Organization of DNA in chromatin.

Abstract

Conformational changes in DNA that accompany drug intercalation suggests the possibility that DNA first bends or kinks to accept an intercalative drug or dye. Kinking is made possible by altering the normal C2'' endo deoxyribose sugar ring puckering in B DNA to a mixed sugar puckering pattern of the type C3'' endo (3''-5'') C2'' endo and partially unstacking base-pairs. A kinking scheme such as this would require minimal stereochemical rearrangement and would involve small energies. A conformational change such as this could possibly be used by proteins in their interactions with nucleic acids. An interesting superhelical DNA structure formed by kinking DNA every 10 base-pairs is described. The structure may be used in the organization of DNA in chromatin.