Title | Theoretical studies of d(A:T)-based parallel-stranded DNA duplexes |
Publication Type | Journal Article |
Year of Publication | 2001 |
Authors | Cubero, E, Luque FJ, Orozco M |
Journal | Journal of the American Chemical Society |
Volume | 123 |
Issue | 48 |
Pagination | 12018 - 12025 |
Date Published | 2001/12/05/ |
Keywords | DNA/chemistry; Models, Molecular; Nucleic Acid Conformation; Poly dA-dT/chemistry |
Abstract | Poly d(A:T) parallel-stranded DNA duplexes based on the Hoogsteen and reverse Watson-Crick hydrogen bond pairing are studied by means of extensive molecular dynamics (MD) simulations and molecular mechanics coupled to Poisson-Boltzmann (MM-PB/SA) calculations. The structural, flexibility, and reactivity characteristics of Hoogsteen and reverse Watson-Crick parallel duplexes are described from the analysis of the trajectories. Theoretical calculations show that the two parallel duplexes are less stable than the antiparallel Watson-Crick duplex. The difference in stability between antiparallel and parallel duplexes increases steadily as the length of the duplex increases. The reverse Watson-Crick arrangement is slightly more stable than the Hoogsteen duplex, the difference being also increased linearly with the length of the duplex. A subtle balance of intramolecular and solvation terms is responsible for the preference of a given helical structure. |