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HIV

In a real tour de force of chemical probing, Kevin Weeks and his collaborators at the University of North Carolina used the SHAPE technology to determine the secondary structure of the complete RNA genome of the HIV-1 virus. Their beautiful paper shows some extremely interesting functional consequences of the HIV-1 secondary structure.

Remarkably, only 31% of the 9142 nucleotides are involved in base pairing, compared to ~60% in ribosomal RNAs. (Also for comparison, ~60% of the nucleotides in long random sequences are predicted to be paired using standard thermodynamic prediction methods, and, if the HIV-1 sequence is shuffled, again ~60% of the nucleotides are predicted to be involved in base pairing.)

There must be some aspects of the composition and arrangement of the sequence in the HIV-1 genome to produce such a small fraction of base pairs. We have undertaken an examination of this issue, and a manuscript is about to be submitted....  
Watch this space!