Structure and dimerization of HIV-1 kissing loop aptamers

Dimerization of two homologous strands of genomic RNA is an essential featu re of the retroviral replication cycle. In HIV-1, genomic RNA dimerization is facilitated by a conserved stem-loop structure located near the 5 ' end of the viral RNA called the dimerization initiation site (DIS). The DIS loo p is comprised of nine nucleotides, six of which define an autocomplementar y sequence flanked by three conserved purine residues. Base-pairing between the loop sequences of two copies of genomic RNA is necessary for efficient dimerization. We previously used in vitro evolution to investigate a possi ble structural basis for the marked sequence conservation of the DIS loop. In this study, chemical structure probing, measurements of the apparent dis sociation constants, and computer structure analysis of dimerization-compet ent aptamers were used to analyze the dimers' structure and binding. The se lected aptamers were variants of the naturally occurring A and B subtypes. The data suggest that a sheared base-pair closing the loop of the DIS is im portant for dimerization in both subtypes. On the other hand, the open or c losed state of the last base-pair in the stem differed in the two subtypes. This base-pair appeared closed in the subtype A DIS dimer and open in subt ype B. Finally, evidence for a cross-talk between nucleotides 2, 5, and 6 w as found in some, but not all, loop contexts, indicating some structural pl asticity depending on loop sequence. Discriminating between the general rul es governing dimer formation and the particular characteristics of individu al DIS aptamers helps to explain the affinity and specificity of loop-loop interactions and could provide the basis for development of drugs targeted against the dimerization step during retroviral replication. (C) 2001 Acade mic Press.