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Nucleic Acids Research, 1987, Vol. 15, No. 10 4241-4255
© 1987

Articles

{alpha}-DNA-III. Characterization by high field 1H-NMR, anti-parallel self-recognition and

conformation of the unnatural hexadeoxyribonucleotides {alpha}-(d(CpApTpGpCpG) and {alpha}-d(CpGpCpApTpG). {alpha}Oligodeoxynucleotides as potential cellular probes for gene control

Francois Morvan, Bernard Rayner, Jean-Louis Imbach, Ding-Kwo Chang* and J.William Lown*

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

Received February 11, 1987. Revised April 23, 1987. Accepted April 23, 1987.

High field 2-D-1H-NMR techniques permitted the assignment of all non-exchangeable protons of the unnatural deoxyribonucleotides {alpha}-[d(CpApTpGpCpG)] and {alpha}-[d(CpGpCpApTpG)]. 1-D and 2-D NOESY experiments show strong H6H8-H4, dipolar interactions for all nucleotides in both sequences. These data, together with COSY and J-reseolved spectra, indicate that these two {alpha}-oligomers adopt 3'-exo conformations of the sugar moieties in solution with anti conformations of the glycosyl linkages. Both 1H-NMR data, and hypochromicity comparison.of {alpha}-CATGCG and ß-CATGCG, demonstrate a higher degree of base stacking in the case of the {alpha}-sequence. The UV hyperchromicity at 260 run, and symmetry considerations in the imino proton NMR experiments reveal antiparallel self-recognition and duplex annealing at positions 1–4 for {alpha}-[d(CATGCG)] and positions 3–6 for {alpha}-[d(CGCATG)] The temperature variation of the imino proton NMR signals suggests that the hydrogen bonding in self-recognition is comparable in strength with that in a ß-DNA duplex, and NOE data are in accord with Watson-Crick rather than Hoogsteen base pairing.


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