SUBSTITUENT EFFECTS ON THE PUCKERING MODE OF THE CYCLOBUTANE RING AND THE GLYCOSYL BOND OF CIS-SYN PHOTODIMERS

The cyclobutane ring (CB) puckering of a cis-syn DNA photodimer (cis-syn d-T[p]T) differs from that of a cis-syn RNA photodimer (cis-syn r-U [p] U) [J.-K. Kim and J. L. Alderfer (1992) Journal of Biomolecular Structure and Dynamics, Vol. 9, p. 1705]. In cis-syn d-T[p]T, interconversion of the CB ring between CB+ and CB- is observed, while in cis-syn r-U[p]U only CB- is observed. In the CB+ conformation, the two thymine rings of the dimer are twisted in a right-handed fashion, as are the bases in B-form DNA. In case of CB- they are twisted in a left-handed fashion. The C5 (base) and/or C2' (sugar) substituents apparently affect the CB ring flexibility in cis-syn d-T[p]T and cis-syn r-U[p]U. To study the effects of the C5 substituent on CB ring flexibility, two-dimensional nuclear Overhauser effect (NOE) and P-31-nmr experiments were performed on cis-syn d-T[p]U, cis-syn d-U[p]T, and cis-syn d-U[p]U photodimers to investigate the CB puckering mode and overall molecular conformation and dynamics. The NOE results indicate the 5-methyl group in the photodimer induces conformational flexibility of the CB ring. In cis-syn d-T[p]U and cis-syn d-U[p]T, both CB+ and CB- puckering modes are observed. This indicates interconversion between two modes takes place as observed in cis-syn d-T[p]T. In the case of cis-syn d-U[p]U, only the puckering CB- mode is observed. All three DNA-type dimers-cis-syn d-T[p]U, cis-syn d-U[p]T, cis-syn d-U[p]U-show a characteristic flexibility of glycosidic bonds at the 5' residue; cis-syn d-T[p]T demonstrates syn-anti interconversion for both the 3' and 5' sides, while the others are exclusively anti on the 3' side. In contrast, the ribophotodimer, cis-syn r-U[p]U, lacking the C5 methyls and having a C2'-OH, demonstrates no conformational flexibility in the CB ring or in either of the glycosidic bonds. Differential flexibility of the three DNA-type dimers (cis-syn d-T[p]U, cis-syn d-U[p]T, cis-syn d-U[p]U) and the RNA dimer (cis-syn r-U[p]U) in the sugar-phosphate backbone region is also apparent from the temperature dependence of the P-31 chemical shifts of these photodimers compared to their normal dimer analogues. Over the temperature range 18-63-degrees-C, the chemical shift change is reduced 22-42% in three DNA-type dimers, while it is reduced 71% in cis-syn r-U[p]U, suggesting the RNA-type dimer is more rigid.