COMPARATIVE SPECTROSCOPIC, CALORIMETRIC, AND COMPUTATIONAL STUDIES OFNUCLEIC-ACID COMPLEXES WITH 2',5''-VERSUS 3',5''-PHOSPHODIESTER LINKAGES

We have used a combination of spectroscopic, calorimetric, and computa tional techniques to characterize the properties of nucleic acid compl exes with 2',5''- and 3',5''-phosphodiester linkages. Specifically, we have compared the properties of complexes formed by the association o f 3',5'' single-stranded 16-mers of adenylic acid (A16) and thymidylic acid (T16) with the complexes formed by the corresponding single-stra nded 16-mers with 2',5''-phosphodiester linkages (A16 and T16*). Our results reveal the following differential features: (i) the 3',5'' str ands form either a duplex or a triplex, depending on the sodium ion co ncentration, whereas the 2',5'' strands form either a triplex or no co mplex at all; (ii) the 2',5'' and 3',5'' triplexes exhibit significant ly different CD spectra, suggesting that the two triplex states are co nformationally nonequivalent; (iii) the 2',5'' triplex has a lower cha rge density than the 3',5'' triplex; (iv) the thermal stability of the 3',5'' triplex, as expected, is concentration dependent, whereas the thermal stability of the 2',5'' triplex is concentration independent; (v) relative to their component single strands, the 2',5'' triplex is thermodynamically much less stable than the 3',5'' triplex, despite be ing thermally more stable; (vi) the reduced thermodynamic stability of the 2',5'' triplex relative to the 3',5'' triplex is overwhelmingly e nthalpic in origin. In the aggregate, our results reveal and character ize significant differences in the properties of complexes formed by t he association of strands with identical base sequences but different phosphodiester linkages. We describe a structural model that is consis tent with many of the differential properties observed. We also specul ate on how these differential properties may have provided an evolutio nary advantage for 3',5'' linkages and how the properties of 2',5'' co mplexes might be exploited in antisense strategies.