Influence of cis-syn photodimers on the secondary structure of poly(A) . poly(U)

Cis-syn cyclobutane-type photodimers were induced into poly (A) . poly(U) using photosensitized UV-irradiation and conformational changes were investigated by H-1 and P-31 NMR spectroscopy. Non-exchangeable and imino proton, as well as phosphorus resonance assignments were made based on earlier work with more simple uracil models containing cis-syn dimers such as UpU and poly(U). The non-exchangeable H-1 NMR spectra reveal (1) 12% of the uracil bases to be saturated with cis-syn cyclobutane rings, (2) the polymer T/sub m/ reduced as much as 350C relative to the unirradiated duplex and (3) many uracil bases presumably adjacent to the photodimer not to be base-paired in the duplex even at 10C. Three sets of imino resonances were observed in irradiated poly(A) . poly(U). At 10C, photodimer iminos (10.78, 10.60, and 10.07 ppm) as well as imino protons on adjacent unsaturated uracil bases (11.33 ppm) are not base-paired with complementary adenines. The imino data suggests an average of 10 base-pairs to be disrupted by a cis-syn photodimer. P-31 NMR further supports an extreme destabilization of the secondary structure of the irradiated polymer. In comparison with the analogous DNA polymer containing cis-syn thymine dimers, poly(dA) . poly(dT) [Rycyna and Alderfer (1986) Biophysical j. 49, 128a], a much larger distorted region in the ribohomopolymer is observed suggesting the A-RNA helix is less able to accommodate photodimer-induced distortion