Origin of DNA Helical Structure and Its Sequence Dependence

Conformational analysis of DNA shows that the origin of the B-form double helix can be attributed in large part to the atomic charge pattern in the base pairs. The charge patterns favor specific helical stacking of the base pairs. Base pairs alone—without backbones—have a strong tendency to form helix, indicating that the backbones play a rather passive role in determining the basic helical structure of DNA. It is mainly the electrostatic interactions determined by the charge pattern on base pairs that stabilize a particular helical conformation. The charge pattern in the base pairs appears to be responsible for much of the sequence dependence of DNA conformation, rather than steric clashes.