An EPR study of the transfer and trapping of holes produced by radiation in guanine(thioguanine) hydrochloride single crystals

Single crystals of guanine hydrochloride monohydrate, guanine hydrochloride dihydrate and anhydrous guanine dihydrochloride, doped with thioguanine, were irradiated with X and gamma rays. In all three systems the dominant radicals were associated with thioguanine. In the former two systems the stabilized species is the thiyl radical, formed by initial loss of an electron at some of the guanines in the crystal lattice, followed by hole migration to thioguanine and subsequent deprotonation of the radical formed. In the anhydrous guanine(thioguanine) dihydrochloride, that process is followed by acquisition of a chlorine ion. In the guanine hydrochloride monohydrate and guanine hydrochloride dihydrate lattices, systems of interacting closely spaced stacked bases and strings of chloride ions might support the migration of electrons and/or holes. In anhydrous guanine dihydrochloride, neither the bases nor the Cl- ions alone are capable of providing the means for the long-range electron, energy and spin transfer. It is the interchangeable sequence of the charged bases and the Cl- ions that makes the supporting strings or networks. The ultimate chlorination of the thioguanine-centered electron-loss radicals depends mainly on the availability of the Cl- ions and the space for their accommodation in the vicinity of the sulfur atom.     

EPR and ENDOR study of crystalline cytosine x HCl doped with 5-methylcytosine. Radiation-induced radical formation and hole transfer

Radical formation and hole transfer were investigated in crystals of cytosine.HCl (C.HCl) doped with 0-1.1 mol-% 5-methylcytosine x HCl (5MC x HCl). The doping level was determined by NMR spectroscopy. Crystals and polycrystalline samples were X-irradiated at 295 K, 77 K and 12 K and studied with EPR, ENDOR and FSE spectroscopy at these temperatures. At 295 K the dominant radicals were the so-called 3alphaH radical, formed in 5MC by a net H-abstraction from the methyl group, and the cytosine C6 H-addition (5-yl) radical. At 12 K five radicals were identified. These were the 3alphaH radical, cytosine reduction and oxidation products, and the cytosine C6 and C5 H-addition (5-yl and 6-yl, respectively) radicals. The spectroscopic parameters for the 3alphaH radical are very similar to those of a radical observed previously in the crystalline cytosine derivatives cytidine (CR), 2'deoxycytidine hydrochloride (CdR x HCl), 5'dCMP and 3'CMP as well as in the uracil derivative 2-thiouracil (2-TU). It was shown that amounts of the order of tenths of a percent 5MC x HCl doped into crystals of C.HCl give rise to a considerable yield of 3alphaH radicals after exposure to ionizing radiation both at room temperature and at lower temperatures. This supports a previous suggestion that naturally occurring 5-methylated cytosine impurities may be responsible for the formation of 3alphaH radicals in the crystalline cytosine derivatives CR, CdR.HCl, 5'dCMP and 3'CMP and suggests that the 3alphaH radical in these systems is a 5-methylated base-centered radical. The total radical yield in doped C x HCl crystals increased considerably with the doping level, both at low temperatures and at room temperature, implying that the 3alphaH radical is more stable than the primary cytosine radicals. The relative amounts of the 3alphaH radical were obtained by using simulated benchmark spectra to reconstruct experimental EPR spectra of doped polycrystalline samples. Evidence is presented suggesting that the enhanced yield of the 3alphaH radical in doped samples is due to holes originally formed at cytosine bases and transferred to 5-methylcytosine bases in addition to the 3alphaH radical being less exposed to recombination than other cytosine radicals.     

Sugar radicals in DNA: isolation of neutral radicals in gamma-irradiated DNA by hole and electron scavenging

In this investigation of the radical formation and the reaction of radicals in gamma-irradiated DNA, we report the isolation of putative neutral radicals by the scavenging of holes by Fe(CN)6(4-) and of electrons by Fe(CN)6(3-). Experiments are performed under conditions that emphasize direct and quasi-direct effects (collectively called direct-type effects.) Samples containing Fe(CN)6(4-) show effective scavenging of holes and the ESR spectra obtained arise principally from DNA anion radicals and neutral radicals. On the other hand, for samples containing Fe(CN)6(3-), electron scavenging is highly efficient, and the resulting spectra arise principally from guanine cation radicals and neutral radicals. When both Fe(CN)6(4-) and Fe(CN)6(3-) are present, a near complete scavenging of cation radicals and anion radicals is observed at 77 K, and the ESR spectra that result originate predominantly with neutral radicals which are assigned predominantly to radicals on the sugar phosphate backbone. A notable finding is the presence of spectral components that indicate the formation, through the rupture of the C3'-O bond, of a neutral deoxyribose radical; a concurrent strand break must accompany formation of this radical. This radical was previously reported in argon-ion-irradiated DNA and now, for the first time, is reported in DNA irradiated with low-LET radiation.     

