Functional monomers and polymers. XCIV. Photochemical reactions on the synthetic polymers containing thymine bases in the presence of adenine derivatives

Photodimerization reactions of polyacrylate and polymethacrylate derivatives and the dimer model compound containing thymine bases were studied in the presence of adenine derivatives in dimethyl sulfoxide; N,N-dimethylformamide; and dimethyl sulfoxide–ethylene glycol solutions. The photodimerization of thymine bases both in the polymers and in the dimer model compound was found to be quenched by the addition of adenine derivatives. Base-base interaction in the ground state was also studied by ultraviolet (UV) spectroscopy in the three solvents. The quenching of the photodimerizationof thymine bases in the presence of adenine derivatives was discussed in terms of the specific interaction between adenine and thymine bases both in ground and excited states.     

Selective determination of guanine and its nucleosides and nucleotides by reaction with phenylglyoxal as a fluorogenic reagent

A fluorimetric method is described for determining guanine in its nucleosides and nucleotides. The method is based on the reaction of the compounds with phenylglyoxal as a fluorogenic reagent in a weakly acidic solution (pH 4.0). The fluorescences produced show excitation and emission maxima around 365 and 510 nm, respectively. The conditions established for the reaction do not produce fluorescence from other nucleic acid bases such as adenine, cytosine, uracil and thymine, and their nucleosides and nucleotides. The method is sensitive and selective for guanine and its derivatives, with a detection limit of 47–310 pmol ml^?1 in the reaction mixture.     

UV laser photolysis of DNA: effect of duplex stability on charge-transfer efficiency.

The distribution of the final base damage was determined within isolated DNA exposed to pulses of 266 nm laser light. Studied lesions included oxidation products arising from biphotonic ionization of DNA bases and pyrimidine dimeric photoproducts arising from monophotonic processes. The distribution of the latter class of damage was found to be correlated with the stability of the DNA duplex. The quantum yield for formation of 8-oxo-7,8-dihydroguanine was much higher than that of other oxidized nucleosides arising from the degradation of thymine and adenine. This observation, together with the shape of the intensity dependence curves, provided evidence for the occurrence of charge-transfer processes within DNA. In addition, increase in the ionic strength of the irradiated DNA and stabilization of the DNA duplex were found to induce a drastic decrease in the yield of thymine and adenine oxidation products. Concurrently, an increase in the yield of 8-oxo-7,8-dihydroguanine was observed. This was rationalized in terms of an increase in the overall charge-transfer efficiency. Therefore, it may be concluded that stabilization of the double-helix favors charge-transfer process toward guanine bases.     

Sequence, structure and energy transfer in DNA

Excitation energy transfer in DNA has similarities to charge transfer, but the transport is of an excited state, not of mass or charge. Use of the fluorescent, modified adenine base 2‐aminopurine (2AP) as an energy trap in short (3‐ to 20‐base) single‐ and double‐stranded DNA oligomers is reviewed. Variation of 2AP’s neighboring sequence shows (1) relatively efficient transfer from adenine compared to that from cytosine and thymine, (2) efficient transfer from guanine, but only when 2AP is at the 3′ end, (3) approximate equality of efficiencies for 3′ to 5′ and 5′ to 3′ directional transfer in adenine tracks. The overall, average transfer distance at room temperature is about four adenine bases or less before de‐excitation. The transfer fluorescence excitation spectral shape is similar to that of the absorption spectrum of the neighboring normal bases, confirming that initial excitation of the normal bases, followed by emission from 2AP (i.e. energy transfer), is occurring. Transfer apparently may take place both along one strand and cross‐strand, depending on the oligomer sequence. Efficiency increases when the temperature is decreased, rising above 50% (overall efficiency) in decamers of adenine below ?60°C (frozen media). Modeling of the efficiencies of transfer from the nearest several adenine neighbors of 2AP in these oligomers suggests that the nearest two neighbors transfer with near 100% efficiency. As bases in B DNA, as well as in single‐stranded DNA, are separated by less than 5 Å (less than the size of a base), standard Förster transfer theory should not apply. Indeed, while both theory and experiment show efficiency decreasing with donor–acceptor distance, the experimental dependence clearly disagrees with Förster 1/r⁶ dependence. It is not yet clear what the best theoretical approach is, but any calculation must deal accurately with the excited states of bases, including strong base–base interactions and structural fluctuations, and should reflect the increase of efficiency with temperature decrease and the relative insensitivity to strandedness (single, double). Attempts to use DNA as a molecular “fiber optic” face three primary challenges. First, reasonable efficiency over more than a base or two occurs only in adenine stretches at temperatures well below freezing. Second, transfer in these adenine tracks is efficient in both directions. Third, absorption of UV light occurs randomly, making excitation at a specific site on this “fiber optic” a challenge.     

