An NMR and conformational investigation of the trans-syn cyclobutane photodimers of dUpdT.

Both trans-syn cyclobutane-type photodimers of 2'-deoxyuridylyl (3'-5') thymidine (dUpdT) were formed by deamination of the corresponding trans-syn cyclobutane photodimers of 2'-deoxycytidylyl (3'-5') thymidine (dCpdT) and were examined by 1H-, 13C-, and 31P-nmr spectroscopy. One- and two-dimensional nmr experiments provided a nearly complete assignment of the 1H, 13C, and 31P resonances. Scalar and nuclear Overhauser effect contacts were used to determine the conformation of the deoxyribose rings, exocyclic bonds, cyclobutane rings, and glycosidic linkages. Isomer I (S-type class; CB-; SYN-ANTI) and isomer II (N-type class; CB+; ANTI-SYN) exhibit markedly different conformational features. 31P chemical shifts show that the relative flexibility is dUpdT > isomer II > isomer I. The conformations of these species are very similar to those of other previously examined trans-syn photodimers. Among bipyrimidine photodimers of a given diastereomeric form (i.e., trans-syn I or II), the nmr-derived conformational parameters are nearly invariant, regardless of base substitution pattern. This contrasts with the substituent-dependent variation of cyclobutane ring conformation observed by Kim et al. (Biopolymers, 1993, Vol. 33, pp. 713-721) for an analogous series of cis-syn photodimers. Steric crowding of cyclobutane ring substituents is offered as an explanation for the difference in substituent effects between the families of cis-syn and trans-syn photodimers.

An NMR and conformational investigation of the trans-syn cyclobutane photodimers of dTpdU.

Two trans-syn cyclobutane photodimers of thymidylyl (3'-5') deoxyuridine were formed by deamination of the corresponding trans-syn cyclobutane photodimers of thymidylyl (3'-5') deoxycytidine and were examined by 1H-, 13C-, and 31P-nmr spectroscopy. Correlation spectroscopy, nuclear Overhauser enhancement spectroscopy, and one-dimensional heterodecoupling experiments allowed a more complete assignment of the 1H spectra, compared with previous reports by Koning et al. [(1991) European Journal of Biochemistry, Vol. 195, pp. 29-40] and Liu and Yang [(1978) Biochemistry, Vol. 17, pp. 4865-4876]. Deoxyribose ring conformations were calculated from 1H coupling constants by pseudorotational analysis, and rotamer distributions of exocyclic bonds were calculated from the observed homonuclear and heteronuclear coupling constants. The cyclobutane ring configuration (CB) of each isomer was identified, using arguments based upon observed scalar and dipolar couplings. Glycosidic bond conformation was ascertained from nuclear Overhauser enhancements observed between base and deoxyribose protons. Isomer I (S-type class; CB-; SYN-ANTI) and isomer II (N-type class; CB+; ANTI-SYN) exhibit markedly different conformational features. 31P chemical shifts and exocyclic bond rotamer distributions indicate diminished backbone flexibility for both photoproducts relative to parent thymidylyl (3'-5') deoxyuridine. Isomer I (SYN-ANTI) is particularly rigid, while isomer II (ANTI-SYN) maintains some flexibility. Also, 13C spectra were acquired and assigned unequivocally with the aid of short- and long-range two-dimensional heteronuclear shift correlation experiments.

Quantum yields and secondary photoreactions of the photoproducts of dTpdT, dTpdC and dTpdU.

The photoproducts of the dinucleoside monophosphates, dTpdT, dTpdC and dTpdU, have been purified by high performance liquid chromatography and characterized by UV absorption spectroscopy, fast atom bombardment mass spectrometry and by secondary thermal and photoreactions. Four types of photoproducts were analyzed: (1) cyclobutane dimers including cis-syn isomers and two diastereomers of the trans-syn isomers; (2) 6-4 photoadducts and the corresponding Dewar valence isomers; (3) photohydrates comprising two diastereomers and (4) a new photoproduct resembling nucleobase amine adducts, which occurs only for dTpdC. The quantum yields of formation of these photoproducts and for some secondary photoreactions were measured by kinetic analysis of the photoproduct yield as a function of photon fluence. These results indicate that cis-syn cyclobutane dimers are the photoproducts formed with highest efficiency with dT[p]dC dimers being formed with 50-75% the efficiency of dT[p]dT dimers. The 6-4 photoadducts are formed with 5-10% the efficiency of cis-syn cyclobutane dimers and the 6-4 photoadduct of dTpdC is formed two to three times more efficiently than that of dTpdT. Photohydrates are also formed efficiently due to an equilibrium between stacked and unstacked complexes of the dinucleoside monophosphates. It is shown that three of these photoproducts, namely the cyclobutane dimers of dTpdC, the 6-4 photoadducts and the possible nucleobase amine adduct, undergo photolysis in the UV-B region resulting in either photoreversion or secondary photoreaction.

