Conformation of adenosine bulge-containing deoxytridecanucleotide duplexes in solution. Extra adenosine stacks into duplex independent of flanking sequence and temperature

M. W. Kalnik, D. G. Norman, P. F. Swann, D. J. Patel

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    62 Citations (Scopus)

    Abstract

    Structural features at the extra adenosine bulge sites in DNA duplexes have been elucidated from an NMR analysis of two-dimensional through space and through bond connectivities in the self-complementary d(C-C-G-C-A-A-T-T-C-A-C-G-G) (CAC 13-mer) and d(C-C-G-A-G-A-A-T-T-C-C-G-G-) (GAG 13-mer) duplexes in aqueous solution. These studies establish that the extra adenosine stacks into the helix at all temperatures below the onset of the melting transition in solution, and the results are independent of whether the extra adenosine is flanked by cytidines (CAC 13-mer) or guanosines (GAG 13-mer). The NMR parameters establish that the extra adenosine can be accommodated into the helix with the flanking base pairs adopting a wedge-shaped orientation. The resulting perturbation extends out to the C10-G11 phosphodiester backbone adjacent to the bulge segment in both the CAC 13-mer and GAG 13-mer duplexes.

    Original languageEnglish
    Pages (from-to)3702-3712
    Number of pages11
    JournalJournal of Biological Chemistry
    Volume264
    Issue number7
    Publication statusPublished - 1989

    ASJC Scopus subject areas

    • Biochemistry
    • Molecular Biology
    • Cell Biology

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