In Vitro Selection of DNA Aptamers Against the HIV-1 TAR RNA Hairpin

Abstract

In vitro selection was performed to identify DNA aptamers against the TAR RNA stem-loop structure of HIV1. A counterselection step allowed the elimination of kissing complex-forming aptamers previously selected (Boiziau et al. J. Biol. Chem. 1999; 274:12730). This led to the emergence of oligonucleotides, most of which contained two consensus sequences, one targeted to the stem 3′-strand (5′-CCCTAGTTA) and the other complementary to the TAR apical loop (5′-CTCCC). The best aptamer could be shortened to a 19-mer oligonucleotide, characterized by a dissociation constant of 50 nM. A 16-mer oligonucleotide complementary to the TAR stem 3′-strand could also be derived from the identified aptamers, with an equal affinity (K_d = 50 nM). Experiments performed to elucidate the interaction between TAR and the aptamers (UV melting measures, enzymatic and chemical footprints) demonstrated that the TAR stem 5′-strand was not simply displaced as a result of the complex formation but unexpectedly remained associated on contact with the antisense oligonucleotide. We suggest that a multistranded structure could be formed.