A glossary of DNA structures from A to Z.

The right-handed double-helical Watson-Crick model for B-form DNA is the most commonly known DNA structure. In addition to this classic structure, several other forms of DNA have been observed and it is clear that the DNA molecule can assume different structures depending on the base sequence and environment. The various forms of DNA have been identified as A, B, C etc. In fact, a detailed inspection of the literature reveals that only the letters F, Q, U, V and Y are now available to describe any new DNA structure that may appear in the future. It is also apparent that it may be more relevant to talk about the A, B or C type dinucleotide steps, since several recent structures show mixtures of various different geometries and a careful analysis is essential before identifying it as a 'new structure'. This review provides a glossary of currently identified DNA structures and is quite timely as it outlines the present understanding of DNA structure exactly 50 Years after the original discovery of DNA structure by Watson and Crick.

[1]  M. Viswamitra,et al.  Visualisation of a 2'-5' parallel stranded double helix at atomic resolution: crystal structure of cytidylyl-2',5'-adenosine. , 1991, Nucleic Acids Research.

[2]  H M Berman,et al.  A standard reference frame for the description of nucleic acid base-pair geometry. , 2001, Journal of molecular biology.

[3]  R. Chandrasekaran,et al.  Structure of poly d(A).poly d(T). , 1992, Journal of biomolecular structure & dynamics.

[4]  M. Bansal,et al.  Conformational polymorphism in G-tetraplex structures: strand reversal by base flipover or sugar flipover. , 1993, Nucleic acids research.

[5]  S. Neidle Oxford handbook of nucleic acid structure , 1998 .

[6]  L. Betts,et al.  A Nucleic Acid Triple Helix Formed by a Peptide Nucleic Acid-DNA Complex , 1995, Science.

[7]  M. Guéron,et al.  A tetrameric DNA structure with protonated cytosine-cytosine base pairs , 1993, Nature.

[8]  A. Wang,et al.  Evidence for a new Z-type left-handed DNA helix: properties of Z(WC)-DNA. , 1990, Nucleic acids research.

[9]  S. Diekmann,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, The EMBO journal.

[10]  S. Arnott,et al.  Structural details of double-helix observed for DNAs containing alternating purine and pyrimidine sequences. , 1974, Journal of molecular biology.

[11]  L. Arnold,et al.  The unusual X-form DNA in oligodeoxynucleotides: dependence of stability on the base sequence and length. , 1996, Journal of biomolecular structure & dynamics.

[12]  F. Crick,et al.  Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid , 1953, Nature.

[13]  G. G. Stokes "J." , 1890, The New Yale Book of Quotations.

[14]  L. Delbaere,et al.  M-DNA: A complex between divalent metal ions and DNA which behaves as a molecular wire. , 1999, Journal of molecular biology.

[15]  T. Koller,et al.  Preparation and characterization of form V DNA, the duplex DNA resulting from association of complementary, circular single-stranded DNA. , 1979, Journal of molecular biology.

[16]  V. P. Chuprina,et al.  The structure of poly(dA):poly(dT) in a condensed state and in solution. , 1987, Nucleic acids research.

[17]  S C Schultz,et al.  DNA G-quartets in a 1.86 A resolution structure of an Oxytricha nova telomeric protein-DNA complex. , 2001, Journal of molecular biology.

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

[19]  W. Saenger,et al.  Molecular structure of deoxyadenylyl-3'-methylphosphonate-5'-thymidine dihydrate, (d-ApT x 2H2O), a dinucleoside monophosphate with neutral phosphodiester backbone. An X-ray crystal study. , 1983, Nucleic acids research.

[20]  Fritz Eckstein,et al.  Chiral phosphorothioate analogues of B-DNA: The crystal structure of Rp-d¦Gp(S)CpGp(S)CpGp(S)C¦☆ , 1993 .

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

[22]  H. R. Wilson,et al.  THE MOLECULAR CONFIGURATION OF DEOXYRIBONUCLEIC ACID. IV. X-RAY DIFFRACTION STUDY OF THE A FORM. , 1965, Journal of molecular biology.

[23]  W. Olson,et al.  A-form conformational motifs in ligand-bound DNA structures. , 2000, Journal of molecular biology.

[24]  A. Leslie,et al.  Left-handed DNA helices , 1980, Nature.

[25]  H. Urata [Effect of chirality of ribose on nucleic acid structure and function]. , 1999, Yakugaku zasshi : Journal of the Pharmaceutical Society of Japan.

[26]  C. Cantor,et al.  Sequences that adopt non-B-DNA conformation in form V DNA as probed by enzymic methylation. , 1987, Journal of molecular biology.

[27]  T. Maniatis,et al.  The structure of DNA , 1992 .

[28]  J. Dahlberg,et al.  Single strands, triple strands, and kinks in H-DNA. , 1988, Science.

[29]  J. Goodfellow,et al.  The intrinsic curvature of a 51 bp K-DNA fragment of Leishmania tarentolae: a molecular model. , 1998, Journal of biomolecular structure & dynamics.

[30]  J. Dahlberg,et al.  Topology and formation of triple-stranded H-DNA. , 1989, Science.

[31]  A G Leslie,et al.  Polymorphism of DNA double helices. , 1980, Journal of molecular biology.

[32]  K. Hoogsteen,et al.  The structure of crystals containing a hydrogen‐bonded complex of 1‐methylthymine and 9‐methyladenine , 1959 .

[33]  Struther Arnott,et al.  The structure of B-DNA in oriented fibers. , 1996, Journal of biomolecular structure & dynamics.

[34]  Stephen Neidle,et al.  Crystal structure of the potassium form of an Oxytricha nova G-quadruplex. , 2002, Journal of molecular biology.

[35]  A. Rich,et al.  The crystal structures of purines, pyrimidines and their intermolecular complexes. , 1970, Progress in nucleic acid research and molecular biology.

[36]  N. Seeman,et al.  Three-Dimensional Tertiary Structure of Yeast Phenylalanine Transfer RNA , 1974, Science.

[37]  Yoshiaki Ueda,et al.  Synthesis and properties of mirror-image DNA , 1992, Nucleic Acids Res..

[38]  M. Bansal,et al.  Hairpin and parallel quartet structures for telomeric sequences. , 1992, Nucleic acids research.

[39]  J. Wengel,et al.  The solution structure of a locked nucleic acid (LNA) hybridized to DNA. , 1999, Journal of biomolecular structure & dynamics.

[40]  E. Blackburn The molecular structure of centromeres and telomeres. , 1984, Annual review of biochemistry.