THE PHOTOCHEMISTRY OF 14 C-5-BROMO-2''-DEOXYURIDYLYL-(3''→5'')-THYMIDINE DETERMINATION OF QUANTUM YIELDS AS A FUNCTION OF pH

Abstract— Quantum yields for the formation of the major photoproduct of 2-¹⁴C-5-bromo-2'-deoxyuridylyl-(3'→5')-thymidine (BrdUpT) have been determined by irradiation of the 2-¹⁴C-BrU-labeled dinucleotide at pH 2.3, 5.9, 7.05, 8.0 and 10.25 with U.V. light at 280nm. At acidic and neutral pH the quantum yield was 0.0063; the value decreased markedly above pH 8.0 to 0.0025 at pH 10.25. Some evidence of the formation of additional photoproducts at high and low pH was found. Some aspects of the mechanism of the reaction are discussed.
Consideration of p K_a values calculated for singlet and triplet excited states indicates that the decrease in the quantum yield of main photoproduct at high pH is due to dissociation of the excited bromodeoxyuridine moiety. It is suggested that the formation of BrdUpT photoproduct and the debromination of bromouracil-labeled DN A occur via different excited states.     

QUANTUM YIELDS AND SECONDARY PHOTOREACTIONS OF THE PHOTOPRODUCTS OF dTpdT, dTpdC AND dTpdU

Abstract— 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.     

The photophysics of a luminescent ruthenium polypyridyl complex with pendant β-cylodextrin; pH modulation of lifetime and photoinduced electron transfer

At room temperature, [Ru(bpy)₂(phen-CD)][PF₆]₂, (phen-CD is 6 ^A -(5-amino-1, 10-phenanthroline)-6 ^A -deoxy- β-Cyclodextrin and bpy is 2,2'-bipyridine) exhibits an intense metal ligand charge transfer (MLCT) transition at 452 nm and a long lived luminescence, centred at 618 nm. We demonstrate, for the first time, that the luminescence quantum yield and lifetime of the Ru (II) polypyridyl centre depends markedly on the solution pH. The pH sensitive range extends from pH 3.9 to pH 13.2 and the luminescence quantum yield changes by more than 60% over this range. This pH sensitivity is attributed to protonation/deprotonation of the secondary amine group bridge between the phenanthroline unit and CD. The complex exhibits strong host-guest binding to anthraquinone and anthraquinone-2-carboxylic acid, with concomitant quenching of the [Ru(bpy)₂(phen-CD)]²⁺ excited state. This quenching arises from efficient intramolecular electron transfer. The sensitivity of this photoinduced process to the protonation state of the bridge is discussed.     

FLUORESCENCE LIFETIME AND QUANTUM YIELD OF PHENYLALANINE AQUEOUS SOLUTIONS. TEMPERATURE AND CONCENTRATION EFFECTS

Abstract— –The influence of concentration and temperature on the fluorescence quantum yield and lifetime (measured by a monophoton technique) of phenylalanine is studied in neutral aqueous solutions (8 × 10^-4-10^-1 M ) over the temperature range 0–70°C. The rate constants for emission, internal conversion and intersystem crossing are evaluated and show that both non radiative processes contribute efficiently to the deactivation of the singlet state. Evidence for excited dimer formation at high concentration is presented. The binding energy of excimers was found to be 0.19 e V.     

