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Nucleic Acids Research, 1984, Vol. 12, No. 5 2519-2533
© 1984

CHEMISTRY

Synthesis complete 1H assignments and conformations of the self-complementary hexadeoxyribonucleotide [d(CpGpApTpCpG)]2 and its fragments by high field NMR

J.W. Lown, C.C. Hanstock, R.C. Bleackley*, J.L. Imbach+, B. Rayner+ and J.J. Vasseur+

Department of Chemistry, University of Alberta, Edmonton Alberta T6G 2G2 *Department of Biochemistry, University of Alberta, Edmonton Alberta T6G 2H7, Canada +Department of Chemistry, Université des Sciences et Techniques du Languedoc 34060 Monotpellier, France

Received November 28, 1983. Accepted February 6, 1984.

The two deoxyribonucleotides [d(CpGpApTpCpG)]2 and [d(CpGpCpG)]2 were synthesized by the phosphotriester method. Their duplex form under the conditions of the 1H-nmr experiments was proven by end 32p labeling with T4 polynucleotide kinase followed by butt end joining employing the absolute specificity of T4 ligase for double stranded DNA and analysis ysing gel electrophoresis and autoradiography. Complete nmr assignment of the 1H chemical shifts and coupling constants was achieved. The assignments were secured using sequential decoupling, NOE difference measurements, and two-dimensional COSY and SECSY experiments. Spectrum simulation confirmed the experimental values of chemical shifts and coupling constants. The techniques for the assignment outlined together with 31P and 2-D heteronuclear shift correlation permit an approach to a systematic analysis of more complex single-strand and duplex oligodeoxyribonucleotides.


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