Kinetic analysis of the deamination reactions of cyclobutane dimers of thymidylyl-3',5'-2'-deoxycytidine and 2'-deoxycytidylyl-3',5'-thymidine.

The cyclobutane dimer photoproducts of dTpdC and dCpdT have been produced by acetophenone photosensitization and separated by reverse-phase HPLC. Each dinucleoside monophosphate was shown to produce one cis,syn isomer and two trans,syn isomers. Three of these photoproducts, namely, the cis,syn isomers of dTpdC and dCpdT and one trans,syn isomer (the syn-anti glycosidic isomer) of dTpdC were selected to study the deamination kinetics. Analysis of the pH dependence indicates that the deamination proceeds by the hydrolysis of the imido amide group of the 5,6-saturated cytosine base with the formation of a carbinolamine intermediate. Determination of the kinetic parameters showed that, for these three cyclobutane dimers, the rate-determining step at physiological pH is a cyclobutane dimers, the rate-determining step at physiological pH is a nucleophilic attack of hydroxide ion on the protonated 5,6-saturated cytosine base. The kinetic analysis showed that the cis,syn isomers deaminate approximately 3 times faster than the trans,syn isomer, which is due to a large difference in pKa of the 5,6-saturated cytosine moiety. An electrostatic interaction between the iminium group of cytosine and the carbonyl group of thymine is proposed to account for the increase in pKa for the cis,syn isomers relative to the trans,syn isomer. A similar interaction is proposed to explain the relative difference in reactivity between the cis,syn isomers and the trans,syn isomer with regard to the breakdown of the carbinolamine intermediate.

Gamma-radiolysis of poly(A) in aqueous solution: efficiency of strand break formation by primary water radicals.

gamma-Radiation-induced single-strand break formation (ssb) in polyadenylic acid (poly(A] has been determined in Ar and N2O-saturated aqueous solution in the presence of different concentrations of t-butanol. Strand breaks were monitored by a low-angle laser light-scattering technique. The efficiencies for strand breakage caused by solvated electrons, hydrogen atoms and OH radicals have been found to be 0.25, 0.20 and 7.8 per cent, respectively. The efficiency of OH radicals depends only slightly on pH (pH 5.0, 7.5 and 9.0) and is independent of the presence of salt (0.01 mol dm-3 NaC1O4) and of the irradiation temperature (20 degrees C and 70 degrees C). The efficiency of OH for ssb formation obtained in this work with poly(A) is much smaller than that of poly(dA). This is explained by the different molecular conformations of the sugar moiety of poly(A) (3'-endo) and poly(dA) (2'-endo). With increasing t-butanol concentration more strand breaks are formed than expected from simple homogeneous competition kinetics of poly(A) and t-butanol for OH radicals. This result is considered to be due to nonhomogeneous reaction kinetics in the above-mentioned competition. The rate constants for the reaction of OH and H with poly(A) have been determined.

Hydroxyl radical-induced strand break formation of poly(U) in anoxic solution. Effect of dithiothreitol and tetranitromethane.

The role of dithiothreitol (DTT) and tetranitromethane (TNM) on the yields of radiation-induced strand break formation in polyuridylic acid (poly(U] was studied in anoxic aqueous solutions at neutral pH by low-angle laser light-scattering. From G (single-strand breaks) as a function of DTT concentration it follows that two different processes lead to OH radical-induced single-strand break (ssb) formation. Only one of the two processes, which accounts for 80 per cent of the ssb formation, is inhibited by DTT, the other one, 20 per cent, is not inhibited. The 'repair' process is attributed to H-donation to the C-6-yl radical of the uracil moiety. The C-6-yl radical is produced by OH addition to the C-5 position of the uracil moiety. It follows that the sugar radicals, in contrast to earlier suggestions, do not seem to be repaired by DTT at the low concentrations used. The strand break formation not inhibited by DTT is induced by radicals other than the uracil-6-yl radical, e.g. the uracil-5-yl or the OH radicals reacting with the sugar moiety. The strong reduction of G(ssb) from 2.3 to 0.2 on addition of TNM is also discussed.

Yields of radiation-induced main chain scission of poly U in aqueous solution: strand break formation via base radicals.

The G values for single-strand breaks G(ssb) in polyuridylic acid (poly U) have been measured by low-angle laser light scattering in aqueous solutions under various conditions (e.g. in the presence of N2O, Ar and t-butanol). In N2O-saturated solutions at room temperature and pH 5.6, the G(ssb) is 2.3. The efficiency of ssb formation was found to be 41 per cent for OH radicals, 19 per cent for H atoms and congruent to zero for e-aq. On the basis of 20 per cent and less than 5 per cent attack on the sugar moiety by OH radicals and H atoms, respectively, the large G(ssb) values obtained cannot be explained solely as resulting from radicals produced by reaction of OH radicals and H atoms on the sugar moiety. It is therefore proposed that base radicals produced by the reaction of OH radicals or H atoms with the uracil moiety can also lead to chain break formation in poly U via radical transfer to the sugar moiety.