Energetic of left and right handed models of DNA

Abstract

It has been shown by model building studies that various right-handed and left-handed models are compatible with x-ray data of B-DNA and C-DNA. These models are also found to be in good agreement with IR dichroism data. Detailed potential energy calcns. have now been carried out for these models, viz., right- and left-handed B-DNA and right-and left-handed C-DNA. It was found that base sugar stacking and interactions involving the phosphate groups are the dominant forces for stabilizing a particular structure. For some sequences, viz., A-A, T-A, and C-A, left-handed stacking was quite favorable in both B and C structures; however, intranucleotide interactions made the left-handed B-DNA unfavorable, whereas the left-handed C-DNA structure was more stable, for all the sequences, than the right-handed C-DNA structure, proposed from fiber data. For the hexanucleoside pentaphosphate fragments, the same trend was obsd., with the right-handed B-DNA being the most stable of the 4 models studied. However, the left-handed C-DNA structure was only marginally higher in energy, particularly if the shielding effect of the counterions, on the phosphate group was taken into consideration.