Two-Dimensional 1H NMR Studies of 32-Base-Pair Synthetic Immobile Holliday Junctions: Complete Assignments of the Labile Protons and Identification of the Base-Pairing Scheme

Shiow meei Chen, Fred Heffron, Walter J. Chazin

    Research output: Contribution to journalArticle

    26 Scopus citations

    Abstract

    The labile protons of two 32-base-pair, four-arm models of immobile Holliday junctions have been studied by two-dimensional 1H nuclear magnetic resonance (NMR) spectroscopy. Overlap of resonances in the imino-imino region of two-dimensional nuclear Overhauser enhancement (NOE) spectra necessitates the use of a multi-pathway approach for obtaining sequence-specific assignments wherein all possible NOE connectivities to the labile protons are utilized, including those from the 2H of adenine, 5CH3 of thymine, and 5H of cytosine. Resonance assignments are obtained for all slowly exchanging imino and cytosine amino protons. Base-pairing up to and including the junction point is found in all four arms of both Holliday junctions. Several cross-arm NOE connectivities are identified and can be used to infer the geometry of the helical stacking domains. The two Holliday junctions studied, which differ only by the exchange of two base pairs at the branch point, appear to have opposite arm stacking geometries. These assignments form an important part of the critical background for detailed NMR analysis of Holliday junction structure and dynamics.

    Original languageEnglish (US)
    Pages (from-to)319-326
    Number of pages8
    JournalBiochemistry
    Volume32
    Issue number1
    DOIs
    StatePublished - Jan 1 1993

    ASJC Scopus subject areas

    • Biochemistry

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