Optical Activity of Single-Strand Oligonucleotides

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Abstract
The circular-dichroism (CD) spectra of several dinucleoside phosphates containing guanine and cytosine in aqueous solution at −17°C are reported in the range 210–300 mμ. The results differ from previously reported dinucleoside phosphate curves in that the CD bands do not appear in pairs of nearby positive and negative bands. This is in disagreement with the exciton treatment which has been successfully used to interpret other dinucleoside phosphate CD and ORD. Tinoco's general theory of polymer optical activity is examined in an attempt to explain the nonconservative CD curves we observe. Both the cases of base planes perpendicular to the helix axis and that of the base planes tilted with respect to the helix axis are considered. We conclude that tilting cannot be expected to give large nonconservative rotational strengths. In addition we show by means of a polarizability approximation, that interaction of the far-uv transitions can give rise to rotational strengths such as those we observe, even for the case of base planes perpendicular to the helix axis. This nonconservative contribution is composed of the Kirkwood polarizability term and an analogous term containing the magnetic transition moment and the polarizability perpendicular to the base plane. The contribution also depends on the direction of the electronic transition dipole moment of the transition whose rotational strength is being calculated. We propose that it is through this dependence that the nonconservative effect is not present in the CD of dinucleoside phosphates previously measured but is prominent in the curves reported for dinucleoside phosphates containing guanine or cytosine. The study suggests that the adenosyl—adenosine CD curve, which is conservative, is a special case due to its electronic structure and that the geometry of several dinucleoside phosphates is the same as that of single-strand RNA whose CD curve is nonconservative.