Structure and conformation in solution of the parallel-stranded hybrid α-d(CGCAATTCGC)·β-d(GCGTTAAGCG) by high-resolution 2D NMR

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Abstract
Summary The unnatural duplex oligonucleotide α-d(CGCAATTCGC)·β-d(GCGTTAAGCG) was analyzed by high-resolution NMR methods. All of the exchangeable imino and nonexchangeable protons of the duplex were assigned. Detection of all 10 of the exchangeable imino protons confirms that a parallel, unsymmetrical duplex is formed. The thermal stability of the parallel duplex is similar to the analogous antiparallel β-β duplex. The right handedness of the helix is confirmed by inter-residue [H8/H6-H1′] and [H8/H6-H2″] NOEs to the 5′-neighbor in the β-strand and [H8/H6-H1′] NOEs to the 3′-neighbor in the α-strand. Intra-residue and inter-residue distances between base protons and deoxyribose protons in both strands were determined using the isolated spin-pair approximation for NOESY cross peaks acquired with mixing times 50 ms or less. The NOE data are consistent with a B-form geometry adopted by the α/β hybrid decamer.