High-resolution NMR studies of chimeric DNA-RNA-DNA duplexes, heteronomous base pairing, and continuous base stacking at junctions
- Howard Hughes Medical Inst., Seattle, WA (United States) Univ. of Washington, Seattle (United States)
- Univ. of Washington, Seattle (United States)
Two symmetrical DNA-RNA-DNA duplex chimeras, d(CGCG)r(AAUU)d(CGCG) (designated rAAUU) and d(CGCG)r(UAUA)d(CGCG) (designated rUAUA), and a nonsymmetrical chimeric duplex, d(CGTT)r(AUAA)d(TGCG)/d(CGCA)r(UUAU)d(AACG) (designated rAUAA), as well as their pure DNA analogues, containing dU instead of T, have been synthesized by solid-phase phosphoramidite methods and studied by high-resolution NMR techniques. The 1D imino proton NOE spectra of these d-r-d chimeras indicate normal Watson-Crick hydrogen bonding and base stacking at the junction region. Preliminary qualitative NOESY, COSY, and chemical shift data suggest that the internal RNA segment contains C3{prime}-endo (A-type) sugar conformations except for the first RNA residues (position 5 and 17) following the 3{prime} end of the DNA block, which, unlike the other six ribonucleotides, exhibit detectable H1{prime}-H2{prime} J coupling. The nucleosides of the two flanking DNA segments appear to adopt a fairly normal C2{prime}-endo B-DNA conformation except at the junction with the RNA blocks (residues 4 and 16), where the last DNA residue appears to adopt an intermediate sugar conformation. The data indicate that A-type and B-type conformations can coexist in a single short continuous nucleic acid duplex, but these results differ somewhat from previous theoretical model studies.
- OSTI ID:
- 5077705
- Journal Information:
- Biochemistry; (United States), Vol. 30:21; ISSN 0006-2960
- Country of Publication:
- United States
- Language:
- English
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