Book of Abstracts: Albany 2003

category image Albany 2003
Conversation 13
Abstract Book
June 17-21 2003

Breaking Base Pairs in a DNA Double Helix

We have been using restrained molecular dynamics simulation techniques on the nanosecond timescale to investigate the conformational and free energy changes upon DNA deformation. Amongst the larger deformations of the double helix, base pair disruption plays important roles in the biological functioning of nucleic acids. This initial step is necessary to making reactive sites on the bases, normally buried in the interior of the helix, accessible for chemical transformation. We have characterized single and multiple openings of the A, T, G, and C bases into both the minor and major grooves of B-DNA in solution. Further rotation of bases out of the double helix leads to base flipping, a phenomenon first observed in crystal structures of DNA modifying enzymes complexed with their target sequences. We have studied the flipping of a cytosine in the target sequence of HhaI methyltransferase in solution and in the protein environment to understand better the role of the enzyme in the flipping process.

Breaking the base pair in a DNA oligomer reveals the energetics of pairing and stacking interactions and shows its coupling to a number of factors including DNA bending, backbone flexibility, hydration patterns, and ion distribution. Partial opening leads to the creation of potentially stabilizing water bridging sites. The associated free energy is compatible with current experimental data for imino proton exchange in solution. Base flipping, however, requires higher free energy along either the minor or major groove pathways, which points to the need for active enzyme participation in extracting a base. In this connection, key protein residues are shown to be involved in the initial perturbation of the base pair and further stabilization of the flipping and orphan bases.

Péter Várnai
Emmanuel Giudice
Richard Lavery

Laboratoire de Biochimie Théorique
Institut de Biologie
13 rue Pierre et Marie Curie
Paris 75005, France

References and Footnotes
  1. Giudice, E., Várnai, P., Lavery, R. ChemPhysChem, 2, 673 (2001).
  2. Várnai, P., Lavery, R. J. Am. Chem. Soc., 124, 7272 (2002)
  3. Giudice, E., Várnai, P., Lavery, R. Nucleic Acids Res., 31, 1434, (2003)