PHOTOPRODUCTS OF BROMOURACIL-LABELED DNA AND THE STRUCTURE OF 5-BROMODEOXYURIDYLYL-(3' → 5')-THYMIDINE PHOTOPRODUCT

Abstract— –An attempt was made to identify some of the ultraviolet (u.v.) photoproducts of 5-bromouracil-labeled DNA (BrU-DNA). Two synthetic dinucleotides, 5-bromodeoxyuridylyl-(3' →5 ')-thymidine (BrdUpT) and 5-bromodeoxyuridylyl-(3' → 5')-deoxycytidine (BrdUpdC), were prepared. Each gave a single u.v. photoproduct which in turn gave a single acid hydrolysis product. 2-¹⁴C-BrU-DNA. prepared from E. coli B3, was irradiated (275–280 nm), hydrolyzed, and paper chromatographed in four systems. Comparison with the two synthetic photoproducts showed that if present at all, BrdUpT and BrdUpdC photoproducts could account for no more than 10 and 3.5 per cent respectively of the total photoproducts. At 55 per cent conversion of BrU into photoproducts, the major ¹⁴C-photoproduct was uracil (78 per cent); the remaining 22 per cent was made up of at least six products, three of which were reversed by 232 nm irradiation.
The debrominated cyclobutane structure proposed by Haug for BrdUpT photoproduct has been shown to be incorrect. It was found to contain one atom of bromine per molecule. On the basis of nuclear magnetic resonance and u.v. spectra, two possible structures are proposed for the photoproduct, each containing an eight-membered ring.     

Crystal structure and photochemical behavior in solution of the 3'-N-sulfamate analogue of thymidylyl(3'-5')thymidine

The 3'-N-sulfamate analogue of thymidylyl(3'-5')thymidine (TnsoT, 1) exhibits a preference for a C3'-endo conformation in the solution and solid states. Its photochemical behavior in solution is compared to that of its natural counterpart, thymidylyl(3'-5')thymidine (TpT, 2), to get further insight into the significance of the C3'-endo conformation on the photoproduct formation at the single-stranded dinucleotide level. Irradiation at 254 nm of 1 led to the same type of photoproducts as observed with 2. However, 1 was significantly more photoreactive than 2, and accordingly, the initial rate of photoproduct formation was enhanced in accordance with its propensity to base stack compared to 2. The corresponding quantum yields were determined and showed that the enhancement factor (1 compared to 2) is moderate for the cyclobutane pyrimidine dimer (CPD) (1.26) and much higher for the (6-4) photoproduct (1.8). These data strongly suggest that the CPD and (6-4) photoproduct arise from distinct minor stacked conformations.     

THYMINE HYDRATE FORMED BY ULTRAVIOLET AND GAMMA IRRADIATION OF AQUEOUS SOLUTIONS

Abstract— Evidence is presented for the formation of a thymine hydrate upon ultraviolet (UV) or gamma irradiation of aqueous solutions. The UV quantum efficiency exhibits a dependence on pH similar to that shown for uracil hydration, but the yield is three orders of magnitude smaller than for uracil. Hydration is not affected by wavelength, oxygen, or concentration of thymine. The reversal rate of the photohydrate to thymine is similar to the reversal rates of both isomers of the thymine hydrate formed by γ radiolysis, and depends on pH in the same way as the rate for the uracil photohydrate. The photohydrate of thymine is chromatographically identical to the cis isomer of 6-hydroxy-5, 6-dihydrothymine.     

Photochemistry of purine 3-oxides in hydroxylic solvents

UV irradiation of the potent oncogen hypoxanthine 3-oxide in aqueous solution induces elimination of and rearrangement of the nitrogen-bound oxygen. The extent of each reaction shows a complex variation over the pH range 0–7. The variations in quantum yield for product formation are shown to result from the presence in the neutral molecule of tautomeric species with differing photochemistries that ionize in the excited state (pK_a^* ～ 3.5) just above the protonation pK_a (1.2). The photochemical reactivity of each ionic and each tautomeric form was assigned by comparing the effect of pH changes between 0 and 11 on the quantum yields for formation of each photoproduct from hypoxanthine 3-oxide with those of two model compounds, 1-hydroxyhypoxanthine and 6-methoxypurine 3-oxide. Photoreduction of the 3-oxides occurs via the triplet state. This process has a relatively consistent low quantum yield (Φ = 0.005 to 0.04) for most ionic and tautomeric forms of both purine 1-oxides and purine 3-oxides. Photorearrangement is a much more efficient process for purine 3-oxides (Φ = 0.3) than for purine 1-oxides (Φ = 0.04).     

