Probing possible left-and right-handed polynucleotide helical conformations from n-h plots. Glycosyl and backbone torsional variation on handedness of helix

Abstract

The helical parameters n (the number of nucleotide residues per turn) and h (the residue height along the helical axis) have been evaluated for single stranded polynucleotide chains and are found to be dependent on the nature of the sugar ring pucker and the nucleotide backbone torsions. The n-h plot reveals that both the familiar right-handed and possible types of left-handed helical conformations fall within the same broad domain, thus conformation transitions from right-handed to left-handed helix and vice versa affect only slightly the backbone torsions. The glycosyl angle apparently suffers the greatest change in the reversal of the helix sense. The normal (χ ' 0-80°) found in right-handed polynucleotides increases to the anti (χ '125°) as exemplified by the Ikehara polymers: synthetic poly (A s ) and poly (U o ) where the monomeric cyclonucleoside units are fixed in the high χ by a covalent linkage between the base C8/C6 and sugar C2' atoms. Conformational energy calculations [Fujii and Tomita, Nucl. Acids Res. 3, 1973 (1976)] on model compounds of Ikehara polymers have shown that the backbone conformations of the left-handed polynucleotides are in silimar conformational domains as the known right-handed polynucleotides, and are in agreement with the work of Yathindra and Sundaralingam [Nucl. Acids Res. 3, 729 (1976)]. These studies indicate that the molecular mechanics of untwisting a helix, leading eventually to a change in helical sense, may involve a combined process of adjusting the glycosyl angle, the pseudorotation phase angle, and the backbone torsions, that is, helix untwisting perhaps involves synchronous rotations around the glycosyl and backbone bonds. In nucleic acids the left-handed helical conformations are as a rule not favored because the high χ is not particularly favored. But under certain situations the left-handed base stack and left-handed helical backbone may occur, especially in short segments around the loop and folded regions of the tertiary structure.