A new simple method of representing relative orientation of bases in DNA helical structures

It is shown that the strandwise correlation of the torsion angles in Nucleic acid structures can throw light on the aspects like helical distortion, in double helical and other associated forms. The single crystal X-ray coordinates for 7 A-DNA, 29 B-DNA, 8 Z-DNA and 4 tRNA structures are used to calculate the glycosyl angle chi and they are plotted in a two dimensional plot. A new torsion angle pi is defined as O4'-C1'-N1(9)-X, where X is a fictitious atom on the normal at N1(9). The chi 1 vs. chi 2 plots (where 1 and 2 refer to I and II-strand of DNA respectively) show the characteristic clustering features of A, B and Z DNAs. They are also compactly reflected in the modified graphical representation like (chi 1 + chi 2) vs. magnitude of chi 1 - chi 2 plot. chi 1 vs. chi 2 plot of the Hoogsteen type of base pairing obtained from the tRNA structures is off diagonal. The distortions due to complexing of the structures under each category, in particular, B-DNAs is readily observed. The observed points of A/B hybrid form clusters between A and B uncomplexed forms. The new torsion angle pi shows similar behavior as that of chi.