Tracking excited state decay mechanisms of pyrimidine nucleosides in real time.

DNA owes its remarkable photostability to its building blocks-the nucleosides-that efficiently dissipate the energy acquired upon ultraviolet light absorption. The mechanism occurring on a sub-picosecond time scale has been a matter of intense debate. Here we combine sub-30-fs transient absorption spectroscopy experiments with broad spectral coverage and state-of-the-art mixed quantum-classical dynamics with spectral signal simulations to resolve the early steps of the deactivation mechanisms of uridine (Urd) and 5-methyluridine (5mUrd) in aqueous solution. We track the wave packet motion from the Franck-Condon region to the conical intersections (CIs) with the ground state and observe spectral signatures of excited-state vibrational modes. 5mUrd exhibits an order of magnitude longer lifetime with respect to Urd due to the solvent reorganization needed to facilitate bulky methyl group motions leading to the CI. This activates potentially lesion-inducing dynamics such as ring opening. Involvement of the 1nπ* state is found to be negligible.

Gas-phase study on uridine: Conformation and X-ray photofragmentation.

Fragmentation of RNA nucleoside uridine, induced by carbon 1s core ionization, has been studied. The measurements by combined electron and ion spectroscopy have been performed in gas phase utilizing synchrotron radiation. As uridine is a combination of d-ribose and uracil, which have been studied earlier with the same method, this study also considers the effect of chemical environment and the relevant functional groups. Furthermore, since in core ionization the initial core hole is always highly localized, charge migration prior to fragmentation has been studied here. This study also demonstrates the destructive nature of core ionization as in most cases the C 1s ionization of uridine leads to concerted explosions producing only small fragments with masses ≤43 amu. In addition to fragmentation patterns, we found out that upon evaporation the sugar part of the uridine molecule attains hexagonal form.

Photochemical generation and reactivity of the 5,6-dihydrouridin-6-yl radical.

Nucleobase radicals are the major family of reactive intermediates formed when nucleic acids are exposed to hydroxyl radical, which is produced by gamma-radiolysis and Fe.EDTA. Significant advances have been made in understanding the role of nucleobase radicals in oxidative DNA damage by independently generating these species from photochemical precursors. However, this approach has been used much less frequently to study RNA molecules. Norrish type I photocleavage of the tert-butyl ketone (2b) enabled studying the reactivity of 5'-benzoyl-5,6-dihydrouridin-6-yl (1b). High mass balances were observed under aerobic or anaerobic conditions, and O(2) did not affect the photochemical conversion of the ketone (2b) to 1b. Competition studies with O(2) indicate that the radical abstracts hydrogen atoms from beta-mercaptoethanol with a bimolecular rate constant = 2.6 +/- 0.5 x 10(6) M(-1)s(-1). The major product formed in the presence of O(2) was 5'-benzoyl-6-hydroxy-5,6-dihydrouridine (6). In contrast, 5-benzoyl-ribonolactone (7), a hypothetical product resulting from C1'-hydrogen atom abstraction by the peroxyl radical, could not be detected. Overall, tert-butyl ketone 2b is a clean source of 5'-benzoyl-5,6-dihydrouridin-6-yl (1b) and should prove useful for studying the reactivity of the respective radical in RNA.

Photodegradation of penoxsulam.

This study was carried out to characterize the photodegradation of penoxsulam and to evaluate the significance of photolysis for its fate and dissipation. Degradation studies of (14)C-labeled isotopes of penoxsulam in a "merry-go-round" reactor suggest that aqueous photodegradation proceeds via three possible pathways: cleavage of the sulfonamide bridge, stepwise degradation of the triazolopyrimidine system and its substituents, and photooxidation of the sulfonyl group. Seven major photoproducts were found, and six were identified. Two of the identified photodegradation products seem to be either rapidly biodegraded when formed or not formed in significant amounts in environmental conditions.

Light-induced reactions of Escherichia coli DNA photolyase monitored by Fourier transform infrared spectroscopy.