RATE CONSTANTS FOR THE DEHYDRATION OF SINGLE AND DOUBLE HYDRATES OF CYTIDYLYL (3''-5'')–CYTIDINE

Abstract— Cytidylyl (3'-5') cytidine (CpC) was irradiated with ultraviolet light (u.v.) to produce the single hydrate (a mixture of C*pC and CpC*) and the double hydrate C*pC* which were separated by electrophoresis. These photoproducts rapidly dehydrate to CpC and deaminate to a mixture of U*pC and CpU*. The rate constants for dehydration and deamination of the hydrates were evaluated for a range of pH values from 3 to 8 at 0°C. It is observed that the rate constants for decay of C*pC* lie between those for C*pC and CpC* for all pH values studied. Both single and double hydrates show minimum stability around pH 4·5 and maximum stability around pH 8. The maximum rate constants for dehydration of C*pC*, C*pC and CpC* are 0·26, 0·145 and 0.35 hr^-1 respectively and the minimum values are 0.024, 0.011 and 0.091 hr^-1 respectively all at 0°C. The rate constants for deamination of C*pC to U*pC for a range of pH values at 0°C were measured. The amount of deamination product varies from about 2 to 10 per cent of the hydrate depending on pH with the maximum amount being produced around pH 8.     

Mechanism of the alkali degradation of (6-4) photoproduct-containing DNA

The (6-4) photoproduct is one of the major damaged bases produced by ultraviolet light in DNA. This lesion is known to be alkali-labile, and strand breaks occur at its sites when UV-irradiated DNA is treated with hot alkali. We have analyzed the product obtained by the alkali treatment of a dinucleoside monophosphate containing the (6-4) photoproduct, by HPLC, NMR spectroscopy, and mass spectrometry. We previously found that the N3-C4 bond of the 5' component was hydrolyzed by a mild alkali treatment, and the present study revealed that the following reaction was the hydrolysis of the glycosidic bond at the 3' component. The sugar moiety of this component was lost, even when a 3'-flanking nucleotide was not present. Glycosidic bond hydrolysis was also observed for a dimer and a trimer containing 5-methyl-2-pyrimidinone, which was used as an analog of the 3' component of the (6-4) photoproduct, and its mechanism was elucidated. Finally, the alkali treatment of a tetramer, d(GT(6-4)TC), yielded 2'-deoxycytidine 5'-monophosphate, while 2'-deoxyguanosine 3'-monophosphate was not detected. This result demonstrated the hydrolysis of the glycosidic bond at the 3' component of the (6-4) photoproduct and the subsequent strand break by β-elimination. It was also shown that the glycosidic bond at the 3' component of the Dewar valence isomer was more alkali-labile than that of the (6-4) photoproduct.     

Role of sequence and conformation on the photochemistry and the photophysics of A-T DNA dimers: an experimental and computational approach

The role of base sequence and conformation on the photochemistry and photophysics of thymidylyl (3'-5')-2'-deoxyadenosine sodium salt (TpdA) and 2-deoxyadenylyl (3'-5')-thymidine ammonium salt (dApT) was studied. To this end, nanosecond transient absorption at 266 nm, steady-state irradiation at 254 nm, and quantum chemical calculations were used. The transient absorption spectra show the solvated electron broad band in the visible region for each dinucleotide. In addition, low-intensity absorption bands are observed in the UV region, which are attributed to the deprotonated and protonated neutral radicals of adenine and thymine bases. Photoionization (PI) occurs by one- and two-photon pathways; the latter accounting for approximately 70% of the net PI yield. A diffusion-limited rate constant of 2.0 x 10(10) M(-1) s(-1) was obtained for the reaction of the neutral molecule with the photoejected electron in both sequences. The photodestruction yield, measured from the chromophore loss at 260 nm, decreases in the presence of well-known electron scavengers. This suggests the participation of base radical anions as one of the photodegradation pathways, which is higher in TpdA than in dApT. The intermediacy of a radical ion pair (charge separated state) between the adjacent adenine and thymine bases is proposed in the formation of the [2 + 2] cycloadduct intermediate. The [2 + 2] cycloadduct intermediate is known to be the precursor of the thymine-adenine eight-member ring photoproduct (TA*). Conformational constrains in the radical ion pair are suggested to explain the absence of the TA* photoproduct in dApT. This hypothesis is supported by semiempirical calculations performed on all relevant reactive intermediates proposed to participate in the mechanism of formation of TA*. Altogether, the results show that sequence and conformation profoundly influence the photochemistry and the photophysics of these DNA model systems.     

