Structure and dynamics of nucleic acids photoproducts

Thesis/Dissertation · Wed Jan 01 04:00:00 EST 1992

OSTI ID:7042701

Kim, J K

Sensitized UV-B irradiation of the dinucleoside monophosphate, d-TpF and d-FpT (F = fluorouracil), produces a defluorinated (5-5) photoadduct, d-T5p5U and d-U5p5T. 2D-NOE experiments and restrained molecular dynamics calculation produced three dimensional structures of the two (5-5) photoadducts, where a 5R-6R and a 5S-6S configuration were obtained as the most probable chiralities of the TC5 and TC6 atoms in d-T5p5U and d-U5p5T. The conformation of cyclobutane-ring (CB-ring) of cis-syn type photodimer revealed potential importance in the photolyase-substrate interactions and conformational impacts on normal nucleic acid regions. In the two puckering modes (CB[sup +] and CB[sup [minus]]) cyclobutane rings are twisted in right-handed fashion as are the base in B-DNA (CB[sup +]) or are left-handed twisted (CB[sup [minus]]). c-s d-T[p]T shows a flexibilities of the CB-ring (CB[sup +] [leftrightarrow] CB[sup [minus]]) and the glycosidic bonds (syn [leftrightarrow] anti), while in c-s-r-U[p]U only the CB[sup [minus]] mode was observed with syn and anti at the 5'-side and 3'-side glycosidic bond. In the ROESY experiment of d(T)[sub 4] containing photodimer, the CB-ring and the 5'-side glycosidic bond at the dimers site showed reduced flexibility. In studies of c-s d-T[p]U, c-s d-U[p]T and c-s d-U[p]U, the methyl group in DNA type photodimer is crucial for inducing the CB-ring flexibility, and 2'-OH group affect the flexibility of 5'-side glycosidic bond in the dimer. Molecular modeling, mechanics and dynamics were used to investigate the conformational behaviors of the photodimerized DNA and RNA structure. Photodimerized RNA structure produced the large structural distortions over the wide regions including the dimer site with the least RMS values of intradimer backbone torsions, while in the dimerized DNA, structural distortions were observed at the first and third residues to the 5'-side and the 3'-side of the dimer site, respectively, but not at the dimer site.

• Research Organization: State Univ. of New York, Buffalo, NY (United States)
• OSTI ID: 7042701
• Country of Publication: United States
• Language: English

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
400500 -- Photochemistry
550200* -- Biochemistry
59 BASIC BIOLOGICAL SCIENCES
ADDUCTS
ALKANES
ANTIMETABOLITES
AZINES
CHEMICAL REACTIONS
CONFORMATIONAL CHANGES
CYCLOALKANES
DRUGS
ELECTROMAGNETIC RADIATION
FLEXIBILITY
FLUOROURACILS
HETEROCYCLIC COMPOUNDS
HYDROCARBONS
HYDROXY COMPOUNDS
MECHANICAL PROPERTIES
MOLECULAR BIOLOGY
MOLECULAR STRUCTURE
ORGANIC COMPOUNDS
ORGANIC FLUORINE COMPOUNDS
ORGANIC HALOGEN COMPOUNDS
ORGANIC NITROGEN COMPOUNDS
PHOTOCHEMICAL REACTIONS
PYRIMIDINES
RADIATIONS
STEREOCHEMISTRY
TENSILE PROPERTIES
ULTRAVIOLET RADIATION
URACILS