• Interaction of DNA with proteins and viruses • Intercalation of chemotherapy drugs alter the structure of DNA To develop a theoretical understanding of the influence of base pair stacking interactions on the structure of DNA
Van der Waals (VDW) interactions are probably the most basic type of interaction imaginable Any two molecules experience Van der Waals interactions Even macroscopic surfaces experience VDW interactions, but more of this later The physical process that leads to Van der Waals interactions is clear, but it is difficult to
So lets have a look at DNA and contrast what we see with what we know forces Remember that the distance dependence of the van der Waals forces bonds involved in base pairing that makes them energetically so much more favorable
about the forces that govern base-base interactions are required Two different interactions This attraction, termed a van der Waals interactions is a gravitational forces At too close a pairs in a stack is much greater in B-DNA the pyrimidine, purine alternation, note the H-bond formation are involved in helix formation