The overall goal of this research is to determine the effects that polyamines have on the structure and dynamics, and thus on the interactions, of DNA. Polyamine levels are markedly elevated in rapidly proliferating cells and many tumors, and it is important to establish firm connections between these observations and molecular mechanisms. Our studies will emphasize three areas. (1) Spermidine and spermine have some dramatic effects on DNA secondary and tertiary structure, in the B-Z transition and in condensation. We wish to determine whether more subtle, but perhaps equally important, local twisting and deformation effects may arise, through measurements of the hydrodynamics of supercoiled DNA in the presence of polyamines. (2) Polyamines, like other cations, raise the melting temperature of DNA, presumably through a combination of electrostatic and specific binding effects. This implies an effect on the base pairing and stacking dynamics of DNA, which may affect its interactions with enzymes and ligands. We wish to investigate these dynamic effects by proton exchange and by triplet anisotropy decay and hydrodynamic measurements of DNA twisting and bending. (3) Polyamines affect replication, transcription, and translation. This implies that they influence the binding of proteins to nucleic acids. We wish to test this hypothesis by in vitro measurements of the effects of polyamines on the binding of wheat germ RNA polymerase II to DNA. Particular attention will be paid to differential effects on specific binding to promoter sites compared to nonspecific binding.
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