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Nucleic Acids Research, 1983, Vol. 11, No. 16 5717-5738
© 1983

CHEMISTRY

Proton NMR studies on the covalently linked RNA-DNA hybrid r(GCG)d(TATACGO). Assignment of proton resonances by application of the nuclear Overhauser effect

J.-R. Mellema, C.A.G. Haasnoot*, G.A. van der Marel, G. Wille, C.A.A. van Boeckel, J.H. van Boom and C. Altona

Gorlaeus Laboratories, State University of Leiden PO Box 9502, 2300 RA Leiden *Faculty of Science, University of Nijmegen, Biophysical Department Toernooiveld 6525 ED Nijmegen, The Netherlands

Received June 15, 1983. Accepted July 21, 1983.

Proton NMR spectra of a covalently linked self-complementary RNA•DNA hybrid, r(GCG)-d(TATACGC), are recorded in H2O and D2O. Imino proton resonances as well as the non-exchangeable base and H-1' resonances are unambiguously assigned by means of nuclear Overhauser effect measurements. Additional information was obtained by 21P NMR and circular dichroism spectra. The RNA parts in the duplex attain full conformational purity and adopt the usual A-RNA conformation. The DNA residues opposite the RNA tract do not adopt an A-type structure completely. Their respective sugar rings still appear to possess a certain conformational freedom. The same holds true for the central d(-TATA-) sequence which forms a DNA•DNA duplex. There appears to be a structural break in this part: the first two residues, T(4) and A(5), are clearly influenced by the adjacent RNA structure, whereas residues T(6) and A(7) behave quite similar to what usually is found in DNA duplexes in aqueous solution.


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[Abstract] [PDF]


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