DIAMOD: display and modeling of DNA bending

MOTIVATION DIAMOD (Displayandmodeling ofDNA) was created as a user-friendly software for exploring and better understanding DNA structural variations, particularly DNA bending. It was intended to be as open as possible so that any of the existing or future predictive models can be used with it. RESULTS DIAMOD features graphic display and interactive manipulation of DNA molecules on the screen. Since it works with di-, tri- or tetranucleotide models supplied as external files of angular parameters, it was recently used to evaluate critically all available predictive models for DNA bending. The program has a unique option to insert bends at defined positions in DNA sequence independently of the currently used model, which enables the simulation of both intrinsic and protein-induced kinking. Finally, many output file formats facilitate the sharing of data with other programs and the creation of visually pleasing images. AVAILABILITY The program is available on request to academic users free of charge. It will be distributed via the WWW (http://www-personal.umich.edu/ mensur/software.html). Users with no network access can get a copy directly from the author. CONTACT mensur@umich.edu

[1]  E. Paleček,et al.  Local supercoil-stabilized DNA structures. , 1991, Critical reviews in biochemistry and molecular biology.

[2]  A M Gronenborn,et al.  Intercalation, DNA Kinking, and the Control of Transcription , 1996, Science.

[3]  R. Dickerson,et al.  How proteins recognize the TATA box. , 1996, Journal of molecular biology.

[4]  D. Goodsell,et al.  MPD and DNA bending in crystals and in solution. , 1996, Journal of molecular biology.

[5]  D. Goodsell,et al.  The crystal structure of C-C-A-T-T-A-A-T-G-G. Implications for bending of B-DNA at T-A steps. , 1994, Journal of molecular biology.

[6]  C. Bustamante,et al.  DNA bending by Cro protein in specific and nonspecific complexes: implications for protein site recognition and specificity. , 1994, Science.

[7]  R E Harrington,et al.  New concepts in protein-DNA recognition: sequence-directed DNA bending and flexibility. , 1994, Progress in nucleic acid research and molecular biology.

[8]  A. Travers,et al.  DNA conformation and protein binding. , 1989, Annual review of biochemistry.

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

[10]  P. Sharp,et al.  Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor , 1995, Nature.

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

[12]  I. Brukner,et al.  Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. , 1994, Journal of molecular biology.

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

[14]  T. Richmond,et al.  Crystal structure of a yeast TFIIA/TBP/DNA complex , 1996, Nature.

[15]  C. Pabo,et al.  Distinctive DNA conformation with enlarged major groove is found in Zn-finger-DNA and other protein-DNA complexes. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[16]  D. Lilley,et al.  DNA supercoiling and transcription: topological coupling of promoters , 1996, Quarterly Reviews of Biophysics.

[17]  Edward N. Trifonov,et al.  CURVATURE: software for the analysis of curved DNA , 1993, Comput. Appl. Biosci..

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

[19]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[20]  Paul J. Hagerman,et al.  Sequence-directed curvature of DNA , 1986, Nature.

[21]  H R Drew,et al.  DNA bending and its relation to nucleosome positioning. , 1985, Journal of molecular biology.

[22]  T. James,et al.  Statistical analysis of DNA duplex structural features. , 1995, Methods in enzymology.

[23]  Hans Neurath,et al.  The Kinemage: A tool for scientific communication , 1996 .

[24]  R. Harrington,et al.  Kinked DNA , 1997, Nature.

[25]  D M Crothers,et al.  Intrinsically bent DNA. , 1990, The Journal of biological chemistry.

[26]  I. Brukner,et al.  Trinucleotide models for DNA bending propensity: comparison of models based on DNaseI digestion and nucleosome packaging data. , 1995, Journal of biomolecular structure & dynamics.

[27]  D. Goodsell,et al.  Bending and curvature calculations in B-DNA. , 1994, Nucleic acids research.

[28]  A. Palleschi,et al.  Validity of the nearest-neighbor approximation in the evaluation of the electrophoretic manifestations of DNA curvature. , 1990, Biochemistry.

[29]  H. Drew,et al.  Sequence periodicities in chicken nucleosome core DNA. , 1986, Journal of molecular biology.

[30]  R E Harrington,et al.  Bending and Torsional Flexibility of G/C-rich Sequences as Determined by Cyclization Assays (*) , 1995, The Journal of Biological Chemistry.

[31]  R. Dickerson,et al.  DNA structure from A to Z. , 1992, Methods in enzymology.

[32]  D. K. Hawley,et al.  DNA bending is an important component of site-specific recognition by the TATA binding protein. , 1995, Journal of molecular biology.

[33]  S. Harvey,et al.  The Organic Crystallizing Agent 2-Methyl-2,4-pentanediol Reduces DNA Curvature by Means of Structural Changes in A-tracts* , 1996, The Journal of Biological Chemistry.

[34]  Stephen K. Burley,et al.  Co-crystal structure of TBP recognizing the minor groove of a TATA element , 1993, Nature.

[35]  R. Harrington,et al.  Strained DNA is kinked by low concentrations of Zn2+. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[36]  R E Harrington,et al.  The effects of sequence context on DNA curvature. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[37]  S C Harvey,et al.  What is the basis of sequence-directed curvature in DNAs containing A tracts? , 1995, Journal of biomolecular structure & dynamics.

[38]  D M Crothers,et al.  Sequence elements responsible for DNA curvature. , 1994, Journal of molecular biology.

[39]  D C Richardson,et al.  Kinemages--simple macromolecular graphics for interactive teaching and publication. , 1994, Trends in biochemical sciences.

[40]  S. Diekmann,et al.  Definitions and nomenclature of nucleic acid structure parameters. , 1989, Journal of molecular biology.

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

[42]  R E Harrington,et al.  Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. , 1991, Proceedings of the National Academy of Sciences of the United States of America.