Polynucleotide models. II. Prediction of the radial position and tilt of the bases from the helical parameters

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Abstract
A simple geometrical analysis is applied to base‐stacking interactions in helical polynucleotides. A base‐pair or other H‐bonded arrangement of bases is represented by a corresponding plane. In a helical structure, these planes will intersect each other if the bases are not perpendicular to the helix axis. The tilt of the bases and the position of intersection of these planes are geometrically related, and demonstrate the interrelation of the tilt of the bases with their radial position. This approach may be coupled with a constraint which predicts the radial position of the bases based solely upon the helical parameters. These two constraints taken together allow a simple means to predict the approximate position and tilt of a given H‐bonded arrangement of bases placed according to specified helical parameters. For a number of polydeoxyribonucleotides, there is more than one base position and tilt consistent with these constraints, while there is only one base position and tilt indicated for each of the polyribonucleotides examined.