The Oxford Handbook of Nucleic Acid Structure is a comprehensive reference text on all aspects of nucleic acid sturcture. Particular emphasis is placed on the results from X-ray crystallography and NMR studies, with both methods being given equal weight. The nineteen chapters describe in detail the variety of DNA and RNA structural types discovered to date with all the major 'native' structures being represented. The text progresses systematically through the polymorphs of double helical DNA through to the higher-order organizations of triplexes, quadruplexes, and junctions, then to RNA structures in their various degrees of complexity. Each chapter has been written by authorities in the field who have worked together to provide this comprehensive text on nucleic acid structure. The whole project has been brought together and edited by Professor Stephen Neidle who is Director of the CRC Biomolecular Structure Unit at the Institute of Cancer Research.
List of contributors xiii Abbreviations xvii Polynucleotide secondary structures: an historical perspective 1(38) Struther Arnott Introduction 1(3) The DNA duplex: discovery and definition 4(4) Expansion 8(1) Discrimination and exploration 8(1) Polymorphism 9(3) Homopolymers 12(4) Polyoligonucleotide duplexes 16(6) Envoi 22(1) Appendix: further details of fibrous polynucleotide structures together with some comments 22(14) References 36(3) Base and base pair morphologies, helical parameters, and definitions 39(38) Richard Lavery Krystyna Zakrzewska Introduction 39(1) Nucleic acid bases 39(4) Base pairing 43(8) Helical parameter definitions 51(3) Helical parameter calculations 54(6) Examples of helical analysis 60(12) Analysing nucleic acid dynamics 72(1) Conclusions 73(1) References 74(3) The nucleic acid database: a research and teaching tool 77(18) Helen M. Berman Christine Zardecki John Westbrook Introduction 77(1) The infrastructure of the NDB 78(5) Production characteristics of the NDB 83(4) Practical uses of the NDB for research and training 87(5) Prospects 92(1) References 92(3) Simulation of nucleic acid structure 95(22) Jennifer L. Miller Thomas E. Cheatham III Peter A. Kollman Force fields for nucleic acids 95(3) Introduction to simulation methods 98(3) Applications of molecular mechanics and dynamics to nucleic acid systems 101(10) References 111(6) A-DNA duplexes in the crystal 117(28) Markus C. Wahl Muttaiya Sundaralingam Introduction 117(1) The A-DNA conformation 117(4) A-DNA crystal packing 121(5) Sequence-structure relationships 126(2) Interconversions between A-, B-, and Z-forms 128(1) Chemical modifications of backbone and bases 129(1) Mispairs 130(2) A-DNA deformability 132(1) A-DNA interaction with ligands 133(6) Comparison with solution studies 139(1) Conclusions 140(1) References 141(4) Helix structure and molecular recognition by B-DNA 145(54) Richard E. Dickerson Introduction 145(1) Early sequence-structure correlations 145(10) Molecular properties of B-DNA 155(3) Differences between individual base steps 158(5) DNA behaviour in crystals and in protein: DNA complexes 163(19) Roll/slide/twist correlations in protein: DNA complexes 182(7) Summary and conclusions 189(2) References 191(8) The single-crystal structures of Z-DNA 199(54) Beth Basham Brandt F. Eichman P. Shing Ho Introduction 199(1) The prototypical Z-DNA structure of d(CGCGCG) 200(22) Sequence and substituent effects on the structure and stability of Z-DNA 222(23) Summary: sequence effects on the structure and stability of Z-DNA 245(4) References 249(4) Standard DNA duplexes and RNA:DNA hybrids in solution 253(42) Uli Schmitz Forrest J.H. Blocker Thomas L. James Introduction 253(1) Data and methods for high resolution structure determination 254(7) DNA duplex structures 261(19) RNA:DNA hybrid structures 280(8) Outlook for the future 288(1) References 289(6) Nucleic acid hydration 295(18) Helen M. Berman Bohdan Schneider Introduction 295(1) Macroscopic studies 295(2) Structural analyses of nucleic acid hydration 297(13) Summary 310(1) References 310(3) Single-crystal X-ray diffraction studies on the non-Watson-Crick base associations of mismatches, modified bases, and non-duplex oligonucleotide structures 313(18) William N. Hunter Tom Brown Introduction 313(1) Mismatches 314(7) Pairings with modified bases 321(3) Non-Watson-Crick associations stabilize higher order structures 324(4) References 328(3) DNA mismatches in solution 331(24) Shan-Ho Chou Brian R. Reid Introduction 331(1) Mismatch pairing in antiparallel GA, GGA, and GGGA repeats 332(3) Mismatches between parallel-stranded CGA triplets and their repeats 335(3) Tandem sheared G:A mismatches separated by Watson-Crick base pairs 338(6) Sheared G:A mismatches closing single-residue hairpin loops 344(5) Sheared G:A mismatches closing two-residue hairpin loops 349(1) Conclusion 349(1) References 350(5) Structures of nucleic acid triplexes 355(34) Edmond Wang Juli Feigon Introduction 355(10) Structures of parallel triplexes 365(11) Structures of antiparallel triplexes 376(4) PNA triplex structures 380(1) Conclusion 380(1) References 381(8) Structures of guanine-rich and cytosine-rich quadruplexes formed in vitro by telomeric, centromeric, and triplet repeat disease DNA sequences 389(66) Dinshaw J. Patel Serge Bouaziz Abdelali Kettani Yong Wang Introduction 389(1) Telomeric sequence G quadruplexes 390(28) G:C:G:C tetrad-containing quadruplexes 418(13) i-motif quadruplexes containing intercalated C:CH+ mismatch pairs 431(16) Future directions 447(2) References 449(6) DNA bending by adenine-thymine tracts 455(16) Donald M. Crothers Zippora Shakked Global and spectroscopic properties of DNA curvature induced by A-tracts 455(4) X-ray crystallographic studies 459(7) The stereochemical basis of A-tract-dependent curvature 466(2) References 468(3) Structures and interactions of helical junctions in nucleic acids 471(28) David M.J. Lilley The occurrence of helical junctions in biology 471(1) Approaches to the study of branched nucleic acids 472(3) The four-way DNA junction 475(6) The three-way DNA junction 481(4) The four-way RNA junction 485(3) Interaction between DNA junctions and proteins 488(4) Some final conclusions 492(2) References 494(5) DNA higher-order structures 499(34) Wilma K. Olson Overview 499(1) DNA supercoiling 499(5) Computational issues 504(6) Equilibrium structures 510(16) Summary 526(1) References 527(6) Crystallographic structures of RNA oligoribonucleotides and ribozymes 533(34) Benoit Masquida Eric Westhof Introduction 533(1) Crystallization 533(6) Oligoribonucleotide crystals 539(9) Catalytic RNAs 548(12) Conclusions 560(2) References 562(5) RNA structure in solution 567(36) Jacek Nowakowski Ignacio Tinoco, Jr Introduction 567(1) RNA structural elements 567(2) Secondary structures 569(20) Tertiary structures, interactions between secondary structures 589(10) References 599(4) Transfer RNA 603(50) John G. Arnez Dino Moras Introduction 603(1) The free tRNA 604(19) tRNA in aminoacylation 623(19) tRNA in protein synthesis 642(3) Perspectives 645(1) References 646(7) Index 653