Reaction of disodium cromoglycate with hydrated electrons

A possible mechanism by which disodium cromoglycate (DSCG) prevents a decrease in regional cerebral blood flow but not hypotension in primates following whole body gamma-irradiation was studied. Several studies have implicated superoxide radicals (O2-.) in intestinal and cerebral vascular disorders following ischemia and ionizing radiation, respectively. O2-. is formed during radiolysis in the reaction between hydrated electrons (e-aq) and dissolved oxygen. For this reason, the efficiency of DSCG to scavenge e-q and possibly prevent the formation of O2-. was studied. Hydrated electrons were produced by photolysis of potassium ferrocyanide solutions. The rate constant, k = 2.92 x 10(10) M-1s-1 for the reaction between e-aq and DSCG was determined in competition experiments using the spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO). This spin trap reacts rapidly with e-aq followed by protonation to yield the ESR observable DMPO-H spin adduct. The results show that DSCG is an efficient e-aq scavenger and may effectively compete with oxygen for e-aq preventing the radiolytic formation of O2-..     

Formation of longitudinal nonlinear structures in the electron cloud of an electron-string ion source

Accumulation of oscillating electrons in an electron-string ion source is simulated by the particle-in-cell method. The electrons are accumulated in a long trap into which an electron beam is injected. It is shown that a chain of alternating phase holes and squeezed states forms in the trap. The dynamical features of such a longitudinal structure, such as the double-pulse waveform and strong high-frequency oscillations of the accumulation current and the broadening of the electron distribution function, are qualitatively similar to those previously observed in experiments with the Krion-2 ion source operating in the electron-string mode.     

Skin Effects in a Dusty Plasma

A multifluid MHD model is applied to study the magnetic field dynamics in a dusty plasma. The motion of plasma electrons and ions is treated against the background of arbitrarily charged, immobile dust grains. When the dust density gradient is nonzero and when the inertia of the ions and electrons and the dissipation from their collisions with dust grains are neglected, we are dealing with a nonlinear convective penetration of the magnetic field into the plasma. When the dust density is uniform, the magnetic field dynamics is described by the nonlinear diffusion equations. The limiting cases of diffusion equations are analyzed for different parameter values of the problem (i.e., different rates of the collisions of ions and electrons with the dust grains and different ratios between the concentrations of the plasma components), and some of their solutions (including self-similar ones) are found. The results obtained can also be useful for research in solid-state physics, in which case the electrons and holes in a semiconductor may be analogues of plasma electrons and ions and the role of dust grains may be played by the crystal lattice and impurity atoms.     

Radical formation in salts of pyrimidines III. Cytosine . H2O cyrstals.

The radicals produced by X-irradiation at 77 K and at 300 K in cytosine monohydrate crystals have been analysed by electron-spin-resonance (e.s.r.) spectroscopy. Three radicals have been identified at 77 K: the anion radical and the cation radical of the cytosine molecule, together with the radical resutling from H-abstraction from the nitrogen N1. Irradiation at 300 K produces radicals resulting from H-adition at three different positions of the cytosine molecule. These are the C5-addition radical, the C6-addition radical, and the O2-addition radical. The results are compared with those found previously by other authors.     

Free radical formation in X-irradiated crystals of 2'-deoxycytidine hydrochloride. Electron magnetic resonance studies at 10 K

Single crystals of deoxycytidine hydrochloride (CdR.HCl) have been X-irradiated at 10 K with doses up to about 150 kGy and studied using 24 GHz (K-band) EPR, ENDOR and FSE spectroscopy. In this system, the cytosine base is protonated at the N3 position. Nine different radicals were characterized and identified. Three of these are ascribed to three versions of the one-electron reduced species, probably differing in their protonation state. Radicals formed by net hydrogen addition to the cytosine C5 and C6 positions were observed at 10 K. The hydrogen-abstraction radical at the deoxyribose C1' position most probably results from initial oxidation of the base. The remaining radical species are all localized to the sugar moiety, representing products formed by net hydrogen abstraction from three of the five available carbons of the deoxyribose sugar. The lack of base-centered oxidation products as well as the structures of the one-electron reduced species is rationalized by considering the specific proton donor-acceptor properties of this crystalline lattice in comparison with similar systems.     

