Sequence-dependent dynamics of TATA-Box binding sites.

[1]  H. Berendsen,et al.  ALGORITHMS FOR MACROMOLECULAR DYNAMICS AND CONSTRAINT DYNAMICS , 1977 .

[2]  G. Ciccotti,et al.  Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes , 1977 .

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

[4]  W. L. Jorgensen Quantum and statistical mechanical studies of liquids. 10. Transferable intermolecular potential functions for water, alcohols, and ethers. Application to liquid water , 2002 .

[5]  H R Drew,et al.  Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure. , 1981, Journal of molecular biology.

[6]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[7]  N. Ulyanov,et al.  Sequence-dependent anisotropic flexibility of B-DNA. A conformational study. , 1984, Journal of biomolecular structure & dynamics.

[8]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[9]  R. H. Ritchie,et al.  Dielectric effects in biopolymers: The theory of ionic saturation revisited , 1985 .

[10]  P. Kollman,et al.  An all atom force field for simulations of proteins and nucleic acids , 1986, Journal of computational chemistry.

[11]  U Heinemann,et al.  Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. , 1987, Science.

[12]  T. Tullius,et al.  The unusual conformation adopted by the adenine tracts in kinetoplast DNA , 1987, Cell.

[13]  Y. Kyōgoku,et al.  One- and two-dimensional NMR studies on the conformation of DNA containing the oligo(dA)oligo(dT) tract. , 1988, Nucleic acids research.

[14]  M. Guéron,et al.  Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. , 1988, Biochemistry.

[15]  D. Crothers,et al.  Structural basis for DNA bending. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[16]  R. Lavery,et al.  Defining the structure of irregular nucleic acids: conventions and principles. , 1989, Journal of biomolecular structure & dynamics.

[17]  Bhyravabhotla Jayaram,et al.  Monte Carlo Simulation Studies on the Structure of the Counterion Atmosphere of B-DNA. Variations on the Primitive Dielectric Model , 1990 .

[18]  Yeast and human TATA-binding proteins have nearly identical DNA sequence requirements for transcription in vitro. , 1990, Molecular and cellular biology.

[19]  Steven Hahn,et al.  Crystal structure of a yeast TBP/TATA-box complex , 1993, Nature.

[20]  Stephen K. Burley,et al.  Co-crystal structure of TBP recognizing the minor groove of a TATA element , 1993, Nature.

[21]  T. Darden,et al.  Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems , 1993 .

[22]  R. Lavery,et al.  Measuring the geometry of DNA grooves , 1994, Biopolymers.

[23]  D. Goodsell,et al.  Bending and curvature calculations in B-DNA. , 1994, Nucleic acids research.

[24]  Stephen K. Burley,et al.  1.9 Å resolution refined structure of TBP recognizing the minor groove of TATAAAAG , 1994, Nature Structural Biology.

[25]  P. Kollman,et al.  Molecular Dynamics Simulations on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA, and Proteins , 1995 .

[26]  Nikolai B. Ulyanov,et al.  [4] Statistical analysis of DNA duplex structural features , 1995 .

[27]  Heinz Sklenar,et al.  JUMNA (junction minimisation of nucleic acids) , 1995 .

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

[29]  P. Kollman,et al.  A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules , 1995 .

[30]  D. K. Hawley,et al.  DNA bending is an important component of site-specific recognition by the TATA binding protein. , 1995, Journal of molecular biology.

[31]  S C Harvey,et al.  Molecular modelling of (A4T4NN)n and (T4A4NN)n: sequence elements responsible for curvature. , 1996, Nucleic acids research.

[32]  Sarma Rh,et al.  Biological Structure and Dynamics. , 1996, Journal of biomolecular structure & dynamics.

[33]  P A Kollman,et al.  Observation of the A-DNA to B-DNA transition during unrestrained molecular dynamics in aqueous solution. , 1996, Journal of molecular biology.

[34]  R. Dickerson,et al.  How proteins recognize the TATA box. , 1996, Journal of molecular biology.

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

[36]  Z. Shakked,et al.  A novel form of the DNA double helix imposed on the TATA-box by the TATA-binding protein , 1996, Nature Structural Biology.

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

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

[39]  R Lavery,et al.  Local DNA stretching mimics the distortion caused by the TATA box-binding protein. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[40]  R. Lavery,et al.  Conformational properties of the TATA-box binding sequence of DNA. , 1997, Journal of biomolecular structure & dynamics.

[41]  H Weinstein,et al.  Does TATA matter? A structural exploration of the selectivity determinants in its complexes with TATA box-binding protein. , 1997, Biophysical journal.

[42]  Richard Lavery,et al.  Internal coordinate modeling of DNA: Force field comparisons , 1997, J. Comput. Chem..

[43]  D. Beveridge,et al.  A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation. , 1997, Biophysical journal.

[44]  Bhyravabhotla Jayaram,et al.  Intrusion of Counterions into the Spine of Hydration in the Minor Groove of B-DNA: Fractional Occupancy of Electronegative Pockets , 1997 .

[45]  J M Rosenberg,et al.  Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration. , 1997, Journal of molecular biology.