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NMR structure of the chimeric hybrid duplex r(gcaguggc)⋅r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription

Szyperski, Thomas ; Götte, Matthias ; Billeter, Martin ; Perola, Emanuele ; Cellai, Luciano ; Heumann, Hermann ; Wüthrich, Kurt

In: Journal of Biomolecular NMR, 1999, vol. 13, no. 4, p. 343-355

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    Titre
    • NMR structure of the chimeric hybrid duplex r(gcaguggc)⋅r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription
    Auteur
    • Szyperski, Thomas. Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, CH-8093, Zürich, Switzerland
    • Götte, Matthias. Max-Planck-Institut für Biochemie, D-82152, Martinsried, Germany
    • Billeter, Martin. Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, CH-8093, Zürich, Switzerland
    • Perola, Emanuele. Istituto di Strutturistica Chimica, CNR, Monterotondo Stazione, P.O. Box 10, I-00016, Rome, Italy
    • Cellai, Luciano. Istituto di Strutturistica Chimica, CNR, Monterotondo Stazione, P.O. Box 10, I-00016, Rome, Italy
    • Heumann, Hermann. Max-Planck-Institut für Biochemie, D-82152, Martinsried, Germany
    • Wüthrich, Kurt. Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Hönggerberg, CH-8093, Zürich, Switzerland
    Type de document
    • Postprint
    Langue
    • Anglais
    Publié dans
    • Journal of Biomolecular NMR, 1999, vol. 13, no. 4, p. 343-355. Kluwer Academic Publishers
    Autre version électronique
    Identifiant OAI-PMH
    • oai:doc.rero.ch:316092
    Summary
    A high-quality NMR solution structure of the chimeric hybrid duplex r(gcaguggc)⋅r(gcca)d(CTGC) was determined using the program DYANA with its recently implemented new module FOUND, which performs exhaustive conformational grid searches for dinucleotides. To ensure conservative data interpretation, the use of 1H-1H lower distance limit constraints was avoided. The duplex comprises the tRNA-DNA junction formed during the initiation of HIV-1 reverse transcription. It forms an A-type double helix that exhibits distinct structural deviations from a standard A-conformation. In particular, the minor groove is remarkably narrow, and its width decreases from about 7.5Å in the RNA/RNA stem to about 4.5Å in the RNA/DNA segment. This is unexpected, since minor groove widths for A-RNA and RNA/DNA hybrid duplexes of ∼11Å and ∼8.5Å, respectively, were previously reported. The present, new structure supports that reverse transcriptase-associated RNaseH specificity is related primarily to conformational adaptability of the nucleic acid in 'induced-fit'-type interactions, rather than the minor groove width of a predominantly static nucleic acid duplex