Cyclobutane-type pyrimidine dimers generated by ultraviolet irradiation of DNA can be cleaved by DNA photolyase. The enzyme-catalysed reaction is believed to be initiated by the light-induced transfer of an electron from the anionic FADH- chromophore of the enzyme to the pyrimidine dimer. In this contribution, first infrared experiments using a novel E109A mutant of Escherichia coli DNA photolyase, which is catalytically active but unable to bind the second cofactor methenyltetrahydrofolate, are described. A stable blue-coloured form of the enzyme carrying a neutral FADH radical cofactor can be interpreted as an intermediate analogue of the light-driven DNA repair reaction and can be reduced to the enzymatically active FADH- form by red-light irradiation. Difference Fourier transform infrared (FT-IR) spectroscopy was used to monitor vibronic bands of the blue radical form and of the fully reduced FADH- form of the enzyme. Preliminary band assignments are based on experiments with 15N-labelled enzyme and on experiments with D2O as solvent. Difference FT-IR measurements were also used to observe the formation of thymidine dimers by ultraviolet irradiation and their repair by light-driven photolyase catalysis. This study provides the basis for future time-resolved FT-IR studies which are aimed at an elucidation of a detailed molecular picture of the light-driven DNA repair process.

Independent generation and reactivity of 2-deoxy-5-methyleneuridin-5-yl, a significant reactive intermediate produced from thymidine as a result of oxidative stress.

2'-Deoxy-5-methyleneuridin-5-yl (1) is produced in a variety of DNA damage processes and is believed to result in the formation of lesions that are mutagenic and refractory to enzymatic repair. 2'-Deoxy-5-methyleneuridin-5-yl (1) was independently generated under anaerobic conditions via Norrish Type I photocleavage during Pyrex filtered photolysis of the benzyl ketone 7. The radical (1) exhibits behavior consistent with that of a resonance-stabilized radical. The KIE for hydrogen atom transfer from t-BuSH was found to be 7.3 +/- 1.7. Competition studies between radical recombination and hydrogen atom donors (2,5-dimethyltetrahydrofuran, kTrap = 46.1 +/- 15.4 M(-1) s(-1); propan-2-ol, kTrap = 13.6 +/- 3.5 M(-1) s(-1)) chosen to mimic the carbohydrate components of 2'-deoxyribonucleotides suggest that 2'-deoxy-5-methyleneuridin-5-yl (1) may be able to transfer damage from the nucleobase to the deoxyribose of an adjacent nucleotide in DNA under hypoxic conditions.

An RNA tertiary structure of the hepatitis delta agent contains UV-sensitive bases U-712 and U-865 and can form in a bimolecular complex.

Genomic RNA of the hepatitis delta agent has a highly conserved element of local tertiary structure. This element contains two nucleotides which become covalently crosslinked to each other upon irradiation with UV light. Using direct RNA analysis, we now identify the two nucleotides as U-712 and U-865 and show that the UV-induced crosslink can be broken by re-exposure to a 254 nm peak UV light source. In the rod-like secondary structural model of delta RNA, nucleotides U-712 and U-865 are off-set from each other by 5-6 bases, a distance too great to permit crosslinking. This model needs to be modified. Our data indicate that bases U-712 and U-865 closely approximate each other and suggest that the smooth helical contour proposed for delta RNA is interrupted by the UV-sensitive element. The nucleotide sequence shows that the UV-sensitive site does not have a particularly high density of conventional Watson-Crick base pairs compared to the rest of the genome. However, this element may have a number of non-Watson-Crick bonds which confer stability. Following UV-crosslinking and digestion with 1 mg/ml of RNase T1 at 37 degrees C for 45 min in 10 mM Tris-HCl, 1 mM EDTA (conditions expected to give complete digestion), this element can be isolated as part of a 54 nucleotide long partial digestion product containing at least 16 internal G residues. UV-crosslinking analysis shows that this unusual tertiary structural element can form in a bimolecular complex.

An ultraviolet light-induced crosslink in yeast tRNA(Phe).

