Solution-state structure of the Dewar pyrimidinone photoproduct of thymidylyl-(3'----5')-thymidine

Abstract

The preparation, spectroscopic investigation, structure determination, conformational analysis, and modeling of the Dewar pyrimidinone photoproduct of thymidylyl-(3'----5')-thymidine, previously referred to as TpT3 [Johns, H. E., Pearson, M. L., LeBlanc, J. C., & Heilleiner, C. W. (1964) J. Mol. Biol. 9, 503-524], is described. TpT3 was prepared in quantitative yield by photolysis of an aqueous solution of the (6-4) photoproduct of TpT with Pyrex-filtered medium-pressure mercury arc light. TpT3 was analyzed by FAB MS, IR, UV, and 1H, 13C, and 31P NMR spectroscopy. The spectroscopic data led to the conclusion that TpT3 results from the photoisomerization of the pyrimidinone ring of the (6-4) product of TpT to its Dewar valence isomer. Torsion angle and interproton distance information derived from coupling constants and NOE data was used to constrain ring conformation searches by utilizing the SYBYL molecular modeling program subroutine SEARCH. Sets of angles derived from the ring search procedure were then used to construct structures whose geometries were optimized by the energy-minimization subroutine MAXIMIN. A two-state model for the solution-state structure of the Dewar photoproduct was chosen which was energetically sound, fit the experimental coupling constants with an RMS deviation of 1.15 Hz, and was consistent with the NOE data. The model for the Dewar photoproduct was compared to a model for the (6-4) photoproduct and the TpT subunits of the Dickerson dodecamer structure by a least-squares fitting procedure. It was concluded that the Dewar photoproduct more closely resembles a B-form TpT unit than does the (6-4) photoproduct.