Phosphorescence of nucleic acids and DNA components at 77 K

The emission spectra of nucleic acids, pyrimidine and purine nucleotides, nucleosides and bases and a series of pyrimidine derivatives were obtained using UV light excitation in glasses (ethanol and 2:1 mixtures of ethylene glycol and water (EG-H2O); also partly in butyronitrile and 2-methyltetrahydrofuran) at 77 K. The quantum yields of fluorescence phi f and phosphorescence phi p of some 30 compounds are presented; for several substituted uracils they are reported for the first time. The values cover a range from phi f = 0.0002 and phi p = 0.001 for uracil in ethanol to phi f = 0.50 for guanosine in acidic ethanol and phi p = 0.095 for guanosine-5'-monophosphate in EG-H2O (pH 6-7). The phosphorescence lifetime tau p at 77 K ranges from about 0.3 s (uracil moiety) to 3 s (adenine moiety). The measured tau p, phi f and phi p values are compared with those available in the literature.     

Transient absorption spectra and quenching of coumarin excited states by nucleic acid bases.

Triplet-triplet absorption spectra of coumarin show different profiles and maxima in ethanol from those in water, which are very similar to those reported in benzene. Long-lived transient species other than triplet states were generated as initial photoproducts between coumarins and nucleic acid bases. The excited singlet and triplet states of coumarins were quenched by nucleic acid bases. Adenine base quenched the excited singlet state of coumarins more efficiently than thymine base. However, photocycloadducts of furocoumarins are formed predominantly with thymine, and not with adenine. Moreover, it is reported that the poly[dA-dT].poly[dA-dT] sequence region is the most favourable site for the photocycloaddition reaction of furocoumarins. The results imply that adenine contributes to singlet-state photocycloaddition reaction of furocoumarins with thymine, probably through an adenine-furocoumarin-thymine termolecular interaction.     

Interaction of low-energy electrons with the purine bases, nucleosides, and nucleotides of DNA

The authors report results from computational studies of the interaction of low-energy electrons with the purine bases of DNA, adenine and guanine, as well as with the associated nucleosides, deoxyadenosine and deoxyguanosine, and the nucleotide deoxyadenosine monophosphate. Their calculations focus on the characterization of the pi* shape resonances associated with the bases and also provide general information on the scattering of slow electrons by these targets. Results are obtained for adenine and guanine both with and without inclusion of polarization effects, and the resonance energy shifts observed due to polarization are used to predict pi* resonance energies in associated nucleosides and nucleotides, for which static-exchange calculations were carried out. They observe slight shifts between the resonance energies in the isolated bases and those in the nucleosides.     

Interaction of phenazine with water and DNA bases

The fluorescence spectrum of aqueous phenazine (PZ), an N-heterocyclic compound, shows some interesting features that indicate the formation of PZ-water complex in the excited state. Two types of complexes are postulated; Type I, formed by the association of water molecule with one of the nitrogen of PZ and Type II, formed by the association of water molecules with both the nitrogen of PZ. In addition, PZ also interacts with the DNA bases, adenine and thymine and the corresponding nucleosides, adenosine and thymidine. Fluorescence and laser flash photolysis studies indicate that the mode of interaction may be photoinduced electron transfer.     

ON THE LUMINESCENCE OF L-TRYPTOPHANE AND l-TYROSINE IN AQUEOUS SOLUTION AT 77dK INDUCED BY X-RAYS AND U.V.-LIGHT

Abstract— The lumincscence arising from L-tryptophane and L-tyrosine in aqueous solutions at 77K during irradiation with u.v.-light and with X-rays has been studied. The spectra obtained with the two types of radiation were largely similar, differing only in that the yields of phosphorescence relative to fluorescence were considerably enhanced in the case of X-irradiation. The decay times observed for the exponentially decaying phosphorescence, being 6.6 sec and 2.7 sec for tryptophane and tyrosine respectively, were the same for both kinds of irradiation. The G-value of the X-ray induced luminescence was about 10 for both tryptophane and tyrosine. Thus, about 30 per cent of the total energy absorbed from X-rays in these compounds was re-emitted as light.
It was concluded that the X-ray induced fluorescence and phosphorescence originate from the same levels as does the luminescence caused by u.v.-light, i.e. the lowest excited singlet and the lowest triplet level of the aromatic structure of these compounds. In the case of X-irradiation the enhanced ratios between the yields of phosphorescence and fluorescence indicated that some process other than excitation directly from the ground state contributed considerably to the luminescence yields. Assuming this process to be a recombination between the ionized molecule and its electron, it was calculated that the contribution to the luminescence yield from excitations directly from the ground state relative to that from ionizations, was negligible for both compounds.     