The irradiation of native or unmodified yeast tRNA(Phe) by short wavelength UV light (260 nM) results in an intramolecular crosslink that has been mapped to occur between C48 in the variable loop and U59 in the T loop. Photo-reversibility of the crosslink and the absence of fluorescent photo adducts suggest that the crosslink product is a cytidine-uridine cyclobutane dimer. This is consistent with the relative geometries of C48 and U59 in the crystal structure of yeast tRNA(Phe). Evaluation of the crosslinking efficiency of the mutants of tRNA(Phe) indicates that the reaction depends on the correct tertiary structure of the RNA.

Enhancement of radiation-induced base release from nucleosides in alkaline solution: essential role of the O.- radical.

The effect of pH on base release in the gamma-radiolysis of N2O-saturated solutions of a number of nucleosides (including uridine, 3-methyluridine, 2',3'-O-isopropylidene-uridine, and adenosine) has been investigated. For all these nucleotides, independent of the base or sugar moiety, base release is very low at pH below 10 (G approximately (0.3-0.7) x 10(-7) mol J-1), but increases drastically to G approximately (3-4) x 10(-7) mol J-1 at pH greater than or equal to 13. This phenomenon had already been previously reported and attributed to an OH(-)-induced transfer of a base radical into a sugar radical. However, it is now shown that at pH 12, where base release starts to increase, a lowering of the dose-rate does not affect the yield of free base. The increase in base release is accompanied by an overall reduction of chromophore loss of similar magnitude (with 2',3'-O-isopropylidene-uridine and 3-methyluridine), as well as by an increase in the yield of oxidizing radicals by a factor of 2 (with uridine). The measured rate constant of the reaction of .OH/O.- with the nucleosides is also pH-dependent, as .OH reacts faster than O.- with the nucleosides by a factor of 6-7. It is concluded that the increase in base release at high pH is caused by the increasing participation of O.-, which, unlike .OH, attacks the nucleosides preferentially at their sugar moieties, and is not due to an OH(-)-induced radical transfer from the base to the sugar moiety.

Ultraviolet irradiation of nucleic acids: formation, purification, and solution conformational analyses of the cis-syn and trans-syn photodimers of UpU.

Uridylyl(3'-5')uridine (UpU) is subjected to aqueous acetone photosensitized radiation with sunlamps. These irradiation conditions form only cyclobutane-type photodimers. Purification of a specific configurational photodimer is accomplished by using C-18 reverse-phase high-performance liquid chromatography. Multinuclear NMR analysis is used to analyze photoproduct formation and to determine conformational features of these photodimers. Four photodimers are identified, with the cis-syn isomer predominant. The cis-syn and trans-syn photodimers of UpU exhibit markedly different furanose and exocyclic bond conformations. A comparison of the properties of the cis-syn dimers of UpU with those of dTpdT reveal many similar conformational features but also some that are different.

[Photochemical transformations of nucleic acid components in the presence of lunar soil]. / Fotokhimicheskie prevrashcheniia komponentov nukleinovykh kislot v prisutstvii lunnogo grunta.

It has been demonstrated that lunar soil is an effective catalyzer of photolysis of thin-solid films of uracil and uridine. Uracil photolysis proceeds more intensively both in the presence of the lunar soil and in absence of the latter as compared to the photolysis of uridine. Together with photodestruction of uracil, the extension in the initial molecular structure takes place.

OH-induced free radicals in uridine studied by a method combining ESR, spin-trapping, and liquid chromatography.

Free radicals produced by the reactions of OH radicals with uridine were investigated by a method combining ESR, spin-trapping, and liquid chromatography. A N2O-saturated aqueous solution of uridine, containing 2-methyl-2-nitrosopropane as a spin-trap, was X-irradiated and the resulting spin-adducts were separated by gel permeation chromatography and reverse-phase HPLC. ESR and uv-absorbance spectra obtained from the separated spin-adducts show that 5-yl and 6-yl radicals are produced by OH addition to the 5,6 double bond of the base moiety. It is also shown that radicals due to H abstraction from the sugar moiety at the C-4' and C-5' positions are produced.

Radiolysis of nucleosides in aqueous solutions: base liberation by the base attack mechanism.

