.  Superhelical torsion in cellular DNA responds directly to environmental and genetic factors. , 1990, Proceedings of the National Academy of Sciences of the United States of America.

[155]  J. Wang,et al.  Helical repeat of DNA in solution. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[156]  Ralf Everaers,et al.  Structure and Dynamics of Interphase Chromosomes , 2008, PLoS Comput. Biol..

[157]  J. Stivers,et al.  Uracil DNA glycosylase uses DNA hopping and short-range sliding to trap extrahelical uracils , 2008, Proceedings of the National Academy of Sciences.

[158]  Carlos Bustamante,et al.  Supplemental data for : The Bacteriophage ø 29 Portal Motor can Package DNA Against a Large Internal Force , 2001 .

[159]  R. L. Baldwin,et al.  Cation-induced toroidal condensation of DNA studies with Co3+(NH3)6. , 1980, Journal of molecular biology.

[160]  Maxim D. Frank-Kamenetskii,et al.  Sequence-Dependent Basepair Opening in DNA Double Helix , 2006 .

[161]  B R Amirikyan,et al.  Determination of DNA cooperativity factor. , 1981, Nucleic acids research.

[162]  D. Lang Regular superstructures of purified DNA in ethanolic solutions. , 1973, Journal of molecular biology.

[163]  N. Seeman,et al.  Paranemic crossover DNA: a generalized Holliday structure with applications in nanotechnology. , 2004, Journal of the American Chemical Society.

[164]  R. Sinden,et al.  Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: Analogous measurements in insect and human cells , 1980, Cell.

[165]  A. V. Lukashin,et al.  Statistical mechanics and topology of polymer chains , 1975, Nature.

[166]  K. Struhl,et al.  Determinants of nucleosome positioning , 2013, Nature Structural &Molecular Biology.

[167]  V. Bloomfield,et al.  Macroion Attraction Due to Electrostatic Correlation between Screening Counterions. 1. Mobile Surface-Adsorbed Ions and Diffuse Ion Cloud , 1996 .

[168]  V. Anshelevich,et al.  Statistical mechanics of supercoils and the torsional stiffness of the DNA double helix , 1979, Nature.

[169]  C. Hentschel Homocopolymer sequences in the spacer of a sea urchin histone gene repeat are sensitive to S1 nuclease , 1982, Nature.

[170]  Mark Akeson,et al.  Automated Forward and Reverse Ratcheting of DNA in a Nanopore at Five Angstrom Precision1 , 2012, Nature Biotechnology.

[171]  N. Cozzarelli,et al.  Use of site-specific recombination as a probe of DNA structure and metabolism in vivo. , 1987, Journal of molecular biology.

[172]  R. Legerski,et al.  Extracellular nucleases of Pseudomonas BAL 31. I. Characterization of single strand-specific deoxyriboendonuclease and double-strand deoxyriboexonuclease activities. , 1975, Nucleic acids research.

[173]  J. Wang,et al.  Variation of the average rotation angle of the DNA helix and the superhelical turns of covalently closed cyclic lambda DNA. , 1969, Journal of molecular biology.

[174]  J. R. Fresco,et al.  Polynucleotides. VII. Spectrophotometric study of the kinetics of formation of the two-stranded helical complex resulting from the interaction of polyriboadenylate and polyribouridylate. , 1966, Journal of molecular biology.

[175]  Simona Cocco,et al.  Overstretching and force-driven strand separation of double-helix DNA. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[176]  G. Budworth The Knot Book , 1983 .

[177]  Barry L. Stoddard,et al.  Natural and engineered nicking endonucleases—from cleavage mechanism to engineering of strand-specificity , 2010, Nucleic Acids Res..

[178]  R. Legerski,et al.  Analysis and optimization of recombinant DNA joining reactions. , 1985, Journal of molecular biology.

[179]  Y. Lyubchenko,et al.  Visualization of supercoiled DNA with atomic force microscopy in situ. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[180]  M. Fixman,et al.  Diffusion‐controlled intrachain reactions of polymers. II Results for a pair of terminal reactive groups , 1974 .

[181]  R. Owen,et al.  Determination of DNA base compositions from melting profiles in dilute buffers , 1969, Biopolymers.

[182]  A. Courey,et al.  Cruciform formation in a negatively supercoiled DNA may be kinetically forbidden under physiological conditions , 1983, Cell.

[183]  Y. Lyubchenko,et al.  Fine structure of DNA melting curves , 1976, Biopolymers.

[184]  D. Case,et al.  Ion counting from explicit-solvent simulations and 3D-RISM. , 2014, Biophysical journal.

[185]  M. Fixman,et al.  Theory of DNA melting curves , 1977, Biopolymers.

[186]  V V Anshelevich,et al.  Variance of writhe for wormlike DNA rings with excluded volume. , 1989, Journal of biomolecular structure & dynamics.

[187]  A Libchaber,et al.  Sequence dependent rigidity of single stranded DNA. , 2000, Physical review letters.

[188]  Phoebe A Rice,et al.  Crystal Structure of an IHF-DNA Complex: A Protein-Induced DNA U-Turn , 1996, Cell.

[189]  R. Wells,et al.  Stabilization of Z DNA in vivo by localized supercoiling. , 1989, Science.

[190]  A. Lyubartsev,et al.  Competitive binding of Mg2+, Ca2+, Na+, and K+ ions to DNA in oriented DNA fibers: experimental and Monte Carlo simulation results. , 1999, Biophysical journal.

[191]  Quan Du,et al.  Protein-induced local DNA bends regulate global topology of recombination products. , 2007, Journal of molecular biology.

[192]  V. P. Kumarev,et al.  Energetics of the B-H transition in supercoiled DNA carrying d(CT)x.d(AG)x and d(C)n.d(G)n inserts. , 1989, Nucleic acids research.

[193]  R. Blake,et al.  Stacking energies in DNA. , 1991, The Journal of biological chemistry.

[194]  P. V. von Hippel,et al.  Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. , 1981, Biochemistry.

[195]  I. Tinoco,et al.  DNA-RNA hybrid duplexes containing oligo(dA:rU) sequences are exceptionally unstable and may facilitate termination of transcription. , 1980, Nucleic acids research.

[196]  T. Pologruto,et al.  Solution structure of an A-tract DNA bend. , 2001, Journal of molecular biology.

[197]  J. Wang,et al.  Conformational fluctuations of DNA helix. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[198]  Michael D. Stone,et al.  Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[199]  Omar A Saleh,et al.  Fast, DNA‐sequence independent translocation by FtsK in a single‐molecule experiment , 2004, The EMBO journal.

[200]  Stephen R Quake,et al.  Behavior of complex knots in single DNA molecules. , 2003, Physical review letters.

[201]  F. Frank-Kamenetskii,et al.  Simplification of the empirical relationship between melting temperature of DNA, its GC content and concentration of sodium ions in solution. , 1971, Biopolymers.

[202]  A. Podtelezhnikov,et al.  Simulations of Polymer Cyclization by Brownian Dynamics , 1997 .

[203]  N. Seeman Nucleic acid junctions and lattices. , 1982, Journal of theoretical biology.

[204]  N. Cozzarelli,et al.  Modeling of long‐range electrostatic interactions in DNA , 1995, Biopolymers.

[205]  J. Brahms,et al.  Structural changes in positively and negatively supercoiled DNA. , 1989, European journal of biochemistry.

[206]  A S Benight,et al.  How many numbers are required to specify sequence‐dependent properties of polynucleotides? , 1992, Biopolymers.

[207]  J. Michael Schurr,et al.  Thermodynamics of the first transition in writhe of a small circular DNA by Monte Carlo simulation , 1996, Biopolymers.

[208]  A Klug,et al.  The helical periodicity of DNA on the nucleosome. , 1981, Nucleic acids research.

[209]  James H. White Self-Linking and the Gauss Integral in Higher Dimensions , 1969 .

