Identification of structural motifs of RNA aptamers interacting with the stem-loop sequence at the Gag-pol junction of HIV-1 RNA

To identify RNA motifs interacting with the stem-loop RNA which plays an important role in the synthesis of gag-pol fusion protein of HIV-1, a SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was performed. RNA aptamers binding to the stem-loop sequence at the gag-pol junction of HIV-1 RNA were selected from a 30-mer random sequence library through 13 rounds of selection. Some of resulting RNA aptamers contained the consensus sequences AAGGGA and GUUGAU. The stem-loop RNA ligand interacted with synthetic RNA fragment containing two conserved sequence motifs AAGGGA and GUUGAU but did not bind to DNA oligonucleotides having the sequences identical to the RNA fragment. These results suggest that a specific tertiary interaction rather than Watson-Crick base-pairing is involved in the complex formation between RNA aptamer and the stem-loop RNA.