Analysis of the possible helical structures of nucleic acids and polynucleotides. Application of (n-h) plots.

Abstract

The two helical parameters n and h where n is the number of nucleotide residues per turn and h is the height per nucleotide residue have been evaluated for single stranded helical polynucleotide chains comprising C(3′) endo and C(2′) endo class of nucleotides. The helical parameters are found to be especially sensitive to the C(4′)–C(3′) (sugar pucker) and the C(4′)–C(5′) torsions. The (n-h) plots display only one important helix forming domain for each class of nucleotides characterized by the sugar pucker and the C(4′)– C(5′) torsion. A correlation between the (n-h) plots and the known RNA (A,A′) and DHA (A,B,C) helical forms has been established. It is found that all forms of helices except the C-DNA possess a favorable combination of P–O torsions. The analysis of the (n-h) plots suggests that C-DNA can have a conformation very similar to B-DNA. Although the (n-h) plots predict the stereochemical possibility of both right-handed and left-handed helices, nucleic acids apparently prefer right-handed conformation because of the energetics associated with the sugar-phosphate backbone and the base.