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.
Collin
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CNRS, Institut de Chimie des Substances Naturelles, 1 Avenue de la Terrasse, F-91190, Gif-sur-Yvette, France.
van Heijenoort
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Boiziau
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Toulmé
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Guittet
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D020029:Base Pairing; D001483:Base Sequence; D016325:HIV Long Terminal Repeat / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics; D008958:Models, Molecular; D018716:Molecular Mimicry; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D011522:Protons; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
D009838:Oligodeoxyribonucleotides; D011522:Protons; D012367:RNA, Viral