Spectroscopic assessment of argon gas discharge induced radiolysis of aqueous adenine and thymine

Ionizing radiation influences life profoundly for it can modify genetic materials. It is a long-standing task to investigate the interaction between energetic particles and DNA together with its components such as nucleotides, nucleosides and bases so as to predict and assess the potential biological effects. In this study, argon gas discharge was employed to produce energetic ions and electrons. The gas discharge caused the radiolysis of aqueous bases and the involved reactions were analyzed by means of spectroscopic tools including UV–vis absorption, fluorescence and Fourier transformation infrared (FTIR) spectroscopy, also assisted by liquid chromatography/mass spectrometry (LC/MS). It was found that the discharge resulted in the adenine-derived lesions such as 4,6-diamino-5-formamidopyrimidine, 8-OH-Ade and 2-OH-Ade in the radiolysis of aqueous adenine, as well as the thymine-derived lesions such as thymine glycol, 5-hydroxy-6-hydrothymine and/or 6-hydroxy-5-hydrothymine, 5-hydroxymethyluracil and 5-formyluracil in the radiolysis of aqueous thymine. The study of radio-sensitivity showed that adenine was more resistant to the discharge. The mechanisms of the involved reactions were studied in detail, confirming that the hydroxyl radical played a dominant role.     

The excited states of adenine and thymine nucleoside and nucleotide in aqueous solution: a comparative study by time-dependent DFT calculations

The effect substitutions at nitrogen atom 1 of thymine and nitrogen atom 9 of adenine have on lowest energy excited electronic states has been studied by means of time-dependent PBE0 calculations in aqueous solution. In agreement with the experimental indications, the vertical excitation energy of the bright state of 1,methyl-thymine, thymine nucleoside and thymine nucleotide is red-shifted with respect to that of thymine. Deoxyribose and deoxyribose-phosphate substituents affect mainly the lowest energy dark state of adenine and thymine, slightly increasing their oscillator strength. The excited states of 9, methyl-adenine and 1, methyl-thymine have also been studied by using the recently developed M052X, CAM-B3LYP and LC-ωPBE density functionals. The computed VEE are in good agreement with those obtained by using PBE0, which, however, provides values closer to the experimental band maximum.     

Dynamics of photoinduced processes in adenine and thymine base pairs

The excited-state dynamics of adenine and thymine dimers and the adenine-thymine base pair were investigated by femtosecond pump-probe ionization spectroscopy with excitation wavelengths of 250-272 nm. The base pairs showed a characteristic ultrafast decay of the initially excited pi pi* state to an n pi* state (lifetime tau(pi pi*) approximately 100 fs) followed by a slower decay of the latter with tau(n pi*) approximately 0.9 ps for (adenine)2, tau(n pi*) = 6-9 ps for (thymine)2, and tau(n pi*) approximately 2.4 ps for the adenine-thymine base pair. In the adenine dimer, a competing decay of the pi pi* state via the pi sigma* state greatly suppressed the n pi* state signals. Similarities of the excited-state decay parameters in the isolated bases and the base pairs suggest an intramonomer relaxation mechanism in the base pairs.     

Thermal desorption behavior and binding properties of DNA bases and nucleosides on gold

A comparison of the binding of DNA bases (adenine, cytosine, guanine, and thymine) and nucleosides (2'deoxyadenosine, 2'deoxycytidine, 2'deoxyguanosine, and thymidine) to gold thin films is presented. Desorption of monolayer/submonolayer and multilayer films of the adsorbates on gold studied via temperature-programmed desorption (TPD) and reflection-absorption infrared (RAIR) spectroscopy reveals that there are major differences in the binding affinities of the different bases to gold, for example, thymine DeltaHdes = 111 +/- 2 kJ/mol compared to guanine DeltaHdes = 146 +/- 2 kJ/mol. The differences can be rationalized by molecular structures of the bases and their binding modes to gold surfaces deduced from IR data. Similar trends in desorption energies, shifted to lower desorption energy by more than 10 kJ/mol, are observed for deoxynucleoside layers on gold thin films.     

Interaction of adenine and thymine with aqueous sugar solutions

The solubility of the nucleic acid bases, adenine and thymine, in aqueous erythritol, xylose, glucose, and sucrose solutions has been studied. The solubility of adenine increases linearly with glucose and sucrose concentration, whereas with the other reagents a nonlinear increase is observed. Below 1.5M reagent concentration, the solubility of adenine increases in the order erythritol < robose, xylose < glucose < sucrose. The solubility of thymine in these solutions, on the other hand, decreases, increases, or does not change depending upon the reagent. The effect of temperature on the solubility of adenine and thymine in sugar solution indicates that the transfer of these molecules from water to sugar solution is exothermic.Presented in part at the VIIth All-India Symposium in Biophysics held at Visva Bharati University during October 1976.     

