Molecular modeling of nucleic acids : developed from a symposium ... at the 213th National Meeting of the American Chemical Society, San Francisco, CA, April 13-17, 1997

Content: The energetics of nucleotide ionization in water-counterion environments / Harshica Fernando, Nancy S. Kim, George A. Papadantonakis, and Pierre R. LeBreton -- Parameterization and simulation of the physical properties of phosphorothioate nucleic acids / Kenneth E. Lind, Luke D. Sherlin, Venkatraman Mohan, Richard H. Griffey, and David M. Ferguson -- Crystallographic studies of RNA internal loops / Stephen R. Holbrook -- Hydrogen-bonding patterns observed in the base pairs of duplex oligonucleotides / William N. Hunter, Gordon A. Leonard, and Tom Brown -- Structure and stability of DNA containing inverted anomeric centers and polarity reversals / James M. Aramini, Johan H. van de Sande, and Markus W. Germann -- Conformational analysis of nucleic acids : problems and solutions / Andrew N. Lane -- NMR structure determination of a 28-nucleotide signal recognition particle RNA with complete relaxation matrix methods using corrected nuclear Overhauser effect intensities / Peter Lukavsky, Todd M. Billeci, Thomas L. James, and Uli Schmitz -- Molecular modeling of DNA using Raman and NMR data, and the nuclease activity of 1,10-phenanthroline-copper ion / W.L. Peticolas, M. Ghomi, A. Spassky, E.M. Evertsz, and T.S. Rush, III -- Three-dimensional NOESY-NOESY hybrid-hybrid matrix refinement of a DNA three-way junction / Varatharasa Thiviyanthan, Nishantha Illangasekare, Elliott Gozansky, Frank Zhu, Neocles B. Leontis, Bruce A. Luxon, and David G. Gorenstein -- Determination of structural ensembles from NMR data : conformational sampling and probability assessment / Nikolai B. Ulyanov, Anwer Mujeeb, Alessandro Donati, Patrick Furrer, He Liu, Shauna Farr-Jones, David E. Konerding, Uli Schmitz, and Thomas L. James -- NMR studies of the binding of an SPXX-containing peptide from high-molecular-weight basic nuclear proteins to an A-T rich DNA hairpin / Ning Zhou and Hans J. Vogel -- Thermodynamics of duplex formation and mismatch discrimination on photolithographically synthesized oligonucleotide arrays / Jonathan E. Forman, Ian D. Walton, David Stern, Richard P. Rava, and Mark O. Trulson -- RNA folding dynamics : computer simulations by a genetic algorithm / A.P. Gultyaev, F.H.D. van Batenburg, and C.W.A. Pleij -- An updated recursive algorithm for RNA secondary structure prediction with improved thermodynamic parameters / David H. Mathews, Troy C. Andre, James Kim, Douglas H. Turner, and Michael Zuker -- Modeling of DNA via molecular dynamics simulation : structure, bending, and conformational t[r]ansitions / D.L. Beveridge, M.A. Young, and D. Sprous -- Molecular dynamics simulations on nucleic acid systems using the Cornell et al. force field and particle mesh Ewald electrostatics / T.E. Cheatham, III, J.L. Miller, T.I. Spector, P. Cieplak, and P.A. Kollman -- Observations on the A versus B equilibrium in molecular dynamics simulations of duplex DNA and RNA / Alexander D. MacKerell, Jr. -- Modeling duplex DNA oligonucleotides with modified pyrimidine bases / John Miller, Michael Cooney, Karol Miaskiewicz, and Roman Osman -- How the TATA box selects its protein partner / Nina Pastor, Leonardo Pardo, and Harel Weinstein -- RNA tectonics and modular modeling of RNA / Eric Westhof, Benoît Masquida, and Luc Jaeger -- Hairpin ribozyme structure and dynamics / A.R. Banerjee, A. Berzal-Herranz, J. Bond, S. Butcher, J.A. Esteban, J.E. Heckman, B. Sargueil, N. Walter, and J.M. Burke -- Molecular modeling studies on the ribosome / Stephen C. Harvey, Margaret S. VanLoock, Thomas R. Rasterwood, and Robert K.-Z. Tan -- Modeling unusual nucleic acid structures / Thomas J. Macke and David A. Case -- Computer RNA three-dimensional modeling from low-resolution data and multiple-sequence information / François Major, Sébastien Lemieux, and Abdelmjid Ftouhi -- Comparative modeling of the three-dimensional structure of signal recognition particle RNA / Christian Zwieb, Krishne Gowda, Niels Larsen, and Florian Müller.
Covering numerous topics in modeling nucleic acids, this volume looks at the role of various spectroscopic methods, simulations of molecular dynamics using particle mesh methods, and dynamic and genetic algorithms for predicting RNA secondary structure. It also covers the thermodynamics of nucleic acid folding and three-dimensional structure prediction based on sequence information.