Circular dichroism of polynucleotides: Dimers as a function of conformation

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Abstract
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.