Solution structure of nucleic acid photoadduct, deoxy-m5HO6-uridylyl(5-5)(3'-5')deoxyuridine by NMR and restrained molecular dynamics.

Sensitized UV-B irradiation (sunlamps) of the dinucleoside monophosphate, d-TpF (F = fluorouracil), produces the usual cyclobutane-type photodimer and an additional defluorinated 5-5 photoadduct, d-T5p5U. In d-T5p5U, the original C5 = C6 structure is modified such that the C5 (d-T5p-) is covalently bonded with the C5 (-p5U) (where the fluorine had been) and the C6 (d-T5p-) acquires an OH group. 2D NOE data and the results of J-coupling analysis are used as constraints to refine structures of d-T5p5U in restrained molecular dynamics calculations. The structures obtained show the most probable chiralities of the C5 and C6 atoms of the Thy-portion to be 5R and 6R, respectively. The orientation of the CH3- and uracil-groups are pseudo-axial and pseudo-equatorial, respectively, with respect to the C5 atom. Glycosidic angles are high-anti and anti for the d-T5p- and the -p5U residue, respectively. C3'-endo like sugar puckering is predominant in the d-T5p- residue while C2'-endo like puckering is predominant at the -p5U residue.