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DNA

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B-DNA


Contents

History of DNA Structure

The following summary is copied from an Atlas of Macromolecules with permission:

Genes were shown to reside in DNA in 1944 (Avery et al.) and this became widely accepted after the 1952 experiments of Hershey and Chase. The double helical structure of the DNA was predicted by James Watson and Francis Crick in 1953 (Nobel Prize, 1962). Their prediction was based in part upon X-ray diffraction studies by Rosalind Franklin, to whom Watson and Maurice Wilkins gave inadequate credit[8]. The predicted B-form double helix was not confirmed with atomic-resolution crystal structures until 1973, first by using dinucleotides of RNA (Rosenberg et al.). The first crystal structure containing more than a full turn of the double helix was not solved until 1980 (1bna, 1981, 12 base pairs). The lag of more than a quarter century between prediction and empirical confirmation involved development of X-ray crystallography for macromolecules, and the need to produce a short, defined sequence of DNA for crystallization. This brief account is based upon a review by Berman, Gelbin, and Westbrook [9], where the references will be found.

DNA Models

The model of DNA used in the scenes in the present article is a theoretical model[10] (Image:B-DNA.pdb), not available in the Protein Data Bank. The PDB file does not follow certain PDB format conventions:

  • Bases are designated ADE, CYT, GUA, and THY instead of the standard DA, DC, DG and DT.
  • The chains are not named. Typically they would be named A and B.

One chain contains residues numbered 1-12 in sequence CGCG AATT CGCG. The other chain contains residues numbered 13-24 with an identical (antiparallel) sequence.

Theoretical models typically represent idealized DNA conformation, whereas real DNA may have various irregularities including kinks and bends (see examples bound to the Lac repressor). There are plenty of empirical models for DNA, the first having become available in the 1970's and 80's (see above). In May, 2012, the Protein Data Bank contains nearly 4,000 entries containing DNA. Over 1,300 contain only DNA, while over 2,000 contain protein-DNA complexes. Over 100 entries contain protein, DNA and RNA, and over 100 contain DNA/RNA hybrid molecules.

For more interactive visualizations of DNA, see DNA.MolviZ.Org, a tutorial that is available in nine languages.

See Also

Proteopedia Articles

External Resources

Interpretation of X-Ray Diffraction by DNA

References

  1. 1.0 1.1 http://www.genome.gov/25520880
  2. Dahm R. Discovering DNA: Friedrich Miescher and the early years of nucleic acid research. Hum Genet. 2008 Jan;122(6):565-81. Epub 2007 Sep 28. PMID:17901982 doi:10.1007/s00439-007-0433-0
  3. 3.0 3.1 A Structure for Deoxyribose Nucleic Acid Watson J.D. and Crick F.H.C. Nature 171, 737-738 (1953)
  4. 4.0 4.1 4.2 Watson, James D, Nancy H. Hopkins, Jeffrey W. Roberts, Joan Argetsinger Steitz, Alan M.Weiner Molecular Biology of Gene (4th ed.). The Benjamin/Cummings Publishing Company Inc.pp. 239-249. ISBN 0-8053-9612-8
  5. SantaLucia J Jr. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci U S A. 1998 Feb 17;95(4):1460-5. PMID:9465037
  6. Saenger, Wolfram (1984). Principles of Nucleic Acid Structure (1st ed). Springer-Verlag. pp. 398. ISBN 0-12-645750-6.
  7. Rawn,David J. "Biochemistry"(1st ed.) Harper&Row,Publishers, Inc.pp. 1024-1050. ISBN-0-06045335-4
  8. Maddox, Brenda: Rosalind Franklin: Dark Lady of DNA, HarperCollins, 2002
  9. Berman HM, Gelbin A, Westbrook J. Nucleic acid crystallography: a view from the nucleic acid database. Prog Biophys Mol Biol. 1996;66(3):255-88. PMID:9284453
  10. Chandrasekaran R, Arnott S. The structure of B-DNA in oriented fibers. J Biomol Struct Dyn. 1996 Jun;13(6):1015-27. PMID:8832384

Proteopedia Page Contributors and Editors (what is this?)

Adithya Sagar, Eran Hodis, Ala Jelani, Eric Martz, Wayne Decatur, Karl Oberholser, David Canner, Joseph M. Steinberger, Angel Herraez, Joel L. Sussman, Frédéric Dardel

DOI: http://dx.doi.org/10.14576/100853.1391042 (?)
Citation: Jelani A, Hodis E, Martz E, Sussman J L, Sagar A, Decatur W, Canner D, Herraez A, Dardel F, Oberholser K, Steinberger J M, 2012, "DNA", Proteopedia, DOI: http://dx.doi.org/10.14576/100853.1391042
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