[210]  N. Davidson,et al.  Kinetics of renaturation of DNA. , 1968, Journal of molecular biology.

[211]  D. Lilley,et al.  The structure of the four-way junction in DNA. , 1993, Annual review of biophysics and biomolecular structure.

[212]  Johan Elf,et al.  The lac Repressor Displays Facilitated Diffusion in Living Cells , 2012, Science.

[213]  P. Hagerman Flexibility of DNA. , 1988, Annual review of biophysics and biophysical chemistry.

[214]  T. Eickbush,et al.  The compaction of DNA helices into either continuous supercoils or folded-fiber rods and toroids , 1978, Cell.

[215]  Jonathan Widom,et al.  Spontaneous sharp bending of double-stranded DNA. , 2004, Molecular cell.

[216]  Robert D. Wells,et al.  Left-handed Z-DNA is induced by supercoiling in physiological ionic conditions , 1982, Nature.

[217]  D. Crothers,et al.  Stability and properties of double and triple helices: dramatic effects of RNA or DNA backbone composition. , 1992, Science.

[218]  A. Godzik,et al.  Topology fingerprint approach to the inverse protein folding problem. , 1992, Journal of molecular biology.

[219]  A. Vologodskii Monte Carlo Simulation of DNA Topological Properties , 2007 .

[220]  J. Champoux,et al.  An activity from mammalian cells that untwists superhelical DNA--a possible swivel for DNA replication (polyoma-ethidium bromide-mouse-embryo cells-dye binding assay). , 1972, Proceedings of the National Academy of Sciences of the United States of America.

[221]  Alexander D. MacKerell,et al.  Atomistic view of base flipping in DNA , 2004, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[222]  C. Dekker,et al.  Friction and torque govern the relaxation of DNA supercoils by eukaryotic topoisomerase IB , 2005, Nature.

[223]  P. Hagerman,et al.  Investigation of the flexibility of DNA using transient electric birefringence , 1981, Biopolymers.

[224]  W. Bauer,et al.  Interaction of closed circular DNA with intercalative dyes. II. The free energy of superhelix formation in SV40 DNA. , 1970, Journal of molecular biology.

[225]  A. Slesarev Positive supercoiling catalysed in vitro by ATP-dependent topoisomerase from Desulfurococcus amylolyticus. , 1988, European journal of biochemistry.

[226]  B. Berne,et al.  Dynamic Light Scattering: With Applications to Chemistry, Biology, and Physics , 1976 .

[227]  L. Nordenskiöld,et al.  Sequence-specific Mg2+-DNA interactions: a molecular dynamics simulation study. , 2011, The journal of physical chemistry. B.

[228]  Joseph A. Bank,et al.  Supporting Online Material Materials and Methods Figs. S1 to S10 Table S1 References Movies S1 to S3 Atomic-level Characterization of the Structural Dynamics of Proteins , 2022 .

[229]  B R Amirikyan,et al.  The ionic strength dependence of the cooperativity factor for DNA melting. , 1987, Journal of biomolecular structure & dynamics.

[230]  J. Wang,et al.  DNA transport by a type II topoisomerase: direct evidence for a two-gate mechanism. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[231]  B. Zimm,et al.  Kinetics of the helix‐coil transition in DNA , 1972, Biopolymers.

[232]  Jeff Gore,et al.  Sequence-Directed DNA Translocation by Purified FtsK , 2005, Science.

[233]  J. SantaLucia,et al.  Nearest-neighbor thermodynamics and NMR of DNA sequences with internal A.A, C.C, G.G, and T.T mismatches. , 1999, Biochemistry.

[234]  J. Dubochet,et al.  Sedimentation and electrophoretic migration of DNA knots and catenanes. , 1998, Journal of molecular biology.

[235]  S. Mirkin,et al.  Structures of homopurine-homopyrimidine tract in superhelical DNA. , 1986, Journal of biomolecular structure & dynamics.

[236]  J. Sturtevant,et al.  Heats of thermally induced helix–coil transitions of DNA in aqueous solution , 1973, Biopolymers.

[237]  F. Pohl,et al.  Antibodies to Z-DNA interact with form V DNA , 1982, Nature.

[238]  A. Vologodskii Theoretical models of DNA topology simplification by type IIA DNA topoisomerases , 2009, Nucleic acids research.

[239]  Bishop,et al.  Statistical mechanics of a nonlinear model for DNA denaturation. , 1989, Physical review letters.

[240]  D. Patel,et al.  Conformational transitions in cytidine bulge-containing deoxytridecanucleotide duplexes: extra cytidine equilibrates between looped out (low temperature) and stacked (elevated temperature) conformations in solution. , 1989, Biochemistry.

[241]  C. Bustamante,et al.  Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules , 1996, Science.

[242]  D. Pulleyblank,et al.  Transition of a cloned d(AT)n-d(AT)n tract to a cruciform in vivo. , 1985, Nucleic acids research.

[243]  N. Hud,et al.  Toroidal DNA condensates: unraveling the fine structure and the role of nucleation in determining size. , 2005, Annual review of biophysics and biomolecular structure.

[244]  Y. Lyubchenko,et al.  Fluctuational opening of the double helix as revealed by theoretical and experimental study of DNA interaction with formaldehyde. , 1976, Journal of molecular biology.

[245]  N. Cozzarelli,et al.  Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements. , 2000, Genes & development.

[246]  J. Langowski,et al.  Brownian dynamics simulations of supercoiled DNA with bent sequences. , 1996, Biophysical journal.

[247]  Charlie Gosse,et al.  Magnetic tweezers: micromanipulation and force measurement at the molecular level. , 2002, Biophysical journal.

[248]  D. Turner,et al.  Improved free-energy parameters for predictions of RNA duplex stability. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[249]  D. Pulleyblank,et al.  The in-vivo occurrence of Z DNA. , 1983, Journal of biomolecular structure & dynamics.

[250]  J. Michael Schurr,et al.  Effect of anisotropy of the bending rigidity on the supercoiling free energy of small circular DNAs , 1995, Biopolymers.

[251]  N. Cozzarelli,et al.  Simplification of DNA topology below equilibrium values by type II topoisomerases. , 1997, Science.

[252]  J. Moe,et al.  Proton exchange and base-pair opening kinetics in 5'-d(CGCGAATTCGCG)-3' and related dodecamers. , 1990, Nucleic acids research.

[253]  K. Loth,et al.  Sliding and target location of DNA-binding proteins:an NMR view of the lac repressor system , 2013, Journal of biomolecular NMR.

[254]  S. Mirkin,et al.  The absence of cruciform structures from pAO3 plasmid DNA in vivo. , 1984, Journal of biomolecular structure & dynamics.

[255]  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.

[256]  A. Turberfield,et al.  A DNA-fuelled molecular machine made of DNA , 2022 .

[257]  I. Panyutin,et al.  Kinetics of cruciform formation and stability of cruciform structure in superhelical DNA. , 1984, Journal of biomolecular structure & dynamics.

[258]  C J Benham,et al.  The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA. , 1993, Journal of molecular biology.

[259]  R. Watson,et al.  Early and late helix-coil transitions in closed circular DNA. The number of superhelical turns in polyoma DNA. , 1968, Journal of molecular biology.

[260]  P. Hagerman,et al.  Sequence-directed curvature of DNA. , 1986, Nature.

[261]  D. Davies,et al.  Helix formation by guanylic acid. , 1962, Proceedings of the National Academy of Sciences of the United States of America.

[262]  H. Leaderman,et al.  Physical properties of polymers , 1962 .

[263]  S. Prager,et al.  Variational Treatment of Hydrodynamic Interaction in Polymers , 1969 .

[264]  M. Frank-Kamenetskii,et al.  Base-stacking and base-pairing contributions into thermal stability of the DNA double helix , 2006, Nucleic acids research.

[265]  S. Rice,et al.  The Thermal Denaturation of Desoxyribose Nucleic Acid , 1957 .

