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Curvature and Deformation of Nucleic Acids : Recent Advances, New Paradigms - Nancy C. Stellwagen

Curvature and Deformation of Nucleic Acids

Recent Advances, New Paradigms

By: Nancy C. Stellwagen (Editor), Udayan Mohanty (Editor)

Hardcover Published: 15th June 2004
ISBN: 9780841238626
Number Of Pages: 376

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Curvature and Deformation of Nucleic Acids: Recent Advances, New Paradigms presents an up-to-date review on the curvature and deformation of nucleic acids. Chapter 1 sets the various chapters in context, as well as describing several controversial topics. Chapter 2 gives a comprehensive review of the literature on DNA bending and describes the current status of molecular dynamics simulations of DNA and protein-DNA complexes. Chapter 3 describes the structural basis for A-tract DNA helix bending, based on recent NMR structures and other biophysical measurements. Chapter 4 describes the localization of Mg++ ions in the crystal structure of a B-form DNA dodecamer and discusses the relevance of these bound ions to sequence-dependent bending. Chapter 5 discusses the electrostatic energy penalties that result from phosphate crowding in curved DNA oligomers. Chapter 6 presents a quantitative model that predicts the magnitude of the bend caused by asymmetric charge neutralization of DNA phosphate residues. Chapter 7 reviews the structural and dynamic properties of four-way DNA junctions in the presence of metal ions, and it describes the exchange between alternative stacking conformers in solution. Chapter 8 documents the fact that a conserved pseudouridine residue in an RNA duplex containing a precursor messenger branch site makes an important contribution to the structure of the molecule. Chapter 9 describes structural perturbations that are observed in disease-related mutants of human mitochondrial transfer RNAs. Chapter 10 reviews the thermodynamics of the folding and unfolding of DNA oligomers distorted by the binding of small ligands. Chapter 11 describes a method of constructing DNA fragments for cyclization studies that uses single strand gaps as flexible hinges that allow the correct torsional orientation of the helix ends. Chapter 12 reviews a statistical mechanical model that predicts the stability of reconstituted nucleosomes based on sequence-dependent DNA curvature and flexibility.

Preface 1: Nancy C. Stellwagen and Udayan Mohanty: Curvature and Deformation of Nucleic Acids: Overview 2: D.L. Beveridge, Surjit B. Dixit, K. Suzie Byun, Gabriela Barreiro, Kelly M. Thayer, and S. Ponomarev: Molecular Dynamics of DNA and Protein-DNA Complexes: Progress on Sequence Effects, Conformational Stability, Axis Curvature, and Structural Bioinformatics 3: Douglas MacDonald and Ponzy Lu: The Structural Basis for A-Tract DNA Helix Bending 4: Martin Engli and Valentina Tereshko: Lattice-and Sequence-Dependent Binding of Mg2+ in the Crystal Structure of a B-DNA Dodecamer 5: P.R. Hardwidge, Y.-P. Pang, J.M. Zimmerman, M. Vaghefi, R. Hogrefe, and L.J. Maher, III: Phosphate Crowding and DNA Bending 6: A. Spasic, G. Hess, K. Becker, M. Hansen, R. Bleil, and U. Mohanty: Asymmetric Charge Neutralization of DNA 7: David M.J. Lilley: Structural and Dynamic Properties of Four-Way Helical Junctions in DNA Molecules 8: Nancy L. Greenbaum and Meredith Newby Lambert: Role of a Conserved Pseudouridine in Spliceosomal Pre-mRNA Branch Site Conformation 9: Shana O. Kelley, Lisa Wittenhagen, and Marc D. Roy: Structural Perturbations in Disease-Related Human tRNAs 10: Luis A. Marky, Karen Alessi, Ronald Shikiya, Jian-Sen Li, and Barry Gold: Folding of Bent Oligodeoxynucleotide Duplexes: Energetics, Ion Binding, and Hydration 11: Alexander Vologodskii: Measuring Protein-Induced DNA Bending by Cyclization of Short DNA Fragments Containing Single-Stranded Region 12: P. De Santis, M. Savino, A. Scipioni, and C. Anselmi: DNA Sequence-Dependent Curvature and Flexability in Stability and Organization of Nucleosomes Author Index Subject Index

ISBN: 9780841238626
ISBN-10: 0841238626
Series: ACS Symposium
Audience: Professional
Format: Hardcover
Language: English
Number Of Pages: 376
Published: 15th June 2004
Publisher: Oxford University Press Inc
Country of Publication: US
Dimensions (cm): 23.83 x 15.49  x 1.88
Weight (kg): 0.47

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