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Nucleic Acids Research, 1987, Vol. 15, No. 17 7027-7044
© 1987

Articles

{alpha}-DNA-V. Parallel annealing, handedness and conformation of the duplex of the unnatural {alpha}-hexadeoxyribonucleotide {alpha}-[d(CpApTpGpCpG)] with its ß-complement ß-[d(GpTpApCpGpC)] deduced from high field 1H-NMR

Francois Morvan, Bernard Rayner, Jean-Louis Imbach, Moses Lee1, John A. Hartley1, Ding-Kwo Chang1 and J.William Lawn1

Laboratoire de Chimie Bio-Organique, Université des Sciences et Techniques du Languedoc UA 488 du CNRS, 34060 Montpellier, France 1Department of Chemistry, University of Alberta Edmonton, Alberta T6G 2G2, Canada

Received June 29, 1987. Revised August 12, 1987. Accepted August 12, 1987.

The ß-complementary hexamer, ß-d[GTACGC], to the {alpha}-sequence, {alpha}-d[CATGCG], was synthesized by the phosphotriester method. The non-exchangeable proton assignments were obtained using 1D- and 2D-NMR techniques, including NOE, COSY and NOESY. The ß-strand exists as a random coil at 21°C, however, at 4°C, it forms an antiparallel self-recognition duplex annealing at positions 1–4. The ß-strand was annealed to the {alpha}-strand, and confirmation of complete annealing was obtained by detection and assignment of the six base pair imino protons in H2O/D2O solution at 21°C. 1D-NOE experiments of the {alpha}, ß duplex d [ {alpha}- (CATGCG) ß- (GTACGC) ] reveal that (i) it exists in aqueous solution in a conformation that belongs to the B family, (ii) it is 70±10% right-handed, (iii) the sugar-base orientations of the ß-strand are anti, and the deoxyribose units exist predominantly in the 2'-endo-3'-exo conformation, NOE measurements of the imino proton signals in the {alpha}, ß duplex reveal that the duplex exhibits parallel polarity.


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