Backbone torsion angle analysis of DNA

This work examined DNA conformations based on torsion angles. The sugar–phosphate backbone torsion angles α, β, γ, δ, ε, and ζ between pairs of adjacent phosphates were found to add up to three turns in A- and B-DNA as well as dsRNA, but not in Z-DNA and aptamers. The number of turns ( T p ) therefore is indicative of nucleotides in repeating double stranded regions. Furthermore, plotting cosine of backbone and glycosidic torsion angles gives a direct visual view of the likeness of dsDNA to A- and B-DNA. The cosine of these torsion angles also allows the calculation of relative Manhattan distance tensors that reflect the likeness to A- and B-DNA. Finally, the cos(δ)–cos(ζ) plot gives strong quadrant-specific clustering of A-, B-, and Z-DNA, allowing for easy identification of dsDNA conformations.