On the radiolysis of uridine and some other nucleosides in aqueous solution, a pH-dependent liberation of uracil or the corresponding base was found. e-aq and HO-.2 gave no freed bases, although many oxidizing radicals, including OH, Cl-.2, Br-.2, (CNS)-.2 and SO-.4, did cause the release of unaltered bases, depending on the pH of the solutions. The base yields were generally high at pH greater than or equal to 11, with the exception of SO-.4, which gave a rather high yield of uracil (from uridine) even in the pH region of less than or equal to 11. The pattern of the base formation against pH varied with the reacting radical, but was the same for the different nucleosides. With regard to the OH radical system, bases are considered to be formed after H-abstraction of the sugar moiety at low pH. The other oxidizing radicals, however, may cause base release by attack at the base. It is possible that O-, present at high pH as the dissociated form of OH, may act partly as an oxidizing radical. A plausible mechanism of 31'-radical formation is discussed.

E.S.R. of spin-trapped radicals in aqueous solutions of 5-halo derivatives of nucleic acid constituents: reactions of hydrated electrons, hydroxyl radicals and U.V. photolysis.

In order to obtain information concerning the mechanism of radio- and photosensitization due to 5-halogen substituted nucleic acid constituents, the free radicals produced in iodo-, bromo-, chloro- and fluoro-derivatives of uracil, uridine and deoxyuridine by reaction with hydrated electrons and with hydroxyl radicals and by direct U.V. photolysis have been studied by e.s.r. and spin-trapping. t-Nitrosobutane was used as the spin-trap. From 5-halogenated bases (except 5-fluorouracil) U.V. photolysis and reactions with hydrated electrons produced the uracilyl radical which was subsequently spin-trapped. When hydroxyl radical reactions were studied, the free radical at the N(1) position of the base was identified. From 5-fluorouracil U.V. photolysis generated the alpha-halo radical at the C(5) position of the base. For 5-halogenated ribonucleosides and deoxyribonucleosides, free radicals located on the sugar moiety were observed for reactions with hydrated electrons, hydroxyl radicals and for U.V. photolysis. The implications of these results for understanding the mechanism of radio- and photosensitization by 5-halogenated nucleic acids are discussed.

E.s.r. of spin-trapped radicals in gamma-irradiated aqueous solutions of nucleic acids and their constituents.

The gamma-radiolysis of de-aerated neutral aqueous solutions of uracil, thymine, cytosine and of the corresponding nucleosides and nucleotides and of calf-thymus DNA was investigated. For uracil and thymine, the U.V. photolysis of aqueous solutions containing H2O2 was also studied. The short-lived radicals were spin-trapped by tert-nitrosobutane and identified by electron-spin-resonance spectroscopy. For all compounds two or more radicals were observed, and these could be distinguished by following the thermal decay of the spin adducts. Radicals formed by the addition of H or OH at the C(5) or C(6) positions of the pyrimidine derivatives were observed in all cases. Sodium formate was used as a scavenger for H and OH to identify the radicals formed by eaq-. Spin-trapped radicals in gamma-irradiated aqueous solutions of polynucleotides exhibited broad e.s.r. lines. For DNA gel, additional narrow lines due to scission products were also found.

Isomerisation and conformation studies of (+)- and (-)6-hydroxy-5, 6-dihydrouridine.

(1) "Uridine hydrates" i.e. (+)- and (-)6-hydroxy-5, 6-dihydrouridine were formed under gamma irradiation in a deaerated aqueous solution of uridine. (2) The structures of two diastereoisomers were determined by spectroscopic measurements (infrared, ultraviolet and NMR) and verified by stereospecific synthesis; uridine hydrates were prepared by mild reduction of trans(+)- and (-)iodohydrins with acetic acid and zinc power. (3) The carbon 6 epimerisation of uridine hydrates 6R or 6S was performed in triated water (pH 5.5, 30 degrees C) and at the same time tritium incorporation on carbon 5 was noted. The mechanism of these reactions could be explained by the opening of the N1-C6 bond of the pyrimidine ring, followed by ketoenolisation reaction of carbons 4 and 5. (4) The 250 MHz NMR analysis has allowed us to determine the nucleoside conformations. Nucleosides had mainly the S(C2' endo) conformation. A slight preference of gauche-gauche (gg) rotamer of the exocyclic hydroxymethyl group was noted and the aglycone was in the anti conformation.