Protein-nucleic acid interactions play essential roles in cellular processes and in the functioning of mammalian retroviruses. To study these interactions the triplet states of aromatic residues will be studied using phosphorescence and optical detection of magnetic resonance (ODMR). Alloproteins will incorporate Trp, Phe, and Tyr analogs that can be selectively excited at the red edge in nucleic acid complexes. Of importance is uncovering factors that influence the stability and sequence selectivity of nucleic acid binding and the extent to which they are influenced by aromatic stacking. The primary focus will be HIV-1 and SIV. Foremost will be studies of the interactions of nucleocapsid (NC) proteins with the RNA genome during maturation in RNA encapsidation. The NC proteins are characterized by conserved Cys-X2-Cys-X4-His-X4-Cys retroviral zinc finger motifs containing aromatic residues at specific sites. Zinc fingers have been found to undergo base-stacking with model RNAs. Similar interactions will be sought. RNA substrates will be extended to sequences containing psi, the encapsidation region of genomic RNA. Spin-lattice relaxation of the triplet state will be studied as a possible reporter of structure. Effects of inducer and operator binding on single-W constructs of E. coli lac repressor will be studied. ODMR or interleukin-1-beta alloproteins will be used to test effects of Trp analog incorporation on protein structure.
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