Book of Abstracts: Albany 2005

category image Volume 22
No. 6
June 2005

Sequence-Dependent Fluctuational Opening of Base Pairs in DNA

Thermal motions within the double helix play a critical role in the DNA structure and function. Although very rare, the events of Watson-Crick base-pair make the active groups of DNA bases (which are otherwise buried within the double helix) accessible for interaction with proteins and chemicals. Fluctuational base-pair opening implies the disruption of hydrogen bonds between the complementary bases and flipping of the base out of the helical stack.

The determination of stacking parameters (1) allows us to revisit the issue of base-pair opening probabilities dependence on the DNA sequence. The partition function calculates the base pair opening probability at every position based on the loss of two stacking interactions and one base pairing. Our model also includes a term, which accounts for the unfavorable position of the exposed base.

We find that these thermodynamic parameters suggest non-obvious sequence dependent base-pair opening probabilities. In fact, this model predicts that some AT pairs will behave more like GC pairs in base pair opening events, and vice versa.

We compare the results of our calculations with literature data on base pair opening probabilities obtained by the NMR approach.

References and Footnotes
  1. Protozanova, E., Yakovchuk, P., and Frank-Kamenetskii, M. D. J. Mol. Biol. 342, 775-785 (2004).

Andrew Krueger*
Ekaterina Protozanova
Maxim D. Frank-Kamenetskii

Center for Advanced Biotechnology
Department of Biomedical Engineering
Boston University
36 Cummington Street
Boston, MA 02215, USA

*Phone: (617)353-8492
Fax: (617)353-8501
Email: akrueger@bu.edu