[266]  D. Patel,et al.  Extrahelical adenosine stacks into right-handed DNA: solution conformation of the d(C-G-C-A-G-A-G-C-T-C-G-C-G) duplex deduced from distance geometry analysis of nuclear Overhauser effect spectra. , 1986, Biochemistry.

[267]  H. Ng,et al.  DNA structure from A to B , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[268]  A M Gronenborn,et al.  Intercalation, DNA Kinking, and the Control of Transcription , 1996, Science.

[269]  W. C. Johnson,et al.  Principles of physical biochemistry , 1998 .

[270]  D. Patel,et al.  Guanine residues in d(T2AG3) and d(T2G4) form parallel-stranded potassium cation stabilized G-quadruplexes with anti glycosidic torsion angles in solution. , 1992, Biochemistry.

[271]  V. Ivanov,et al.  The detection of B-form/A-form junction in a deoxyribonucleotide duplex. , 1996, Biophysical journal.

[272]  D. Case,et al.  A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA , 2009, Nucleic acids research.

[273]  V. Zhurkin,et al.  B-DNA twisting correlates with base-pair morphology. , 1995, Journal of molecular biology.

[274]  G. Weisbuch,et al.  Polyelectrolyte theory. I. Counterion accumulation, site‐binding, and their insensitivity to polyelectrolyte shape in solutions containing finite salt concentrations , 1980 .

[275]  H. Stanley,et al.  Statistical physics of macromolecules , 1995 .

[276]  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.

[277]  S. Woodson,et al.  Loop dependence of the stability and dynamics of nucleic acid hairpins , 2007, Nucleic acids research.

[278]  J. Le Pecq,et al.  Decay of fluorescence emission anisotropy of the ethidium bromide-DNA complex. Evidence for an internal motion in DNA. , 1970, Proceedings of the National Academy of Sciences of the United States of America.

[279]  Micah J. McCauley,et al.  DNA overstretching in the presence of glyoxal: structural evidence of force-induced DNA melting. , 2008, Biophysical journal.

[280]  I. Tinoco,et al.  A thermodynamic study of unusually stable RNA and DNA hairpins. , 1991, Nucleic acids research.

[281]  D. K. Chattoraj,et al.  DNA condensation with polyamines. II. Electron microscopic studies. , 1978, Journal of molecular biology.

[282]  I. Tinoco,et al.  Estimation of Secondary Structure in Ribonucleic Acids , 1971, Nature.

[283]  S. Quake,et al.  Relaxation of a single DNA molecule observed by optical microscopy. , 1994, Science.

[284]  I. Rouzina,et al.  Force-induced melting of the DNA double helix 1. Thermodynamic analysis. , 2001, Biophysical journal.

[285]  B. Lee,et al.  Measurement of the repulsive force between polyelectrolyte molecules in ionic solution: hydration forces between parallel DNA double helices. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[286]  J. Sturtevant,et al.  THE KINETICS OF DOUBLE HELIX FORMATION FROM POLYRIBOADENYLIC ACID AND POLYRIBOURIDYLIC ACID. , 1960, Proceedings of the National Academy of Sciences of the United States of America.

[287]  J. Wang,et al.  Supercoiling of the DNA template during transcription. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[288]  R. Sinden DNA Structure and Function , 1994 .

[289]  N R Cozzarelli,et al.  Structure of plectonemically supercoiled DNA. , 1990, Journal of molecular biology.

[290]  P. Beard,et al.  Cleavage of Circular, Superhelical Simian Virus 40 DNA to a Linear Duplex by S1 Nuclease , 1973, Journal of virology.

[291]  Homer Jacobson,et al.  Intramolecular Reaction in Polycondensations. I. The Theory of Linear Systems , 1950 .

[292]  N. Abrescia,et al.  Crystal structure of an antiparallel DNA fragment with Hoogsteen base pairing , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[293]  Shri Jain,et al.  Visualization of drug-nucleic acid interactions at atomic resolution. III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions. , 1977, Journal of molecular biology.

[294]  L. Lerman,et al.  Structural considerations in the interaction of DNA and acridines. , 1961, Journal of molecular biology.

[295]  N R Cozzarelli,et al.  Probability of DNA knotting and the effective diameter of the DNA double helix. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[296]  Wilma K Olson,et al.  Working the kinks out of nucleosomal DNA. , 2011, Current opinion in structural biology.

[297]  D. Poland,et al.  Recursion relation generation of probability profiles for specific‐sequence macromolecules with long‐range correlations , 1974, Biopolymers.

[298]  N. Cozzarelli,et al.  Mechanism of topology simplification by type II DNA topoisomerases , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[299]  N R Cozzarelli,et al.  The effect of ionic conditions on the conformations of supercoiled DNA. I. Sedimentation analysis. , 1997, Journal of molecular biology.

[300]  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.

[301]  J. SantaLucia,et al.  The thermodynamics of DNA structural motifs. , 2004, Annual review of biophysics and biomolecular structure.

[302]  K. Breslauer,et al.  Energetic signatures of single base bulges: thermodynamic consequences and biological implications , 2009, Nucleic acids research.

[303]  L. Shlyakhtenko,et al.  Melting of DNA in ethanol–water solutions , 1974, Biopolymers.

[304]  H. Frisch,et al.  Thermodynamics and equilibrium sedimentation analysis of the close approach of DNA molecules and a molecular ordering transition , 1981, Biopolymers.

[305]  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.

[306]  C. Levinthal,et al.  ON THE UNWINDING OF DNA. , 1956, Proceedings of the National Academy of Sciences of the United States of America.

[307]  F. Pohl Dynamics of the B-to-Z transition in supercoiled DNA. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[308]  I. Andricioaei,et al.  Transient Hoogsteen Base Pairs in Canonical Duplex DNA , 2011, Nature.

[309]  J Langowski,et al.  A Brownian dynamics program for the simulation of linear and circular DNA and other wormlike chain polyelectrolytes. , 1998, Biophysical journal.

[310]  J. Dubochet,et al.  The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo. , 1994, Journal of molecular biology.

[311]  N R Cozzarelli,et al.  The effect of ionic conditions on the conformations of supercoiled DNA. II. Equilibrium catenation. , 1997, Journal of molecular biology.

[312]  N. Seeman,et al.  A precisely controlled DNA biped walking device , 2004 .

[313]  A. Vologodskii,et al.  Probability of the site juxtaposition determines the rate of protein-mediated DNA looping. , 2007, Biophysical journal.

[314]  N. Cozzarelli,et al.  Helical repeat and linking number of surface-wrapped DNA. , 1988, Science.

[315]  P. V. von Hippel,et al.  Facilitated Target Location in Biological Systems* , 2022 .

[316]  M. Frank-Kamenetskii,et al.  Evidence of cruciform structures in superhelical DNA provided by two‐dimensional gel electrophoresis , 1983, FEBS letters.

[317]  D. Rabinovich,et al.  High-resolution structure of a DNA helix containing mismatched base pairs , 1985, Nature.

[318]  Jie Yan,et al.  Two distinct overstretched DNA states , 2010, Nucleic acids research.

[319]  S. Harvey,et al.  Dehydrating agents sharply reduce curvature in DNAs containing A tracts. , 1995, Nucleic acids research.

[320]  A. Engel,et al.  Characterization of complexes between recA protein and duplex DNA by electron microscopy. , 1982, Journal of molecular biology.

[321]  M. Magnasco,et al.  A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases , 1999, Nature.

[322]  M. Guéron,et al.  Proton exchange and base-pair lifetimes in a deoxy-duplex containing a purine-pyrimidine step and in the duplex of inverse sequence. , 1987, Journal of molecular biology.

[323]  Jiro Shimada,et al.  Ring-closure probabilities for twisted wormlike chains: application to DNA , 1984 .

[324]  B. Alberts,et al.  T4 DNA topoisomerase: a new ATP-dependent enzyme essential for initiation of T4 bacteriophage DNA replication , 1979, Nature.

