SOLUTION STRUCTURE OF A NUCLEIC-ACID PHOTOPRODUCT OF DEOXYFLUOROURIDYLYL-(3'-5')-THYMIDINE MONOPHOSPHATE (D-FPT) DETERMINED BY NMR AND RESTRAINED MOLECULAR-DYNAMICS - STRUCTURAL COMPARISON OF 2 SEQUENCE ISOMERPHOTOADDUCTS (D-U5P5T AND D-T5P5U)

Acetone-sensitized irradiation using UV-B (sun lamp, lambda(max) = 313 nm) of deoxyfluorouridytyl-(3'-5')-thymidine monophosphate (d-FpT, F = fluorouracil), produces two major photoproducts, the cis-syn cyclobu tane-type photodimer and a defluorinated (5-5) photoadduct, d-U5p5T. P roduct distribution is dependent on the pH of the irradiation solution , as was the case of irradiated d-TpF. At high pH (8-10) the (5-5) pho toadduct is the major photoproduct. Irradiation of d-FpT shows a much faster photodegradation rate than the sequence isomer d-TpF. Multinucl ear NMR experiments establish the formation of (5-5) covalent bonding between the C5 (d-U5p-, where the fluorine had been) and the C5 (-p5T) and the C6 (-p5T) acquires an OH group. NOE interproton distances and dihedral angles derived from J coupling analysis are constrained to r efine model structures of d-U5p5T in restrained molecular dynamics cal culations. The resultant structures obtained show 5S-6S as the most pr obable chiralities of the C5 and C6 atoms of the thymine, which is the opposite chirality to the corresponding atoms in the sequence isomer d-T5p5U. The orientation of the C5 substituents (-p5T fragment), the C H3 and the uracil are pseudo-axial and pseudo-equatorial respectively. Glycosidic angles are in the anti regions for both the d-U5p- and -p5 T residues. Averaged backbone conformations of the two photoadducts, d -U5p5T and d-T5p5U, are similar, although the overall structure of d-U 5p5T appears much more flexible than that of d-T5p5U. In particular, t he sugar conformations of the 5'-end residues show a remarkable differ ence in flexibility.