NMR characterization of a kissing complex formed between the TAR RNA element of HIV-1 and a DNA aptamer

This work presents the first structural analysis of an RNA–DNA complex consisting of an 18 nt RNA hairpin and a 20 nt DNA aptamer. The DNA molecule was previously selected, from a randomly synthesized library, against the transactivation response element (TAR) involved in transcriptional regulation of the HIV genome. The DNA aptamer used in the present study is an imperfect stem–loop with the sequence 5′-ACTCCCAT-3′, characteristic of the selected candidates, in the apical loop. This octameric motif contains five bases complementary to the TAR loop sequence 5′-CUGGGA-3′. The use of homo- and heteronuclear NMR spectroscopy allowed assignment of the complex resonances and resolution of its secondary structure. Evidence is given for a kissing complex fold, which consists of a quasi-continuous helix formed by one stem of DNA, one stem of RNA and a central hybrid helix comprising 5 bp. Two out of helices residues of DNA and one of RNA connect the DNA–RNA loop–loop helix to the stem of either partner in the complex. In addition, two thymines of the DNA stem are engaged in a non-canonical T·T base pair.