Molecule of the Month: DNA
Atomic structures reveal how the iconic double helix encodes genomic information
A Central Icon
Additional 'extragenetic' information is read from the surfaces that are left exposed in the double helix. In the major groove (the wider of the two grooves in the structure on the left), the different base pairs have a characteristic pattern of chemical groups that carry information, shown by green arrows in the close-up diagrams on the right. These include hydrogen bond donors (D) and acceptors (A) as well as a site with a large, bulky group in adenine-thymine base pairs (large asterisk) or a small group in guanine-cytosine base pairs (small asterisk). In the minor groove, there is a different arrangement of chemical groups that carry additional information, indicated with blue arrows in the diagram on the right and the blue letters in the structure on the left. As revealed in hundreds of structures in the PDB, this extragenetic information is used by proteins to read the genetic code in DNA without unwinding the double helix. It is also targeted by a number of toxins and drugs that attack DNA.
Variations on a Theme
Exploring the Structure
DNA Double Helix
We often think of DNA as a perfect, smooth double helix. In reality, DNA has a lot of local structure. The small piece of DNA shown here, from PDB entry 1bna , shows some of the common variations. At the top, the helix is bent to the left, distorted by the way that the helices are packed into the crystal. At the bottom, two of the bases are strongly propeller twisted--they are not in one perfect plane. This improves the way that the bases stack on top of one another along each strand, stabilizing the whole double helix. As more and more structures of DNA are studied, it is becoming clear that DNA is a dynamic molecule, quite flexible on its own, which is bent, kinked, knotted and unknotted, unwound and rewound by the proteins that interact with it. Click on the image for an interactive JSmol view of this structure.
Topics for Further Discussion
- Researchers have determined the structures of many small DNA helices with mispaired bases, and some of the enzymes that help correct them. Try searching for "DNA mispair" in the main RCSB PDB site to see them.
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- 2dcg: Wang, A.H., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G., Rich, A. (1979) Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature 282: 680-686
- 1bna: Drew, H.R., Wing, R.M., Takano, T., Broka, C., Tanaka, S., Itakura, K., Dickerson, R.E. (1981) Structure of a B-DNA dodecamer: conformation and dynamics. Proceedings of the National Academy of Science USA 78: 2179-2183
- 1ana: Conner, B.N., Yoon, C., Dickerson, J.L., Dickerson, R.E. (1984) Helix geometry and hydration in an A-DNA tetramer: IC-C-G-G Journal of Molecular Biology 174: 663-695
- Richard E. Dickerson (1983) The DNA Helix and How it is Read. Scientific American 249 (December), pp. 94-111.
- Wolfram Saenger (1994) Principles of Nucleic Acid Structure (Springer-Verlag, New York).
- The Nucleic Acid Database, http://ndbserver.rutgers.edu/
November 2001, David Goodselldoi:10.2210/rcsb_pdb/mom_2001_11