Circular dichroism of polynucleotides: Dimers as a function of conformation

Working within the restrictions of a model, we have calculated the circular dichroism of the dinucleoside phosphates ApA, CpC, and CpA for various conformations. Comparing the calculated curves with those measured in aqueous solution we find agreement for ( 1 ) ApA as a right‐handed helix with both bases either as in B‐form DNA, or else rotated 180° around the glycosidic bond, ( 2 ) CpC as the right‐handed conformation with both bases as in DNA, ( 3 ) ApC as either the right‐handed conformation with both bases as in DNA, or else as a left‐handed helix with both bases rotated 180°, and ( 4 ) CpA as either a left‐handed helix with both bases in a left‐handed DNA, or else in the right‐handed conformation with both bases rotated 180°. In addition, we have investigated circular dichroism as a measure of unstacking. We find that opening the bases to a 90° total angle (base planes perpendicular) reduces the intensity of the calculated bands to 20% of their original value. Further, we find that allowing the sliding of one base past the other does not lead to a temperature dependence consistent with experiment.