Conformational variations of the cis-syn cyclobutane-type photodimer in DNA and RNA.
The recent NMR study of a cis-syn photodimer B-DNA 10mer-duplex (Taylor et al., Biochemistry 29, 8858 (1990)) showed the cyclobutane (CB) ring with a puckered-twist in a right-handed sense (CB+). This is opposite to that of the crystal structure of cis-syn d-TpT(cyano-ethyl)(d-T[p]T-CE) which has a left-handed puckered-twist (CB-)(Hruska et al., Biopolymers 25, 1399 (1986)). 2D-NOESY experiments were performed on cis-syn d-T[p]T and cis-syn U[p]U at 25 and 35 degrees C, respectively, to investigate the puckering mode of the cyclobutane ring of isolated cis-syn photodimers of the DNA and RNA types. The DNA photodimers showed interconversion of the puckered-twist of the cyclobutane ring between CB- and CB+ and interconversion of the glycosidic angle between syn and anti in both nucleoside residues. Interestingly, in the RNA photodimer only the CB- puckering mode with syn conformation of the glycosidic angle of the U[p]- was observed. These different dynamical behaviors of the photodimer in DNA and RNA might portend differential conformational effects on their corresponding normal nucleic acid regions. In addition these results indicate differences in the cyclobutane ring conformation of the cis-syn d-T[p]T, not only in solution and crystalline states, but also when the dimer is isolated and in duplex forms.
Kim
J K
JK
Biophysics Department, Roswell Park Cancer Institute, Buffalo, NY 14263.
Alderfer
J L
JL
D003503:Cyclobutanes / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D015226:Dinucleoside Phosphates / Q000737:chemistry; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011740:Pyrimidine Dimers / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*
D003503:Cyclobutanes; D015226:Dinucleoside Phosphates; D011740:Pyrimidine Dimers; C017758:thymidylyl-(3'-5')-thymidine; D012313:RNA; D004247:DNA