PROPERTIES OF THYMINE DIMERS

Abstract— The photochemical and chemical properties of the four dimers of thymine have been studied. The extinction coefficients, reversal cross-sections and quantum yields for reversal are presented as a function of wavelength in the range 200–289 nm. At any wavelength, the dimers have different reversal cross-sections but also different extinction coefficients. The quantum yields for reversal are nearly the same for all four dimers, the values ranging from 0·6 to 0·9 over the wavelength range 200–289 nm. Titration curves for the four dimers show that for each dimer, two groups are involved with two pK's at about 10·5 and 12·2. Dimers A and B are stable at alkali and acid pH's. Dimers C and D are stable from pH 1 to 3 and unstable at other pH's, with thymine the main degradation product.     

A water-soluble Xe@cryptophane-111 complex exhibits very high thermodynamic stability and a peculiar (129)Xe NMR chemical shift

The known xenon-binding (±)-cryptophane-111 (1) has been functionalized with six [(η(5)-C(5)Me(5))Ru(II)](+) ([Cp*Ru](+)) moieties to give, in 89% yield, the first water-soluble cryptophane-111 derivative, namely [(Cp*Ru)(6)1]Cl(6) ([2]Cl(6)). [2]Cl(6) exhibits a very high affinity for xenon in water, with a binding constant of 2.9(2) × 10(4) M(-1) as measured by hyperpolarized (129)Xe NMR spectroscopy. The (129)Xe NMR chemical shift of the aqueous Xe@[2](6+) species (308 ppm) resonates over 275 ppm downfield of the parent Xe@1 species in (CDCl(2))(2) and greatly broadens the practical (129)Xe NMR chemical shift range made available by xenon-binding molecular hosts. Single crystal structures of [2][CF(3)SO(3)](6)·xsolvent and 0.75H(2)O@1·2CHCl(3) reveal the ability of the cryptophane-111 core to adapt its conformation to guests.     

Photoexcitation of the potassium octacyanotungstate(IV)· 5–nitro-1,10–phenanthroline system: kinetics and mechanism of the reaction

The kinetics of thermal reactions of the photochemically-generated species [W(CN)7OH]4− and [W(CN)6–(CNH)(H2O)]2− with 5–nitro-1,10–phenanthroline (nitrophen) in basic and acidic media, respectively, were studied in buffer solutions at pH 4.2–10.6 and ionic strength 7.5×10−2kg−1 at 20°C. The quantum yield for the formation of the photoproduct was calculated and found to depend upon pH and the ligand and [W(CN)8]4− concentrations. The rate constants and quantum yields were less compared with 1,10–phenanthroline due to the electron-withdrawing inductive effect of the nitro group in nitrophen, which makes the latter a weaker ligand. The pseudo-first-order rate constant and quantum yield values in acidic media are higher than in basic media and the mechanisms of the photochemical substitution are different in the two media. This revised version was published online in June 2006 with corrections to the Cover Date.     

Hydrolytic stability of 2',3'-O-methyleneadenos-5'-yl 2',5'-di-O-methylurid-3'-yl 5'-O-methylurid-3'(2')-yl phosphate: implications to feasibility of existence of phosphate-branched RNA under physiological conditions