[325]  P. Hanawalt,et al.  Localized torsional tension in the DNA of human cells. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[326]  J. SantaLucia,et al.  Thermodynamics of internal C.T mismatches in DNA. , 1998, Nucleic acids research.

[327]  V. Ivanov,et al.  The B-A transition in superhelical DNA. , 1990, Nucleic acids research.

[328]  J. Dubochet,et al.  Direct visualization of supercoiled DNA molecules in solution. , 1990, The EMBO journal.

[329]  J. Reeve,et al.  Large scale preparation of positively supercoiled DNA using the archaeal histone HMf. , 1997, Nucleic acids research.

[330]  S. Halford,et al.  Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[331]  J. Wang,et al.  Cyclization of phage DNAs. , 1968, Cold Spring Harbor symposia on quantitative biology.

[332]  S. Mirkin,et al.  H-DNA and related structures. , 1994, Annual review of biophysics and biomolecular structure.

[333]  A. Phan,et al.  HIV-1 integrase inhibitor T30177 forms a stacked dimeric G-quadruplex structure containing bulges , 2011, Nucleic acids research.

[334]  D. Crothers,et al.  The rate of DNA unwinding. , 1969, Journal of molecular biology.

[335]  I. Rouzina,et al.  Heat capacity effects on the melting of DNA. 2. Analysis of nearest-neighbor base pair effects. , 1999, Biophysical journal.

[336]  D. Pulleyblank,et al.  Facile transition of poly[d(TG)·d(CA)] into a left-handed helix in physiological conditions , 1983, Nature.

[337]  C. W. Hilbers,et al.  Nucleic acids and nuclear magnetic resonance. , 1988, European journal of biochemistry.

[338]  D. Porschke,et al.  Dynamics of the B-A transition of DNA double helices. , 2004, Nucleic acids research.

[339]  J. Widom,et al.  Role of DNA sequence in nucleosome stability and dynamics , 2001, Quarterly Reviews of Biophysics.

[340]  Steven M. Block,et al.  Transcription Against an Applied Force , 1995, Science.

[341]  C Blomberg,et al.  Association kinetics with coupled diffusional flows. Special application to the lac repressor--operator system. , 1976, Biophysical chemistry.

[342]  G. Chang,et al.  Crystal Structure of the Lactose Operon Repressor and Its Complexes with DNA and Inducer , 1996, Science.

[343]  Taekjip Ha,et al.  Extreme Bendability of DNA Less than 100 Base Pairs Long Revealed by Single-Molecule Cyclization , 2012, Science.

[344]  M. Duguet,et al.  The helical repeat of DNA at high temperature. , 1993, Nucleic acids research.

[345]  S. Mirkin,et al.  DNA H form requires a homopurine–homopyrimidine mirror repeat , 1987, Nature.

[346]  A nuclear magnetic resonance investigation of the energetics of basepair opening pathways in DNA. , 2005, Biophysical journal.

[347]  A. Grosberg,et al.  On the theory of Ψ‐condensation , 1982 .

[348]  S. Smith,et al.  Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads. , 1992, Science.

[349]  J. Michael Schurr,et al.  Dependence of the torsional rigidity of DNA on base composition , 1990, Nature.

[350]  J. Roca,et al.  DNA transport by a type II DNA topoisomerase: Evidence in favor of a two-gate mechanism , 1994, Cell.

[351]  L. J. Peck,et al.  Sequence dependence of the helical repeat of DNA in solution , 1981, Nature.

[352]  J. Wang,et al.  Bacterial DNA topoisomerase I can relax positively supercoiled DNA containing a single-stranded loop. , 1985, Journal of molecular biology.

[353]  A. Kikuchi,et al.  Reverse gyrase—a topoisomerase which introduces positive superhelical turns into DNA , 1984, Nature.

[354]  S. Mirkin,et al.  A structural transition in d(AT)n.d(AT)n inserts within superhelical DNA. , 1985, Journal of biomolecular structure & dynamics.

[355]  S. Busby,et al.  Effects of nucleoid-associated proteins on bacterial chromosome structure and gene expression. , 2010, Current opinion in microbiology.

[356]  W D Wilson,et al.  Sequence specific thermodynamic and structural properties for DNA.RNA duplexes. , 1994, Biochemistry.

[357]  E. Lesnik,et al.  Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: relationship with base composition and structure. , 1995, Biochemistry.

[358]  Rob Phillips,et al.  Exact theory of kinkable elastic polymers. , 2004, Physical review. E, Statistical, nonlinear, and soft matter physics.

[359]  Frank Dean,et al.  Determination of the absolute handedness of knots and catenanes of DNA , 1983, Nature.

[360]  P. Brown,et al.  A sign inversion mechanism for enzymatic supercoiling of DNA. , 1979, Science.

[361]  M. Ptashne,et al.  Cooperative binding of λ repressors to sites separated by integral turns of the DNA helix , 1986, Cell.

[362]  D. Pörchke Molecular states in single‐stranded adenylate chains by relaxation analysis , 1978 .

[363]  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.

[364]  C. E. Longfellow,et al.  Laser temperature-jump, spectroscopic, and thermodynamic study of salt effects on duplex formation by dGCATGC. , 1989, Biochemistry.

[365]  H M Berman,et al.  Crystal studies of B-DNA: the answers and the questions. , 1997, Biopolymers.

[366]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[367]  Qing Zhang,et al.  The Molecular Biology Toolkit (MBT): a modular platform for developing molecular visualization applications , 2005, BMC Bioinformatics.

[368]  J. W. Alexander Topological invariants of knots and links , 1928 .

[369]  V. Sasisekharan,et al.  Symmetry and molecular structure of a DNA triple helix: d(T)n.d(A)n.d(T)n. , 1993, Biochemistry.

[370]  T Schlick,et al.  Dynamics of site juxtaposition in supercoiled DNA. , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[371]  J. Viovy Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms , 2000 .

[372]  A. R. Srinivasan,et al.  The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.

[373]  V. Anshelevich,et al.  Polyelectrolyte model of DNA , 1987 .

[374]  N. Cozzarelli,et al.  Unlinking of DNA by Topoisomerases During DNA Replication , 1995 .

[375]  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.

[376]  D. Crothers,et al.  Improved estimation of secondary structure in ribonucleic acids. , 1973, Nature: New biology.

[377]  B. Révet,et al.  Short unligated sticky ends enable the observation of circularised DNA by atomic force and electron microscopies. , 1998, Nucleic acids research.

[378]  R. Sidorov,et al.  Mechanism of spontaneous DNA-DNA interaction of homologous linear duplexes. , 2002, Biochemistry.

[379]  V. Anshelevich,et al.  Slow relaxational processes in the melting of linear biopolymers: A theory and its application to nucleic acids , 1984, Biopolymers.

[380]  N. Sugimoto,et al.  Improved thermodynamic parameters and helix initiation factor to predict stability of DNA duplexes. , 1996, Nucleic acids research.

[381]  J. Dubochet,et al.  Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA. , 1995, Journal of molecular biology.

[382]  Ignacio Tinoco,et al.  Base-base mismatches. Thermodynamics of double helix formation for dCA3XA3G + dCT3YT3G (X, Y = A, C, G, T) , 1985, Nucleic Acids Res..

[383]  A. Bax,et al.  Direct measurement of distances and angles in biomolecules by NMR in a dilute liquid crystalline medium. , 1997, Science.

[384]  W. Bauer,et al.  Supercoiling in closed circular DNA: dependence upon ion type and concentration. , 1978, Biochemistry.

[385]  Rolf Boelens,et al.  Toward an integrated model of protein-DNA recognition as inferred from NMR studies on the Lac repressor system. , 2004, Chemical reviews.

[386]  Alfred Nordheim,et al.  THE CHEMISTRY AND BIOLOGY OF LEFT-HANDED Z-DNA , 1984 .

