Book of Abstracts: Albany 2009
June 16-20 2009
© Adenine Press (2008)
Stability of right-handed DNA crossovers mediated by divalent cations in solution
The assembly of DNA duplexes into higher-order structures plays a major role in many vital cellular functions such as recombination, chromatin packaging and gene regulation. However, little is currently known about the molecular structure and stability of direct DNA-DNA interactions that are required for such functions. Although the close approach of DNA segments is usually considered repulsive, recent experimental and theoretical studies have indicated that short-range attraction may exist between DNA double helices in the presence of divalent cations. DNA helices have found natural ways to minimize electrostatic repulsion between double helices in crystal structures of DNA. Within crystals, B-DNA can form either tight right-handed crossovers self-fitted by groove-backbone interaction or left-handed crossovers assembled by groove-groove juxtaposition. In the present work, molecular dynamics simulations are used to evaluate the stability of such crossovers in various ionic conditions. Our results show, for the first time, that right-handed DNA crossovers are thermodynamically stable in a solution environment that contains at least one Mg2+ per four phosphate groups. A structural analysis highlights the importance of sequence-specific phosphate-cytosine interactions in the major groove, reinforced by preferential Mg2+ binding at these anchor sites. Free-energy calculations reveal an attractive force at short-range that stabilises such crossover structures with inter-axial separation of helices within 20 Å. Right-handed crossovers, however, dissociate swiftly in the presence of monovalent ions only, even at 1M concentration. Left-handed crossovers are assembled by sequence-independent juxtaposition of the helices which appeared unstable even at the highest concentration of Mg2+ studied here. Our study provides new molecular insights into chiral association of DNA duplexes and highlights the unique role divalent cations play in stabilization, in agreement with recently published experimental data. These results may serve as a rational basis to understand the role DNA crossovers play in many biological processes.
1 Department of Chemistry and Biochemistry