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-Tp]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 ³¹P-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 ³¹P chemical shifts of these photodimers compared to their normal dimer analogues. Over the temperature range 18-63°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. © 1993 John Wiley & Sons, Inc.