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Updated: Aug 8, 2026

Analyzing and Building Nucleic Acid Structures with 3DNA
Published on: April 26, 2013
Structure and conformation in solution of the parallel-stranded hybrid alpha-d(CGCAATTCGC).beta-d(GCGTTAAGCG) by
W H Gmeiner1, B Rayner, F Morvan
1Department of Chemistry, University of Alberta, Edmonton, Canada.
Abstract:
The unnatural duplex oligonucleotide alpha-d(CGCAATTCGC).beta-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 beta-beta 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 beta-strand and [H8/H6-H1'] NOEs to the 3'-neighbor in the alpha-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 alpha/beta hybrid decamer.
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