OLIGONUCLEOTIDE INTERACTIONS .2. DIFFERENCES IN BASE STACKING IN LINEAR AND CYCLIC DEOXYTHYMIDINE OLIGONUCLEOTIDES

The circular dichroism, ultraviolet absorption, a ndnuclear magnetic resonance of linear and cyclic thymidine diand trinucleotides have been studied. In aqueous solution the long-wavelength Cotton effects of the cyclic dinucleotide are opposite in sign to the corresponding bands of the linearcompound. Thus cyclic thymidine dinucleotide must have a stacked conformation which is quite different from the basestacking geometry of any other known oligonucleotide. Nuclear magnetic resonance spectra of the cyclic dimer suggests that the two bases are magnetically equivalent. It is possible to construct a plausible model of the conformation of the cyclic dimer which explains both the optical and magnetic resonance data. In methanol solution the linear oligothymidylates are unstacked and show optical properties very similar to those of thymidylic acid. Methanol causes substantial changes in the conformation of cyclic thymidine dinucleotide while, in contrast, there is virtually no effect on the cyclic trinucleotide. The vast differences in the base stacking of linear and cyclic oligonucleotides may have implications for the possible structures of loops and hairpins in transfer and ribosomal ribonucleic acids. © 1969, American Chemical Society. All rights reserved.