Base pairing probabilities in a complete HIV-1 RNA

We have calculated the base pair probability distribution for the secondary structure of a full length HIV-1 genome using the partition function approach introduced by McCaskill (1990). By analyzing the full distribution of base pair probabilities instead of a restricted number of secondary structures, we gain more complete and reliable information about the secondary structure of HIV-1. We introduce methods that condense the information in the probability distribution to one value per nucleotide in the sequence. Using these methods we represent the secondary structure as a weighted average of the base pair probabilities, and we can identify interesting secondary structures that have relatively well-defined base pairing. The results show high probabilities for the known secondary structures at the 5'-end of the molecule that have been predicted on the basis of biochemical data. The Rev response element (RRE) appears as a distinct element in the secondary structure, It has a meta-stable domain at the high affinity site for the binding of Rev, The overall structure decomposes into fairly small independent structures in the first 4000 bases of the molecule, The remaining 5000 bases (excluding the terminal repeat) form a single, large structure, on top of which the RRE is located.