Hydrolytic reactions of 2',3'-O-methyleneadenos-5'-yl 2',5'-di-O-methylurid-3'-yl 5'-O-methylurid-3'(2')-yl phosphate (1a,b) have been followed by RP-HPLC over a wide pH range to evaluate the feasibility of occurrence of phosphate-branched RNA under physiological conditions. At pH <2, where the decomposition of is first order in [H3O+], the P-O5' bond is cleaved 1.5 times as rapidly as the P-O3' bond. Under these conditions, the reaction probably proceeds by an attack of the 2'-OH on the phosphotriester monocation. Over a relatively wide range from pH 2 to 5, the hydrolysis is pH-independent, referring to rapid initial deprotonation of the attacking 2'-OH followed by general acid catalyzed departure of the leaving nucleoside. The P-O5' bond is cleaved 3 times as rapidly as the P-O3' bond. At pH 6, the reaction becomes first order in [HO-], consistent with an attack of the 2'-oxyanion on neutral phosphate. The product distribution is gradually inversed: in 10 mmol L(-1) aqueous sodium hydroxide, cleavage of the P-O3' bond is favored over P-O5' by a factor of 7.3. The results of the present study suggest that the half-life for the cleavage of under physiological conditions is only 100 s. Even at pH 2, where is most stable, the half-life for its cleavage is less than one hour and the isomerization between and is even more rapid than cleavage. The mechanisms of the partial reactions are discussed.     

PHOTOCHEMISTRY OF URACIL. INTERSYSTEM CROSSING AND DIMERIZATION IN AQUEOUS SOLUTION

Abstract— Ultraviolet irradiation of ¹⁴C-uracil in aqueous solution results in the formation of hydrate and dimer photoproducts. The rate of dimerization increases with increasing uracil concentration, and decreases with increasing concentration of oxygen in solution. The kinetics are in agreement with a model previously proposed to account for the reactions, in which dimerization occurs by a reaction involving the triplet state of uracil, but hydration occurs from an excited singlet state. Oxygen reduces dimer formation by quenching the triplet. The quantum yield for intersystem crossing (ISC) to the triplet depends on the irradiation wavelength, increasing from 0.0014 at 280 nm to 0.016 at 230 nm. The ratio of rate constants for reaction of the triplet with oxygen and for dimerization is 1.1; the ratio of rate constants for triplet decay and for dimerization is 5.9 × 10^-5 M. The increase in ISC with photon energy suggests that ISC is favoured from excited vibrational levels. The quantum yield for hydration is about 0.002 at pH 4.5 for all wavelengths, but increases as the pH is decreased.     

Extent of formation of a dimeric adenine photoproduct in polynucleotides and DNA

Quantum yields are reported for the formation of a dimeric adenine photoproduct, A = A, in adenine homopolymers and DNA irradiated at 254 nm. The A = A content of irradiated samples was assayed by using reversed-phase HPLC to isolate the 4,6-diamino-5-guanidinopyrimidine (DGPY) which is produced from A = A on acid hydrolysis. Acid hydrolysates derived from DNA radiolabelled with [14C] 2'-deoxyadenosine were spiked with unlabelled DGPY before fractionation on HPLC and the recovered material was further purified by chromatography on Sephadex G-10 followed by co-crystallization with DGPY sulphate. Although A = A is formed with a relatively high quantum yield of 1.6 X 10(-3) mol einstein-1 in single-stranded poly(dA) the photoaddition reaction is strongly quenched in base-paired poly(dA).poly(dT) and undetectable in poly(rA).poly(dT). Respective quantum yields of 6 X 10(-5) and 9 X 10(-6) were estimated for the formation of A = A in single- and double-stranded E. coli DNA implying that the photoproduct has very limited biological significance. From studies with d(ApG), d(GpA), ApG, GpA, d(A)20 and d(A4G)4 it is concluded that adjacent guanine and adenine bases do not form a photoadduct analogous to A = A and also that guanine residues have no local or long-range quenching effect on photodimerization within A-A doublets.     

