NMR STUDIES OF RNA/RNA INTERACTION FOR THE BIMOLECULAR TRANSCRIPTION REGULATIO

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This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Viruses use a diverse set of mechanisms for transcriptional regulation of protein expression. One of the most novel transcription regulation mechanisms is found in the single stranded, bipartite RNA genomes of dianthoviruses. An RNA-RNA interaction between an 20 nucleotide element in the coding region of RNA-2 and an 8 nucleotide element of the coat protein subgenomic mRNA promoter RNA-1 has been previously demonstrated (1). To further characterize this mechanism by the NMR spectroscopy method, a model system of short synthetic oligonucleotides was prepared. The 20mer analog of RNA-2 forms a hairpin loop structure with a stable G:U basepair closing the loop as determined by thermal denaturation and NMR methods:1. The dynamics of the synthetic bi-molecular RNA-2 and RNA-1 complex make it unsuited for determination of a high resolution 3 dimensional structure2. The combination of dianthovirus sequence conservation and NMR results provide structural restrains sufficient to generate a low resolution model3. The general features of the model are two helical regions, the stem of the RNA-2 hairpin and a helix formed by the base pairing between the RNA-2 loop and RNA-1. Seven base pairs are present in the complex . The structure has similarity to the structural features of pseudoknots.