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. This proposal outlines our need for studying viral RNA using small-angle x-ray scattering methods. In particular we focus on relatively well characterized plant viruses (CCMV and BMV), and outline SAXS experiments that would help elucidate the forces governing self-assembly and organization of genomic material (RNA in this case) inside the viral capsid. By comparing the shape and size of the viral RNA in solution with those of various non-viral (e.g., messenger, ribosomal and random) RNAs of the same length, we hope to verify if the secondary/tertiary structure in the first case is fundamentally different from that of the others. Further, we would like to determine how sensitive these biopolymers are to changes in ionic environment. Specifically, under physiological salt conditions, do the changes in conformation correlate with the internal volume restrictions presented by a protein capsid. We hope these studies will eventually lead us towards answering more subtle questions such as: a) does the sequence of nucleotides in viral RNA explicitly code for a special secondary and tertiary structure conducive to packaging, and b) for a given capsid protein, do the sequence and length of RNA therefore control the preferred size (T-number) of the assembled particle over others.
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