Friday, August 14, 2009

What is an RNA Genome?

The idea of an RNA genome is, for now, taken in the context of retroviruses like HIV.
Joseph Watts and Kevin Weeks at UNC (Chapel-Hill), have used a technique called SHAPE (selective 2' hydroxyl acylation analyzed by primer extension), to determine conformational "flexibilities" of nucleotides, and extrapolate their results to secondary structure prediction of the RNA (9173 nucleotides) in HIV. Their results can be found at: DOI. The marketing title of their results is "Architecture and secondary structure of an entire HIV-1 genome".
It seems like these flexibilities are just a determination of whether there is base-pairing or not.