[387]  H. Yamakawa,et al.  Translational Friction Coefficient of Wormlike Chains , 1973 .

[388]  Alexander Vologodskii,et al.  REVIEWS OF TOPICAL PROBLEMS: Topological aspects of the physics of polymers: The theory and its biophysical applications , 1981 .

[389]  K. Maskos,et al.  Nmr studies of an extrahelical cytosine in an A·T rich region of a deoxyribodecanucleotide , 1993, Biopolymers.

[390]  Jacques H. van Boom,et al.  Molecular structure of a left-handed double helical DNA fragment at atomic resolution , 1979, Nature.

[391]  J. SantaLucia,et al.  Improved nearest-neighbor parameters for predicting DNA duplex stability. , 1996, Biochemistry.

[392]  Ashley H. Hardin,et al.  Direct measurement of DNA bending by type IIA topoisomerases: implications for non-equilibrium topology simplification , 2011, Nucleic acids research.

[393]  Y. Lyubchenko,et al.  Effect of base-pair stability on the melting of superhelical DNA , 1981, Nature.

[394]  V. Ivanov,et al.  A-DNA in solution as studied by diverse approaches. , 1992, Methods in enzymology.

[395]  V. P. Kumarev,et al.  The energetics of the B-Z transition in DNA. , 1987, Journal of biomolecular structure & dynamics.

[396]  L. Joshua-Tor,et al.  Mechanism of DNA translocation in a replicative hexameric helicase , 2006, Nature.

[397]  H. Blöcker,et al.  Predicting DNA duplex stability from the base sequence. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[398]  T. Biver Use of UV-Vis Spectrometry to Gain Information on the Mode of Binding of Small Molecules to DNAs and RNAs , 2012 .

[399]  P. Doty,et al.  Thermal renaturation of deoxyribonucleic acids. , 1961, Journal of molecular biology.

[400]  F. Studier Effects of the conformation of single-stranded DNA on renaturation and aggregation. , 1969, Journal of molecular biology.

[401]  J. Gouaux,et al.  Structure of Staphylococcal α-Hemolysin, a Heptameric Transmembrane Pore , 1996, Science.

[402]  Alfred Pingoud,et al.  Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA , 2008, Nucleic acids research.

[403]  D S Goodsell,et al.  The effect of crystal packing on oligonucleotide double helix structure. , 1987, Journal of biomolecular structure & dynamics.

[404]  Guixue Wang,et al.  The persistence length and length per base of single-stranded DNA obtained from fluorescence correlation spectroscopy measurements using mean field theory , 2013 .

[405]  W. Hunter,et al.  Refined crystal structure of an octanucleotide duplex with G . T mismatched base-pairs. , 1986, Journal of molecular biology.

[406]  J. Feigon,et al.  Thrombin-binding DNA aptamer forms a unimolecular quadruplex structure in solution. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[407]  D. Crothers,et al.  Ring closure probabilities for DNA fragments by Monte Carlo simulation. , 1986, Journal of molecular biology.

[408]  A V Lukashin,et al.  Fluctuations in superhelical DNA. , 1979, Nucleic acids research.

[409]  Joost van Mameren,et al.  Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging , 2009, Proceedings of the National Academy of Sciences.

[410]  H. Hiasa,et al.  Topoisomerase III, but not topoisomerase I, can support nascent chain elongation during theta-type DNA replication. , 1994, The Journal of biological chemistry.

[411]  D. Lilley,et al.  The inverted repeat as a recognizable structural feature in supercoiled DNA molecules. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[412]  C. Benham Statistical mechanical analysis of competing conformational transitions in superhelical DNA. , 1983, Cold Spring Harbor symposia on quantitative biology.

[413]  J. Skolnick,et al.  Electrostatic Persistence Length of a Wormlike Polyelectrolyte , 1977 .

[414]  M. Gellert,et al.  Regulation of the genes for E. coli DNA gyrase: Homeostatic control of DNA supercoiling , 1983, Cell.

[415]  Jacob W J Kerssemakers,et al.  Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments , 2010, Nature Methods.

[416]  N. Seeman,et al.  Thermodynamics of forming a parallel DNA crossover. , 2009, Biophysical journal.

[417]  W G Hol,et al.  A model for the mechanism of human topoisomerase I. , 1998, Science.

[418]  N C Seeman,et al.  Thermodynamics of DNA branching. , 1992, Journal of Molecular Biology.

[419]  E. Hayden Nanopore genome sequencer makes its debut , 2012 .

[420]  A. Vologodskii,et al.  The kinetics of oligonucleotide replacements. , 2000, Journal of molecular biology.

[421]  P. V. von Hippel,et al.  Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice. , 1974, Journal of molecular biology.

[422]  T M Jovin,et al.  Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). , 1972, Journal of molecular biology.

[423]  O. Kratky,et al.  Röntgenuntersuchung gelöster Fadenmoleküle , 1949 .

[424]  T. Hsieh,et al.  Thermodynamic properties of superhelical DNAs. , 1975, Biochemistry.

[425]  A. Riggs,et al.  The lac represser-operator interaction , 1970 .

[426]  Alfred Nordheim,et al.  Negatively supercoiled plasmids contain left-handed Z-DNA segments as detected by specific antibody binding , 1982, Cell.

[427]  Sanjay Tyagi,et al.  Molecular Beacons: Probes that Fluoresce upon Hybridization , 1996, Nature Biotechnology.

[428]  J. Berger,et al.  Structural basis for gate-DNA recognition and bending by type IIA topoisomerases , 2007, Nature.

[429]  S. Mirkin,et al.  Transcriptionally driven cruciform formation in vivo. , 1992, Nucleic acids research.

[430]  D. Lilley,et al.  Competing B-Z and helix-coil conformational transitions in supercoiled plasmid DNA. , 1992, The Journal of biological chemistry.

[431]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[432]  N. Seeman,et al.  A nanomechanical device based on the B–Z transition of DNA , 1999, Nature.

[433]  V. Ivanov,et al.  The nature of the – transition of DNA in solution , 1975 .

[434]  D M Crothers,et al.  Relaxation kinetics of dimer formation by self complementary oligonucleotides. , 1971, Journal of molecular biology.

[435]  N. Cozzarelli,et al.  Processive recombination by wild-type gin and an enhancer-independent mutant. Insight into the mechanisms of recombination selectivity and strand exchange. , 1994, Journal of molecular biology.

[436]  J. Thornton,et al.  An overview of the structures of protein-DNA complexes , 2000, Genome Biology.

[437]  Jie Yan,et al.  Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry , 2013, Proceedings of the National Academy of Sciences.

[438]  P. Hagerman,et al.  Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA). , 1999, Journal of molecular biology.

[439]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[440]  D. Wigley,et al.  Structure and mechanism of helicases and nucleic acid translocases. , 2007, Annual review of biochemistry.

[441]  R Lavery,et al.  Modelling extreme stretching of DNA. , 1996, Nucleic acids research.

[442]  Y. Zivanovic,et al.  Helical repeat of DNA in solution. The V curve method. , 1987, Nucleic acids research.

[443]  William M. Shih,et al.  A 1.7-kilobase single-stranded DNA that folds into a nanoscale octahedron , 2004, Nature.

[444]  J. Hearst,et al.  Sedimentation Constants of Broken Chains and Wormlike Coils , 1962 .

[445]  M. Gellert,et al.  DNA gyrase action involves the introduction of transient double-strand breaks into DNA. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[446]  V. Zhurkin,et al.  DNA stretching and compression: large-scale simulations of double helical structures. , 1999, Journal of molecular biology.

[447]  L. Onsager THE EFFECTS OF SHAPE ON THE INTERACTION OF COLLOIDAL PARTICLES , 1949 .

[448]  J. Michael Schurr,et al.  Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments. , 1996, Journal of molecular biology.

