STRUCTURE OF A DNA DUPLEX THAT CONTAINS ALPHA-ANOMERIC NUCLEOTIDES AND 3'-3'-PHOSPHODIESTER AND 5'-5'-PHOSPHODIESTER LINKAGES - COEXISTENCEOF PARALLEL AND ANTIPARALLEL DNA

We report a comparative spectroscopic study of a novel self-complement ary duplex decamer, d(GCGAAT-3'-3'-(alpha T)-5'-5'-CGC)(2), in which a n alpha-anomeric nucleotide has been inserted into the sequence in a p arallel orientation via 3'-3' and 5'-5' phosphodiester bonds, and its unmodified B-DNA analog, d(GCGAATTCGC)(2). Plots of the hyperchromicit y and circular dichroism of these oligonucleotides are virtually ident ical, indicating that the overall base stacking and handedness are pre served in the alpha duplex. Thermodynamic parameters extracted from UV melting experiments show that the alpha duplex is only slightly less stable than the control. A near complete set of H-1 and P-31 nuclear m agnetic resonance (NMR) assignments were obtained for both duplexes us ing classical one- and two-dimensional approaches. Several lines of ev idence, in particular, imino H-1, P-31, nuclear Overhauser enhancement , and deoxyribose ring proton spin-spin coupling data, convincingly de monstrate that the overall structural integrity of the alpha and contr ol duplexes are quite comparable, with any perturbations in the former localized to the regions of the construct encompassing the alpha-nucl eotide and the unique backbone linkages. Specifically, the alpha duple x exhibits normal Watson-Crick type base pairing, it remains antiparal lel except at the inverted nucleotide, all bases are in the anti orien tation, and the sugar ring puckering is predominantly ''S''-type. Howe ver, the J-coupling information for the alpha-nucleotide and the neigh boring (3') cytidine are notably different, and reflect a decrease in the amplitude of the sugar pucker in alpha T7, and a significant shift in the conformational equilibrium of the furanose ring in C8 toward t he ''N''-type pucker. The feasibility of synthesizing oligodeoxynucleo tides containing a combination of alpha sugars and short parallel stra nded segments, their propensity for forming stable duplexes, and the s tructural insights into such complexes reported here are of potential importance in the area of antisense therapy.