High-resolution NMR study of a synthetic DNA-RNA hybrid dodecamer containing the consensus Pribnow promoter sequence
- Univ. of Washington, Seattle (USA)
The nonsymmetrical double-helical hybrid dodecamer d(CGTTATAATGCG){center dot}r(CGCAUUAUAACG) was synthesized with solid-phase phosphoramidite methods and studied by high-resolution 2D-NMR. The imino protons were assigned by one-dimensional nuclear Overhauser methods. All the base protons and H1', H2', H2'', H3', and H4' sugar protons of the DNA strand and the base protons, H1', H2', and most of the H3'-H4' protons of the RNA strand were assigned by 2D NMR techniques. The well-resolved spectra allowed a qualitative analysis of relative proton-proton distances in both strands of the dodecamer. The chemical shifts of the hybrid duplex were compared to those of the pure DNA double helix with the same sequence. The intrastrand and cross-strand NOEs from adenine H2 to H1' resonances of neighboring base pairs exhibited characteristic patterns that were very useful for checking the spectral assignments, and their highly nonsymmetric nature reveals that the conformations of the two strands are quite different. Detailed analysis of the NOESY and COSY spectra, as well as the chemical shift data, indicate that the RNA strand assumes a normal A-type conformation (C3'-endo) whereas the DNA strand is in the general S domain but not exactly in the normal C2'-endo conformation.
- OSTI ID:
- 5476781
- Journal Information:
- Biochemistry; (USA), Vol. 28:6; ISSN 0006-2960
- Country of Publication:
- United States
- Language:
- English
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DNA
HYBRIDIZATION
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NUCLEAR MAGNETIC RESONANCE
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OVERHAUSER EFFECT
PROTONS
TRANSCRIPTION
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ELEMENTARY PARTICLES
FERMIONS
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