95-07-057

#
Abstract:

Base Pairing Probabilities in a Complete HIV-1 RNA

## Martijn A. Huynen, Alan S. Perelson, Wayne A. Vieira, and
Peter F. Stadler

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 MasCaskill (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 strucutre. 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.

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