SPECTROSCOPIC AND THERMODYNAMIC STUDIES OF DNA DUPLEXES CONTAINING ALPHA-ANOMERIC C-NUCLEOTIDE, A-NUCLEOTIDE, AND G-NUCLEOTIDE AND POLARITYREVERSALS - COEXISTENCE OF LOCALIZED PARALLEL AND ANTIPARALLEL DNA

We present a thermodynamic, enzymatic, and spectroscopic study of thre e self-complementary DNA decamer duplexes, d[GCGAATT-3'-3'-(alpha C)-5 '-5'-GC](2) (alphaC), d[GCG-3'-3'-(alpha A)-5'-5'-ATTCGC](2) (alphaA), and d[GC-3'-3'-(alpha G)-5'-5'-AATTCGC](2) (alphaG), which are identi cal in sequence but contain one alpha-anomeric nucleotide per strand i n a parallel orientation via 3'-3' and 5'-5' phosphodiester bonds; the results are placed in the context of our recent studies on the other members of this series, namely alphaT, d[GCGAAT-3'-3'-(alpha T)-5'-5'- CGC](2), and the unmodified control [Aramini, J. M., et al. (1996) Bio chemistry 35, 9355-9365]. On the basis of UV hyperchromicity and melti ng profiles as well as H-1 and P-31 nuclear magnetic resonance (NMR) s pectroscopic data, we conclude that all five constructs form stable du plexes, with very comparable structural features that are consistent w ith an overall right-handed, antiparallel B-DNA motif and Watson-Crick base pairing throughout. However, each of the alpha-containing sequen ces exhibits unique thermodynamic and structural differences ascribed to the nature (and position) of the alpha-nucleotide. First, the therm ostability of these duplexes decreases from the control to alphaC in t he following series: control > alphaT approximate to alphaA approximat e to alphaG > alphaC. Second, in each of the four alpha-duplexes, H-1 and P-31 chemical shift differences compared to those of the control d uplex are largely confined to the region encompassing the alpha-nucleo tide and unnatural phosphodiester linkages, as well as neighboring nuc leotides. Surprisingly, for alphaC, these modifications result in a si gnificant alteration to the backbone conformation at the phosphodieste r group directly across from the 3'-3' linkage. Finally, spin-spin (J) coupling data, specifically Sigma 1', indicate that the vast majority of the furanose rings in these duplexes display a high propensity for adopting the S pucker. However, in alphaC, alphaA, and alphaT (but no t alphaG), the sugar ring conformation in the nucleotide immediately f ollowing the 5'-5' linkage is described by an approximately equal dist ribution between the N and S conformers.