Homologous Pairing between Long DNA Double Helices

Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it has to be invoked to account for various biological data. Using quantum chemistry, molecular mechanics, and hints from recent genetics experiments I show here that direct recognition between homologous dsDNA is possible through formation of short quadruplexes due to direct complementary hydrogen bonding of major groove surfaces in parallel alignment. The constraints imposed by the predicted structures of the recognition units determine the mechanism of complexation between long dsDNA. This mechanism and concomitant predictions agree with available experimental data and shed light upon the sequence effects and the possible involvement of topoisomerase II in the recognition.Comment: 10 pages, 7 figures, Includes Supplemental Material. To appear in Phys. Rev. Let

The torque transfer coefficient in DNA under torsional stress

In recent years, significant progress in understanding the properties of supercoiled DNA has been obtained due to nanotechniques that made stretching and twisting of single molecules possible. Quantitative interpretation of such experiments requires accurate knowledge of torques inside manipulated DNA. This paper argues that it is not possible to transfer the entire magnitudes of external torques to the twisting stress of the double helix, and that a reducing torque transfer coefficient (TTC<1) should always be assumed. This assertion agrees with simple physical intuition and is supported by the results of all-atom molecular dynamics (MD) simulations. According to MD, the TTCs around 0.8 are observed in nearly optimal conditions. Reaching higher values requires special efforts and it should be difficult in practice. The TTC can be partially responsible for the persistent discrepancies between the twisting rigidity of DNA measured by different methods.Comment: 5 pages, 4 figures. To appear in Phys. Rev.