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 cons isting of an 18 nt RNA hairpin and a 20 nt DNA aptamer, The DNA molecule wa s previously selected, from a randomly synthesized library, against the tra nsactivation response element (TAR) involved in transcriptional regulation of the HIV genome. The DNA aptamer used in the present study is an imperfec t stem-loop with the sequence 5'-ACTCCCAT-3', characteristic of the selecte d 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 h eteronuclear 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 ou t of helices residues of DNA and one of RNA connect the DNA-RNA loop-loop h elix to the stem of either partner in the complex. In addition, two thymine s of the DNA stem are engaged in a non-canonical T.T base pair.