[449]  G. Charvin,et al.  Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[450]  N. Cozzarelli,et al.  The helical repeat of double-stranded DNA varies as a function of catenation and supercoiling , 1988, Nature.

[451]  V. Bloomfield,et al.  Condensation of DNA by trivalent cations. 1. Effects of DNA length and topology on the size and shape of condensed particles , 1990, Biopolymers.

[452]  M. Vologodskaia,et al.  Effect of magnesium on cruciform extrusion in supercoiled DNA. , 1999, Journal of molecular biology.

[453]  J. A. Subirana,et al.  Condensation of DNA by basic protiens does not depend on protien composition , 1994 .

[454]  J. SantaLucia,et al.  A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[455]  J. Marko,et al.  Extension of torsionally stressed DNA by external force. , 1997, Biophysical journal.

[456]  J. Berger,et al.  DNA topoisomerases: harnessing and constraining energy to govern chromosome topology , 2008, Quarterly Reviews of Biophysics.

[457]  Michael D. Stone,et al.  Mechanochemical analysis of DNA gyrase using rotor bead tracking , 2006, Nature.

[458]  F. MacKintosh,et al.  Visualizing the formation and collapse of DNA toroids. , 2010, Biophysical journal.

[459]  S. Harvey,et al.  Static contributions to the persistence length of DNA and dynamic contributions to DNA curvature. , 1995, Biophysical chemistry.

[460]  Ad Bax,et al.  Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy , 2003, Journal of biomolecular NMR.

[461]  W. Bauer,et al.  Structure and reactions of closed duplex DNA. , 1978, Annual review of biophysics and bioengineering.

[462]  Robert E. Johnson,et al.  Human DNA polymerase iota incorporates dCTP opposite template G via a G.C + Hoogsteen base pair. , 2005, Structure.

[463]  W. Greenleaf,et al.  Direct observation of base-pair stepping by RNA polymerase , 2005, Nature.

[464]  J. SantaLucia,et al.  NMR solution structure of a DNA dodecamer containing single G.T mismatches. , 1998, Nucleic acids research.

[465]  N. Cozzarelli,et al.  The mechanism of type IA topoisomerases , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[466]  P. Doty,et al.  Heterogeneity in Deoxyribonucleic Acids: I. Dependence on Composition of the Configurational Stability of Deoxyribonucleic Acids , 1959, Nature.

[467]  B. Zimm,et al.  Theory of the Phase Transition between Helix and Random Coil in Polypeptide Chains , 1959 .

[468]  S. Cockroft,et al.  Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures , 2013, Nature Structural &Molecular Biology.

[469]  A. Aksimentiev,et al.  Competitive binding of cations to duplex DNA revealed through molecular dynamics simulations. , 2012, The journal of physical chemistry. B.

[470]  M. Frank-Kamenetskii,et al.  Thermodynamics of the B–Z transition in superhelical DNA , 1984, Nature.

[471]  M. Rief,et al.  Sequence-dependent mechanics of single DNA molecules , 1999, Nature Structural Biology.

[472]  T. Przytycka,et al.  Transcription dependent dynamic supercoiling is a short-range genomic force , 2013, Nature Structural &Molecular Biology.

[473]  D. Branton,et al.  Characterization of individual polynucleotide molecules using a membrane channel. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[474]  Edward N Trifonov,et al.  Cracking the chromatin code: precise rule of nucleosome positioning. , 2011, Physics of life reviews.

[475]  K. Bjornson,et al.  Mechanisms of helicase-catalyzed DNA unwinding. , 1996, Annual review of biochemistry.

[476]  N. Seeman,et al.  Synthesis from DNA of a molecule with the connectivity of a cube , 1991, Nature.

[477]  A. Phan Human telomeric G‐quadruplex: structures of DNA and RNA sequences , 2010, The FEBS journal.

[478]  P. Flory Principles of polymer chemistry , 1953 .

[479]  M. Frank-Kamenetskii,et al.  Fluctuations in the DNA double helix: A critical review. , 2014, Physics of life reviews.

[480]  P. Brown,et al.  Catenation and knotting of duplex DNA by type 1 topoisomerases: a mechanistic parallel with type 2 topoisomerases. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[481]  Hao Yan,et al.  DNA Origami with Complex Curvatures in Three-Dimensional Space , 2011, Science.

[482]  D. Ermak,et al.  Brownian dynamics with hydrodynamic interactions , 1978 .

[483]  Chung-Cheng Liu,et al.  Type II DNA topoisomerases: Enzymes that can unknot a topologically knotted DNA molecule via a reversible double-strand break , 1980, Cell.

[484]  R. Wells,et al.  The B- to Z-DNA equilibrium in vivo is perturbed by biological processes. , 1988, Proceedings of the National Academy of Sciences of the United States of America.

[485]  S. Mirkin,et al.  Triplex DNA structures. , 1995, Annual review of biochemistry.

[486]  E. L. Zechiedrich,et al.  DNA disentangling by type-2 topoisomerases. , 2004, Journal of molecular biology.

[487]  P. Borst,et al.  DNA circles with cruciforms from Isospora (Toxoplasma) gondii. , 1984, Biochimica et biophysica acta.

[488]  S. Wölfl,et al.  Transcription of human c‐myc in permeabilized nuclei is associated with formation of Z‐DNA in three discrete regions of the gene. , 1992, The EMBO journal.

[489]  Nikos Panayotatos,et al.  Cruciform structures in supercoiled DNA , 1981, Nature.

[490]  Y. Lyubchenko,et al.  Atomic force microscopy study of the effects of Mg(2+) and other divalent cations on the end-to-end DNA interactions. , 2002, Biochemistry.

[491]  J. Wang,et al.  Interaction between DNA and an Escherichia coli protein omega. , 1971, Journal of molecular biology.

[492]  M. Frank-Kamenetskii,et al.  Perspectives report: Melting of DNA: Its study and application as a research method , 1970, Biopolymers.

[493]  J. Kjems,et al.  Self-assembly of a nanoscale DNA box with a controllable lid , 2009, Nature.

[494]  L. Lerman,et al.  Length-independent separation of DNA restriction fragments in two-dimensional gel electrophoresis , 1979, Cell.

[495]  Alexandre V. Morozov,et al.  Using DNA mechanics to predict in vitro nucleosome positions and formation energies , 2009, Nucleic acids research.

[496]  V. Zhurkin,et al.  Anisotropic flexibility of DNA and the nucleosomal structure. , 1979, Nucleic acids research.

[497]  Alexander Vologodskii,et al.  Sequence dependence of DNA bending rigidity , 2010, Proceedings of the National Academy of Sciences.

[498]  A. Rich,et al.  A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment. , 1985, Nucleic acids research.

[499]  A. Bensimon,et al.  The Elasticity of a Single Supercoiled DNA Molecule , 1996, Science.

[500]  R. Wartell,et al.  The effect of base sequence on the stability of RNA and DNA single base bulges. , 1999, Biochemistry.

[501]  C. Dekker,et al.  Dynamics of DNA Supercoils , 2012, Science.

[502]  M. L. Bret Catastrophic variation of twist and writhing of circular DNAs with constraint , 1979 .

[503]  A. Ansari,et al.  A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics. , 2012, Biophysical journal.

[504]  J. Champoux DNA topoisomerases: structure, function, and mechanism. , 2001, Annual review of biochemistry.

[505]  J. Reif,et al.  Directed nucleation assembly of DNA tile complexes for barcode-patterned lattices , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[506]  S. Cocco,et al.  Loops in DNA: An overview of experimental and theoretical approaches , 2006, The European physical journal. E, Soft matter.

[507]  A. Riggs,et al.  The lac repressor-operator interaction. 3. Kinetic studies. , 1970, Journal of molecular biology.

[508]  M. Record,et al.  Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications. , 1990, Annual review of biophysics and biophysical chemistry.

[509]  M. Wanunu Nanopores: A journey towards DNA sequencing. , 2012, Physics of Life Reviews.

