Optical properties of ribonucleic acids predicted from oligomers

Abstract

An empirical method has been developed for predicting the optical properties of single-strand polynucleotides from the corresponding properties of oligonucleotides. If only nearest-neighbor interactions are considered, the optical rotatory dispersion of polynucleotides can be predicted from that of dinucleoside phosphates and mononucleosides. These calculations are in good agreement with experimental results for poly A, poly C, poly U and tobacco mosaic virus RNA and other RNA's in the absence of salt at neutral pH. Thus in the limit of low salt concentration, the conformation of tobacco mosaic virus RNA is mostly a single strand with stacked bases. The nearest-neighbor formalism has been extended to take into account double-stranded conformations. At present there are not sufficient experimental data to include the contributions to the optical rotatory dispersion from all of the possible double-stranded dimers. However, the effects of double-strand formation can be estimated from the known optical rotatory dispersion of double- and single-strand homopolynucleotides. With these estimates it was possible to predict the change in optical rotatory dispersion expected when a single strand forms intramolecular base pairs. These calculations agree with the observed change in the optical rotatory dispersion of tobacco mosaic virus RNA when salt is added to a salt-free solution. A model has been constructed for the yeast alanine sRNA which includes the effects of base stacking as well as base pairing. The properties of this model are consistent with much of the experimental data on the conformation of sRNA's. The optical rotatory dispersion of partially double-stranded alanine sRNA is in good agreement with nearest-neighbor predictions.