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 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.(ABSTRACT TRUNCATED AT 250 WORDS)
Kim
J K
JK
Biophysics Department, Roswell Park Cancer Institute, Buffalo, New York 14263.
Wallace
J C
JC
Alderfer
J L
JL
D003503:Cyclobutanes / Q000737:chemistry; D004247:DNA / Q000737:chemistry / Q000528:radiation effects; D004255:Deoxyribodipyrimidine Photo-Lyase / Q000378:metabolism; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D010777:Photochemistry; D011740:Pyrimidine Dimers / Q000737:chemistry* / Q000528:radiation effects; D012313:RNA / Q000737:chemistry / Q000528:radiation effects
D003503:Cyclobutanes; D011740:Pyrimidine Dimers; D012313:RNA; D004247:DNA; D004255:Deoxyribodipyrimidine Photo-Lyase