A standard reference frame for the description of nucleic acid base-pair geometry.

A common point of reference is needed to describe the three-dimensional arrangements of bases and base-pairs in nucleic acid structures. The different standards used in computer programs created for this purpose give rise to con¯icting interpretations of the same structure.1 For example, parts of a structure that appear ``normal'' according to one computational scheme may be highly unusual according to another and vice versa. It is thus dif®cult to carry out comprehensive comparisons of nucleic acid structures and to pinpoint unique conformational features in individual structures

[1]  E Westhof,et al.  On the wobble GoU and related pairs. , 2000, RNA.

[2]  V. Zhurkin,et al.  DNA stretching and compression: large-scale simulations of double helical structures. , 1999, Journal of molecular biology.

[3]  W. Olson,et al.  Overview of nucleic acid analysis programs. , 1999, Journal of biomolecular structure & dynamics.

[4]  W. Olson,et al.  Resolving the discrepancies among nucleic acid conformational analyses. , 1999, Journal of molecular biology.

[5]  V. Zhurkin,et al.  DNA sequence-dependent deformability deduced from protein-DNA crystal complexes. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[6]  R. Dickerson,et al.  DNA bending: the prevalence of kinkiness and the virtues of normality. , 1998, Nucleic acids research.

[7]  M. A. El Hassan,et al.  Structure and conformation of helical nucleic acids: analysis program (SCHNAaP). , 1997, Journal of molecular biology.

[8]  H M Berman,et al.  Conformations of the sugar-phosphate backbone in helical DNA crystal structures. , 1997, Biopolymers.

[9]  A. R. Srinivasan,et al.  Geometric parameters in nucleic acids: Nitrogenous bases , 1996 .

[10]  C R Calladine,et al.  The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme. , 1995, Journal of molecular biology.

[11]  B. Ravi,et al.  NUPARM and NUCGEN: software for analysis and generation of sequence dependent nucleic acid structures , 1995, Comput. Appl. Biosci..

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

[13]  G. Baudoux,et al.  A database study of intermolecular NH⋯O hydrogen bonds for carboxylates, sulfonates and monohydrogen phosphonates , 1995 .

[14]  G. Hummer,et al.  An extension of the rigorous base-unit oriented description of nucleic acid structures. , 1994, Journal of biomolecular structure & dynamics.

[15]  A. Gavezzotti,et al.  Geometry of the Intermolecular X-H.cntdot..cntdot..cntdot.Y (X, Y = N, O) Hydrogen Bond and the Calibration of Empirical Hydrogen-Bond Potentials , 1994 .

[16]  E. Pednault,et al.  Nucleic acid structure analysis. Mathematics for local Cartesian and helical structure parameters that are truly comparable between structures. , 1994, Journal of molecular biology.

[17]  W. Olson,et al.  The effect of mathematics and coordinate system on comparability and "dependencies" of nucleic acid structure parameters. , 1994, Journal of molecular biology.

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

[19]  R L Jernigan,et al.  Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA. , 1993, Journal of molecular biology.

[20]  E. Pednault,et al.  Nucleic acid structure analysis: a users guide to a collection of new analysis programs. , 1993, Journal of biomolecular structure & dynamics.

[21]  A. R. Srinivasan,et al.  The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids. , 1992, Biophysical journal.

[22]  R. Dickerson,et al.  Analysis of local helix geometry in three B-DNA decamers and eight dodecamers. , 1991, Journal of molecular biology.

[23]  R. Dickerson,et al.  Structure of the B-DNA decamer C-C-A-A-C-G-T-T-G-G and comparison with isomorphous decamers C-C-A-A-G-A-T-T-G-G and C-C-A-G-G-C-C-T-G-G. , 1991, Journal of molecular biology.

[24]  C. Foces-Foces,et al.  N⋯Nsp2 hydrogen interactions in organic crystals , 1990 .

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

[26]  M. Bansal,et al.  A self-consistent formulation for analysis and generation of non-uniform DNA structures. , 1989, Journal of biomolecular structure & dynamics.

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

[28]  R. Dickerson,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, Journal of biomolecular structure & dynamics.

[29]  C. Tung,et al.  A rigorous basepair oriented description of DNA structures. , 1988, Journal of biomolecular structure & dynamics.

[30]  R Lavery,et al.  The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids. , 1988, Journal of biomolecular structure & dynamics.

[31]  C. Wilson.  Analysis of conformational parameters in nucleic acid fragments. II. Co-crystal complexes of nucleic acid bases. , 1988, Nucleic acids research.

[32]  W. Hunter,et al.  The structure of guanosine-thymidine mismatches in B-DNA at 2.5-A resolution. , 1993, The Journal of biological chemistry.

[33]  A. Takénaka,et al.  Model for interactions of amino acid side chains with Watson-Crick base pair of guanine and cytosine: crystal structure of 9-(2-carbamoylethyl)guanine and 1-methylcytosine complex. , 1985, Biochemistry.

[34]  H R Drew,et al.  A base-centred explanation of the B-to-A transition in DNA. , 1984, Journal of molecular biology.

[35]  A. Takénaka,et al.  A Model for Interactions of Amino Acid Side Chains with Watson-Crick Base Pair of Guanine and Cytosine. Crystal Structures of 9-(2-Carboxyethyl)guanine and Its Crystalline Complex with 1-Methylcytosine , 1984 .

[36]  H R Drew,et al.  Reversible bending and helix geometry in a B-DNA dodecamer: CGCGAATTBrCGCG. , 1982, The Journal of biological chemistry.

[37]  H R Drew,et al.  Structure of a B-DNA dodecamer: conformation and dynamics. , 1981, Proceedings of the National Academy of Sciences of the United States of America.

[38]  F. Allen,et al.  The Cambridge Crystallographic Data Centre: computer-based search, retrieval, analysis and display of information , 1979 .