Oligonucleotide interactions. III. Circular dichroism studies of the conformation of deoxyoligonucleolides

TLDR

The study measured circular dichroism spectra of deoxynucleotides and used a semi‑empirical nearest‑neighbor model to predict spectra, also exploring simultaneous analysis of sequence isomers. Dimer spectra differ from monomer sums, revealing base‑stacked conformations; terminal phosphate and salt have minimal impact, and simultaneous analysis works for purine runs but not for pyrimidine runs.

Abstract

Abstract The circular dichroism (CD) spectra of the four usual deoxymononucleosides, all sixteen deoxydinucleotides, and a number of trinucleotides have been measured. The dimer spectra are quite different from the sum of the spectra of their constituent monomers. This indicates the presence of base‐stacked conformations analogous to those found for ribonucleoside diphosphates. The CD spectra of several deoxytrinucleotide diphosphates and single‐strand f 1 DNA can be calculated fairly well by using a semi‐empirical nearest‐neighbor approach. There is little or no effect of terminal phosphate or of salt concentration on the optical properties of most deoxy oligomers. The possibility of simultaneous analysis of mixtures of deoxypurine or deoxypyrimidine sequence isomers has been examined. This seems to be a viable approach for the analysis of purine runs but cannot promise much success for pyrimidine runs.