[510]  A. Nordheim,et al.  DNA supercoiling changes the spacing requirement of two lac operators for DNA loop formation with lac repressor. , 1988, The EMBO journal.

[511]  A. Podtelezhnikov,et al.  Multimerization-cyclization of DNA fragments as a method of conformational analysis. , 2000, Biophysical journal.

[512]  G. Cohen,et al.  X-ray fiber diffraction and model-building study of polyguanylic acid and polyinosinic acid. , 1975, Journal of molecular biology.

[513]  H. Vosberg,et al.  Action of nicking-closing enzyme on supercoiled and nonsupercoiled closed circular DNA: formation of a Boltzmann distribution of topological isomers. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[514]  N R Cozzarelli,et al.  The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling. , 1997, Nucleic acids research.

[515]  C. Blomberg,et al.  Association kinetics with coupled diffusion. An extension to coiled-chain macromolecules applied to the lac repressor-operator system. , 1977, Biophysical chemistry.

[516]  T. Steitz,et al.  Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[517]  R. J. Robbins,et al.  Direct observation of the torsional dynamics of DNA and RNA by picosecond spectroscopy. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[518]  K. Swinger,et al.  IHF and HU: flexible architects of bent DNA. , 2004, Current opinion in structural biology.

[519]  A. Rich,et al.  Crystal structure of Z-DNA without an alternating purine-pyrimidine sequence. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[520]  P. Vallone,et al.  Predicting sequence-dependent melting stability of short duplex DNA oligomers. , 1997, Biopolymers.

[521]  I. Tinoco,et al.  The hypochromism of helical polynucleotides. , 1962, Journal of molecular biology.

[522]  S. Yabuki,et al.  Hyperfine structure in melting profile of bacteriophage lambda DNA , 1976, Biopolymers.

[523]  M. Kennedy,et al.  Solution-state structure of a DNA dodecamer duplex containing a Cis-syn thymine cyclobutane dimer, the major UV photoproduct of DNA. , 1998, Journal of molecular biology.

[524]  Eric C Greene,et al.  Visualizing one-dimensional diffusion of proteins along DNA , 2008, Nature Structural &Molecular Biology.

[525]  K Watanabe,et al.  GNA trinucleotide loop sequences producing extraordinarily stable DNA minihairpins. , 1997, Biochemistry.

[526]  N. Pierce,et al.  A synthetic DNA walker for molecular transport. , 2004, Journal of the American Chemical Society.

[527]  E. Siggia,et al.  Entropic elasticity of lambda-phage DNA. , 1994, Science.

[528]  M. Gellert,et al.  DNA gyrase: an enzyme that introduces superhelical turns into DNA. , 1976, Proceedings of the National Academy of Sciences of the United States of America.

[529]  Zesheng Li,et al.  The 3D structures of G-Quadruplexes of HIV-1 integrase inhibitors: molecular dynamics simulations in aqueous solution and in the gas phase , 2010, Journal of molecular modeling.

[530]  Michelle D. Wang,et al.  Stretching DNA with optical tweezers. , 1997, Biophysical journal.

[531]  C. W. Hilbers,et al.  Effects of base sequence on the loop folding in DNA hairpins. , 1989, Biochemistry.

[532]  M. Eigen,et al.  Co-operative non-enzymic base recognition. 3. Kinetics of the helix-coil transition of the oligoribouridylic--oligoriboadenylic acid system and of oligoriboadenylic acid alone at acidic pH. , 1971, Journal of molecular biology.

[533]  Colin Norman US Budget: Escaping the ‘New Realism’ , 1976, Nature.

[534]  M. Frank-Kamenetskii,et al.  Topological interaction between polymer chains , 1975 .

[535]  M. Gellert,et al.  Slow cruciform transitions in palindromic DNA. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[536]  Alexander Vologodskii,et al.  Simulation of DNA catenanes. , 2009, Physical chemistry chemical physics : PCCP.

[537]  L. Lerman A transition to a compact form of DNA in polymer solutions. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[538]  Stormy J. Chamberlain,et al.  Topoisomerases facilitate transcription of long genes linked to autism , 2013, Nature.

[539]  Masahito Yamamoto,et al.  Thermodynamic parameters based on a nearest-neighbor model for DNA sequences with a single-bulge loop. , 2004, Biochemistry.

[540]  H. Mizusawa,et al.  Unwinding of double-stranded DNA helix by dehydration. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[541]  A. Lyubartsev,et al.  Application of polyelectrolyte theories for analysis of DNA melting in the presence of Na+ and Mg2+ ions. , 1998, Biophysical journal.

[542]  Yonggun Jun,et al.  Longest Relaxation Times of Double-Stranded and Single-Stranded DNA , 2007 .

[543]  Robert H. Austin,et al.  Bending and twisting dynamics of short linear DNAs. Analysis of the triplet anisotropy decay of a 209 base pair fragment by Brownian simulation , 1989 .

[544]  J. Wang,et al.  Moving one DNA double helix through another by a type II DNA topoisomerase: the story of a simple molecular machine , 1998, Quarterly Reviews of Biophysics.

[545]  R. Sinden,et al.  Measurement of localized DNA supercoiling and topological domain size in eukaryotic cells. , 1999, Methods in enzymology.

[546]  D. Ecker,et al.  Combinatorially selected guanosine-quartet structure is a potent inhibitor of human immunodeficiency virus envelope-mediated cell fusion. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[547]  Ruojie Sha,et al.  A Bipedal DNA Brownian Motor with Coordinated Legs , 2009, Science.

[548]  D. Crothers,et al.  Preferential location of bulged guanosine internal to a G.C tract by 1H NMR. , 1988, Biochemistry.

[549]  Richard E. Dickerson,et al.  Crystal structure analysis of a complete turn of B-DNA , 1980, Nature.

[550]  S. Smith,et al.  Ionic effects on the elasticity of single DNA molecules. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[551]  P. Bucher,et al.  Natural DNA sequences can form left-handed helices in low salt solution under conditions of topological constraint. , 1982, Journal of molecular biology.

[552]  A. Pingoud,et al.  The rotation-coupled sliding of EcoRV , 2012, Nucleic acids research.

[553]  J. SantaLucia,et al.  Nearest neighbor thermodynamic parameters for internal G.A mismatches in DNA. , 1998, Biochemistry.

[554]  Lingyan Huang,et al.  Effects of sodium ions on DNA duplex oligomers: improved predictions of melting temperatures. , 2004, Biochemistry.

[555]  U. K. Laemmli,et al.  Characterization of DNA condensates induced by poly(ethylene oxide) and polylysine. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[556]  Phoebe A Rice,et al.  Integration host factor: putting a twist on protein-DNA recognition. , 2003, Journal of molecular biology.

[557]  Yong You,et al.  Predicting stability of DNA duplexes in solutions containing magnesium and monovalent cations. , 2008, Biochemistry.

[558]  K. V. van Holde,et al.  Sedimentation of homogeneous double-strand DNA molecules. , 1977, Biochemistry.

[559]  Diffusion of the restriction nuclease EcoRI along DNA. , 2010, Journal of molecular biology.

[560]  R. Schleif,et al.  In vivo DNA loops in araCBAD: size limits and helical repeat. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[561]  J. Vinograd,et al.  THE CYCLIC HELIX AND CYCLIC COIL FORMS OF POLYOMA VIRAL DNA. , 1963, Proceedings of the National Academy of Sciences of the United States of America.

[562]  J. SantaLucia,et al.  Thermodynamics and NMR of internal G.T mismatches in DNA. , 1997, Biochemistry.

[563]  D. Stigter,et al.  Evaluation of the counterion condensation theory of polyelectrolytes. , 1995, Biophysical journal.

[564]  G. Călugăreanu Sur les classes d'isotopie des noeuds tridimensionnels et leurs invariants , 1961 .

