The specific goal of this study is to use solid state NMR to gain a detailed knowledge of the structure and internal dynamics of synthetic oligoribonucleotides which contain secondary structural domains which serve as binding sites for Human immunodeficiency virus (HIV) proteins. Specifically we will use solid state 2H NMR to investigate the dynamics and solid state 13C NMR to investigate the structure of the purine-rich """"""""bubble"""""""" or internal loop which constitutes the binding site for Rev on the RNA Rev Response Element (RRE). The presence of a noncanonical GG base pair in the internal loop is required for binding and can only be replaced by an AA base pair. The GG base pair will be labeled with 2H on the furanose ring and at the 5' position in the backbone in order to investigate the sugar-phosphate configuration of this region .The AA base pair will be similarly labeled in order to investigate the manner in which the structure of this domain influences protein binding. 2H NMR studies will also be conducted of the nucleotides in the bulged loop of TAR, which is the binding site for Tat, another HIV protein. The dynamics and structure of the nucleotides in the bulged loop will be studied in the native form and bound to arginine.
