Transmission, evolution, and helix handedness of nucleic acid conformation

In aqueous solution nucleic acid structures are conformationally pluralistic. The composition of the conformational blend and the preferred intramolecular order are largely determined by the constitution and sequence which control the torsional and flexural movements about the internucleotide phosphodiester bond. At the level of a trimer in many cases an important contributing structure is a bulged configuration in which the central residue is bulged out, allowing the end nucleotide units to interact intramolecularly. Ribonucleic acids transmit conformation through a series of stereochemical domino effects due to the presence of a synchronous (?) coupled set of base sequence dependent conformational parameters and interdependent structural changes linked to base-base stacking interactions. Nucleic acids have 3′5′, and not 2′5′, phosphodiester bonds because the intrinsic molecular stereodynamics of 2′5′ internucleotide systems are such that they cannot support stable helical structures with base stacking interactions at the single-or double-stranded level. Because polynucleotides mostly express themselves in double helical configurations, this probably provided the 3′5′ internucleotide bond an evolutionary advantage over their 2′5′ analogs. The experimental geometry of the miniature double helix of the cyclodimer A5pU0 agrees with that of the novel vertical double helix [W. K. Olson, Proc. Nat. Acad. Sci. US 74, 1775 (1977)] and disagrees with the theoretical helix parameters that Sundaralingam and Yathindra [Int. J. Quant. Chem. Quant. Biol. Symp. No. 4, 285 (1977)] have derived from the rigid nucleotide concept.