[565]  Nancy R. Forde,et al.  Using mechanical force to probe the mechanism of pausing and arrest during continuous elongation by Escherichia coli RNA polymerase , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[566]  D. Crothers,et al.  Determination of the extent of DNA bending by an adenine-thymine tract. , 1990, Biochemistry.

[567]  W. Keller Determination of the number of superhelical turns in simian virus 40 DNA by gel electrophoresis. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[568]  G. Varani Exceptionally stable nucleic acid hairpins. , 1995, Annual review of biophysics and biomolecular structure.

[569]  D. Crothers,et al.  Structural origins of adenine-tract bending , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[570]  T. Strick,et al.  Behavior of supercoiled DNA. , 1998, Biophysical journal.

[571]  J. Eisinger Complex formation between transfer RNA'S with complementary anticodons. , 1971, Biochemical and biophysical research communications.

[572]  G. Charvin,et al.  Topoisomerase IV bends and overtwists DNA upon binding. , 2005, Biophysical journal.

[573]  James C. Wang,et al.  Noncomplementarity in base sequences between the cohesive ends of coliphages 186 and λ and the formation of interlocked rings between the two DNA's , 1967, Biopolymers.

[574]  J. Shimada,et al.  Moments for DNA topoisomers: The helical wormlike chain , 1988, Biopolymers.

[575]  Bruno H. Zimm,et al.  Theory of twisting and bending of chain macromolecules; analysis of the fluorescence depolarization of DNA , 1979 .

[576]  N. Seeman,et al.  DNA double-crossover molecules. , 1993, Biochemistry.

[577]  L. Hurley,et al.  Interstrand cross-linking by bizelesin produces a Watson-Crick to Hoogsteen base-pairing transition region in d(CGTAATTACG)2. , 1993, Biochemistry.

[578]  A. Hoff,et al.  Hysteresis of denaturation of DNA in the melting range , 1972, Biopolymers.

[579]  J. R. Williamson,et al.  G-quartet structures in telomeric DNA. , 1994, Annual review of biophysics and biomolecular structure.

[580]  G. Davey,et al.  The mechanics behind DNA sequence-dependent properties of the nucleosome , 2012, Nucleic acids research.

[581]  Marc Le Bret,et al.  Monte carlo computation of the supercoiling energy, the sedimentation constant, and the radius of gyration of unknotted and knotted circular DNA , 1980, Biopolymers.

[582]  R. J. Kelleher,et al.  Sequence-dependent energetics of the B-Z transition in supercoiled DNA containing nonalternating purine-pyrimidine sequences. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[583]  Andrew V. Colasanti,et al.  A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning. , 2007, Journal of molecular biology.

[584]  Philip Nelson,et al.  Entropic Elasticity of Twist-Storing Polymers , 1997, cond-mat/9712004.

[585]  Sequence-Disorder Effects on DNA Entropic Elasticity , 1997, cond-mat/9711285.

[586]  J. Vinograd,et al.  The number of superhelical turns in native Virion SV40 DNA and Minicol DNA determined by the band counting method , 1976, Cell.

[587]  K. Klenin,et al.  Salt-dependent DNA superhelix diameter studied by small angle neutron scattering measurements and Monte Carlo simulations. , 1998, Biophysical journal.

[588]  P. Bevilacqua,et al.  Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg),d(cCNNGg), and d(gCNNGc). , 2002, Biochemistry.

[589]  F. Arnold,et al.  Structure, dynamics, and thermodynamics of mismatched DNA oligonucleotide duplexes d(CCCAGGG)2 and d(CCCTGGG)2. , 1987, Biochemistry.

[590]  Michelle D. Wang,et al.  Stretching of single collapsed DNA molecules. , 2000, Biophysical journal.

[591]  D. Rolfsen Knots and Links , 2003 .

[592]  D. Crothers,et al.  Free energy of imperfect nucleic acid helices. II. Small hairpin loops. , 1973, Journal of molecular biology.

[593]  Bruno H. Zimm,et al.  Chain Molecule Hydrodynamics by the Monte-Carlo Method and the Validity of the Kirkwood-Riseman Approximation , 1980 .

[594]  T. Richmond,et al.  The structure of DNA in the nucleosome core , 2003, Nature.

[595]  Jie Yan,et al.  Two distinct overstretched DNA structures revealed by single-molecule thermodynamics measurements , 2012, Proceedings of the National Academy of Sciences.

[596]  M J Doktycz,et al.  Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: Evaluation of the nearest‐neighbor stacking interactions in DNA , 1992, Biopolymers.

[597]  Vadim V. Demidov,et al.  Nucleic Acids: Structures, Properties and Functions , 2001 .

[598]  S. Mirkin,et al.  A pH-dependent structural transition in the homopurine-homopyrimidine tract in superhelical DNA. , 1985, Journal of biomolecular structure & dynamics.

[599]  M. Frank-Kamenetskii,et al.  Stacked-unstacked equilibrium at the nick site of DNA. , 2004, Journal of molecular biology.

[600]  A. Vologodskii,et al.  A study of the reversibility of helix-coil transition in DNA. , 1981, Nucleic Acids Research.

[601]  J. Wang,et al.  Interactions between twisted DNAs and enzymes: the effects of superhelical turns. , 1974, Journal of molecular biology.

[602]  P. Dedon,et al.  An improved method for large-scale preparation of negatively and positively supercoiled plasmid DNA. , 2009, BioTechniques.

[603]  D. Lilley,et al.  Stress‐induced cruciform formation in a cloned d(CATG)10 sequence. , 1986, The EMBO journal.

[604]  P. Doty,et al.  The Molecular Weight and Shape of Desoxypentose Nucleic Acid , 1952 .

[605]  M. Rudolph,et al.  Crystal structures of Thermotoga maritima reverse gyrase: inferences for the mechanism of positive DNA supercoiling , 2012, Nucleic acids research.

[606]  R. Dickerson,et al.  DNA bending: the prevalence of kinkiness and the virtues of normality. , 1998, Nucleic acids research.

[607]  Stretching a heteropolymer , 1998 .

[608]  B. Friedman,et al.  SCALING AND UNIVERSALITY IN POLYMER REACTION KINETICS , 1994 .

[609]  A. Vologodskii,et al.  Topological Behavior of Plasmid DNA. , 2015, Microbiology spectrum.

[610]  G. Felsenfeld,et al.  The conformation of polyriboadenylic acid at low temperature and neutral pH. A single‐stranded rodlike structure , 1975, Biopolymers.

[611]  A Libchaber,et al.  Kinetics of conformational fluctuations in DNA hairpin-loops. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[612]  R. Dulbecco,et al.  EVIDENCE FOR A RING STRUCTURE OF POLYOMA VIRUS DNA. , 1963, Proceedings of the National Academy of Sciences of the United States of America.

[613]  F. B. Fuller The writhing number of a space curve. , 1971, Proceedings of the National Academy of Sciences of the United States of America.

[614]  I. Rouzina,et al.  Competitive electrostatic binding of charged ligands to polyelectrolytes: practical approach using the non-linear Poisson-Boltzmann equation. , 1997, Biophysical chemistry.

[615]  M. Hsiang,et al.  Structure of histone H1-DNA complex: effect of histone H1 on DNA condensation. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[616]  C. Kang,et al.  Crystal structure of a DNA decamer containing a cis-syn thymine dimer , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[617]  Charles M. Rice,et al.  Three conformational snapshots of the hepatitis C virus NS3 helicase reveal a ratchet translocation mechanism , 2009, Proceedings of the National Academy of Sciences.

[618]  R. Lavery,et al.  DNA: An Extensible Molecule , 1996, Science.

[619]  R. Sinden,et al.  Perfect palindromic lac operator DNA sequence exists as a stable cruciform structure in supercoiled DNA in vitro but not in vivo. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[620]  K. Klenin,et al.  Diffusion-controlled intrachain reactions of supercoiled DNA: Brownian Dynamics simulations. , 2001, Biophysical journal.