RADICAUX LIBRES INDUITS PAR L''ACTION DU RAYONNEMENT ULTRAVIOLET SUR CERTAINS CONSTITUANTS DE L''ACIDE DEOXYRIBONUCLEIQUE

The action of ultra violet rays of 260 nm on aqueous solutions of bases, nucleosides and nucleotides of DNA at 77°K is studied by electron spin resonance. It is shown that the free radicals observed are similar, with a few noteworthy exceptions to those induced by X-rays, under the same conditions of temperature, in the solid state. Contrary to what might be excepted on the basis of the results obtained by X-rays, the variation in the yield in paramagnetic centres in each sequence studied does not seem to be important.     

ROOM-TEMPERATURE FLUORESCENCE PROPERTIES OF THE POLYNUCLEOTIDE POLYdA POLYdT

The room-temperature fluorescence spectrum of the non-alternating polynucleotide polydA.polydT is found to have its maximum at about 325 nm and, when exciting in the spectral region where both adenine (A) and thymine (T) absorb, to coincide with that obtained for excitation at 293 nm where thymine is selectively excited. The fluorescence anisotropy is found to be equal to 0.18 and independent of the excitation and emission wavelengths. These observations are consistent with: (i) emission stemming from T; and (ii) transfer of electronic energy from A to T being not efficient. These inferences are also supported by the observed dependence of the fluorescence quantum yield on the excitation wavelength.     

Vinylsulfonylethyl derivatives of nucleic acid bases and their graft polymers on polyethyleneimine

Vinylsulfonylethyl (VSE) derivatives of the nucleic acid bases adenine, thymine, cytosine, and the nucleosides inosine and uridine have been prepared via a simple Michael reaction with divinyl sulfone. The VSE derivatives were grafted on a polyethyleneimine (PEI) backbone. PEI of different molecular weights (1400, 1800 and 50,000–100,000) were used and also two different molar ratios (1:1 and 1:2) of monomer to PEI were employed. From the ¹H-NMR and elemental analysis, it appeared that in almost all instances the grafting was quantitative. In one case, both 1-VSE-thymine and 9-VSE-adenine were grafted on the same PEI backbone. Interactions between some of these polymers were investigated by UV spectroscopy. The expected complementary base pairing was observed only in DMSO–ethylene glycol solvent system but not in DMSO. The adenine polymer showed a one-to-one interaction with the thymine polymer.     

Simple ethers as models of sugar molecules in calculations of vertical excitation energies of DNA and RNA nucleosides

The ribose and deoxyribose molecules of RNA and DNA nucleosides are substituted with simple model compounds 1-methoxy-2-ethanol and 1-methoxypropane to mimic the effect of binding to sugars on the vertical excitation energies of purine and pyrimidine bases. The (R)-1-methoxy-2-ethanol, CH(3)OC*HCH(2)OH, for model ribose nucleosides and (R)-1-methoxypropane, CH(3)OC*HC(2)H(5), for model deoxyribose nucleosides have minimal structural characteristics of ribose and deoxyribose molecules when attached to nucleic acid purine and pyrimidine bases. The bases are attached to the C1 carbon atom designated by the asterisk. The vertical excitation energies of these model nucleosides are calculated with the time-dependent density functional theory method at the B3LYP level with 6-311++G(d,p) and aug-cc-pVDZ basis sets. The attachment of the ether molecules qualitatively and quantitatively modifies the excited state energy levels of the model nucleosides when compared to the free bases. These changes can affect the deexcitation mechanisms for photoexcited nucleosides.     

A gas phase ab initio excited state geometry optimization study of thymine, cytosine and uracil

Molecular geometries of the nucleic acid bases thymine, cytosine and uracil in the ground and the lowest two singlet excited states were optimized using the ab initio approach employing the 4-31G basis set for all the atoms except the amino group of cytosine for which the 6-311+G^* basis set was used. The excited state calculations were performed employing configuration interaction involving singly excited configurations (CIS). Vibrational frequencies were computed in order to examine the nature of the stationary points on the potential energy surfaces obtained by geometry optimization. While the ground state geometries of uracil and thymine (except the methyl group hydrogens) are planar, the corresponding excited state geometries were found to be significantly nonplanar. In the case of cytosine, the amino group is pyramidal and the rest of the molecule is only slightly nonplanar in the ground state, but the excited state geometries are appreciably nonplanar. In particular, consequent to the S₂(n–π^*) excitation of cytosine, the amino group plane is strongly rotated. While thymine is stable in the S₂(π–π^*) excited state, uracil appears to be dissociative in the corresponding excited state.