End-group-confined chain walking within a group 4 living polyolefin and well-defined cationic zirconium alkyl complexes for modeling this behavior

Living polymers derived from the polymerization of 1-butene using the cationic zirconium initiator, {Cp*ZrMe[N(Et)C(Me)-N(tBu)]}[B(C6F5)4] (Cp* = eta5-C5Me5) (1), have been shown to undergo end-group-confined chain walking that is competitive with direct beta-hydride elimination and chain release at -10 degrees C. The well-defined complexes, {Cp*Zr(iBu)[N(Et)C(Me)N(tBu)]}[B(C6F5)4] (2) and {Cp*Zr(2-ethylbutyl)[N(Et)C(Me)N(tBu)]}[B(C6F5)4] (3), were prepared, and each was found to possess a strong beta-hydrogen agostic interaction that is absent in the living polymer. The isotopically single- and double-labeled derivatives, {Cp*Zr(2-d-2-methylpropyl)[N(Et)C(Me)N(tBu)]}[B(C6F5)4] (2') and {Cp*Zr(1-13C-2-d-2-methylpropyl)[N(Et)C(Me)N(tBu)]}[B(C6F5)4] (2' '), were also prepared and found to undergo isotopic label scrambling at 0 degrees C. For 2' ', the observation that after scrambling each deuterium label is located on a 13C-labeled carbon atom is consistent with the Busico mechanism for chain-end epimerization rather than the Resconi mechanism. Decomposition of 3 yielded olefinic products also consistent with chain walking prior to beta-hydride elimination and chain release. Finally, the unexpected decrease in stability of the living polymer relative to that of the model complexes reveals the importance of subtle differences in steric and electronic factors in controlling beta-hydride elimination and chain release.     

pH fluorosensors for use in marine systems

In this work we present optical pH sensors especially designed for pH measurements in marine environment. Embedded in an uncharged, highly proton-permeable hydrogel matrix, the two novel lipophilic carboxyfluorescein derivatives 2',7'-dihexyl-5(6)-N-octadecyl-carboxamidofluorescein (DHFA) and 2',7'-dihexyl-5(6)-N-octadecyl-carboxamidofluorescein ethyl ester (DHFAE) have apparent dissociation constants of ca. 8.4. The pH transition range of the sensors perfectly matches the pH range occurring in seawater and marine sediment (ca. pH 7.2-9.2). The cross-sensitivity towards ionic strength (IS) was found to be low for DHFA-containing membranes and was even negligible when using DHFAE as indicator. The quantum yield (QY) of DHFA (0.94(basic)) is similar to that of fluorescein (0.97(basic)). QYs of 0.62(basic) and 0.22(acidic) were found for DHFAE. The optical properties of the indicators enable referenced measuring schemes. Lactonisation of the DHFAE chromophore is prevented by esterification of the carboxyl group in 2 position. Thus, internally referenced dual wavelength measurements are possible since the emission maxima of the basic and acidic form of DHFAE differ by 30 nm. Dual lifetime referenced (DLR) measurements were made with pH sensors incorporating ruthenium-(II)-tris-4,7-diphenyl-1,10-phenanthroline (Ru(dpp)(3))-containing reference particles in addition to the indicator. This type of sensor can be applied for pH imaging or in phase-modulation measurements of pH.     

FLUORESCENCE QUANTUM YIELDS OF 124-kDa PHYTOCHROME FROM OAT UPON EXCITATION WITHIN DIFFERENT ABSORPTION BANDS

Abstract— A fluorescence quantum yield (emission at650–850 nm) of π= (2.3 ± 0.3)10⁻³ was measured for the red-absorbing form (Pr) of 124-kDa phytochrome from etiolated oat seedlings ( Avena sativa ) upon excitation in the Soret band at Λ^exc= 380 nm. The small difference between this value and the previously determined quantum yield with Λ^exc= 640 nm, π= (3.5 ± 0.4)10⁻³is attributed to a blue-absorbing emitter responsible for the "anomalous" or "blue" emission of the chromoprotein in the region from ca. 400 to 550 nm. The absorption of Pr at 380 nm is consequently somewhat lower than that measured directly from the spectrum. Processes from upper excited states of the Pr phytochromobilin-derived chromophore other than rapid relaxation to the emitting state are not important. A quantum yield of Φ ' 1.2 times 10⁻³ is estimated for the blue fluorescence. The proportion of the blue emitters relative to Pr appears to be relatively high.