|Stacking interactions and the Twist of DNA |
Laboratory for Surface Modification
|Valentino Cooper, Physics Department|
12:00 Noon, Chem. 260
The interactions between stacked nucleobase pairs contribute significantly to the stability of DNA. In addition, numerous studies highlight the stabilizing effect of thymine within DNA. As such knowledge of the relative importance of these interactions may be useful for developing a complete theoretical understanding of DNA. I will present our use of the vdW density functional, (Dion, Rydberg, Schröder, Langreth, Lundqvist, PRL 92, 246401, 2004) to investigate the importance of stacking interactions between Watson-Crick DNA base pairs. I will discuss the relative accuracy of this functional for simulations of stacked nucleobases and our application to stacked nucleobase pair steps, a system which is not possible to study using traditional quantum chemical methods. These results indicate that stacking interactions are essential for defining both the base pair step distance and the helical twist angle of DNA. Furthermore, we show that the stability gained from the presence of thymine is due to vdW interactions between the methyl group of the thymine with neighboring bases.