Kinetic assembling of the biologically active secondary structure for CAR, the target sequence for the Rev protein of HIV-1

We predict the metastable secondary structure for the CAR (cis anti-repressor sequence) which is active in the regulation of the interaction with the Rev protein of HIV-1. We prove that the active structure sustained between nts 7364 and 7559 of the env RNA is the most probable metastable structure whose formation is kinetically governed and not thermodynamically determined. The structure is obtained by means of a Monte Carlo simulation which computes refolding events which occur as the CAR portion of the viral RNA is being assembled. Thus, the regulatory role of the secondary structure is determined as soon as the new RNA has been synthesized and it is preserved for further recognition by the Rev protein. In analogy with previous work by the author, it is shown that the destabilization by site-directed mutagenesis of the secondary structure for a non-chain-specific recognition site enhances the Rev response.