Base release in nucleosides induced by low-energy electrons: a DFT study

Low-energy electrons are known to induce strand breaks and base damage in DNA and RNA through fragmentation of molecular bonding. Recently the glycosidic bond cleavage of nucleosides by low-energy electrons has been reported. These experimental results call for a theoretical investigation of the strength of the C(1)'-N link in nucleosides (dA, dC and dT) between the base and deoxyribose before and after electron attachment. Through density functional theory (DFT) calculations, we compare the C(1)'-N bond strength, i.e., the bond dissociation energy of the neutral and its anionic radical, and find that an excess electron effectively weakens the C(1)'- N bond strength in nucleosides by 61-75 kcal/mol in the gas phase and 76-83 kcal/mol in the solvated environment. As a result, electron-induced fragmentation of the C(1)'-N bond in the gas phase is exergonic for dA (DeltaG=-14 kcal/mol) and for dT (DeltaG=-6 kcal/mol) and is endergonic (DeltaG=+1 kcal/ mol) only for dC. In the gas phase all the anionic nucleosides are found to be in valence states. Solvation is found to increase the exergonic nature by an additional 20 kcal, making the fragmentation both exothermic and exergonic for all nucleoside anion radicals. Thus C(1)'-N bond breaking in nucleoside anion radicals is found to be thermodynamically favorable both in the gas phase and under solvation. The activation barrier for the C(1)'-N bond breaking process was found to be about 20 kcal/mol in every case examined, suggesting that a 1 eV electron would induce spontaneous cleavage of the bond and that stabilized anion radicals on the DNA strand would undergo base release at only a modest rate at room temperature. These results suggest that base release from nucleosides and DNA is an expected consequence of low-energy electron-induced damage but that the high barrier would inhibit this process in the stable anion radicals.     

Premelting thermal fluctuational interbase hydrogen-bond disrupted states of a B-DNA guanine-cytosine base pair: significance for amino and imino proton exchange.

Modified self-consistent phonon theory when applied to the DNA double helix indicates the existence of fairly long-lived states in which single interbase H bonds are disrupted. One can then postulate a number of situations in which particular disrupted H bonds can enhance particular proton exchange. In this paper we postulate a number of such partially open states for a B-conformation GC base pair and calculate the probability of each of these states for a B-conformation poly(dG).poly(dC). We compare these probabilities to those probabilities needed to explain various observed proton exchange rates. We propose that, for a GC base pair in B conformation, there are two amino proton exchangeable states--a cytosine amino proton exchangeable state and a guanine amino proton exchangeable state; both require the disruption of only the corresponding interbase H bond. The imino proton exchange, however, requires the disruption of all three interbase H bonds and this defines a third open state. Our calculated probabilities for a GC base pair in these three states are in fair agreement with available experimental estimates from measurements of amino and imino proton exchange.     

Energetics of the lattice: Packing elements in crystals of four-stranded intercalated cytosine-rich DNA molecules

Condensation of single molecules from solution into crystals represents a transition between distinct energetic states. In solution, the atomic interactions within the molecule dominate. In the crystalline state, however, a set of additional interactions are formed between molecules in close contact in the lattice—these are the packing interactions. The crystal structures of d(CCCT), d(TAACCC), d(CCCAAT), and d(AACCCC) have in common a four-stranded intercalated cytosine segment, built by stacked layers of cytosine · cytosine⁺ (C · C⁺) base pairs coming from two parallel duplexes that intercalate into each other with opposite polarity. The intercalated cytosine segments in these structures are similar in their geometry, even though the sequences crystallized in different space groups. In the crystals, adenine and thymine residues of the sequences are used to build the three-dimensional crystal lattice by elaborately interacting with symmetry-related molecules. The packing elements observed provide novel insight about the copious ways in which nucleic acid molecules can interact with each other—for example, when folded in more complicated higher order structures, such as mRNA and chromatin. © 1998 John Wiley & Sons, Inc. Biopoly 44: 257–267, 1997     

Effects of 60Co gamma-irradiation on chondromucoprotein.

Pulse radiolysis and 60Co gamma-radiolysis have been used to study the effects of ionizing radiations on the protein-polysaccharide complex, chondromucoprotein. Both hydroxyl radicals and hydrated electrons readily react with the complex, with second-order rate-constants of 4-55 X 10(8)M-1s-1, respectively. Depolymerization of the carbohydrate component, which is initiated by reaction of OH, readily occurs after irradiation in aqueous solution, as is evidenced by an increase in the formation of reducing-end groups and a decrease in the viscosity of the solution. The ability of the anionic carbohydrate component to bind cationic counter-ions also decreases.     

Electron and hole transfer from DNA base radicals to oxidized products of guanine in DNA

An investigation of electron and hole transfer to oxidized guanine bases in DNA is reported. Guanine in DNA was preferentially oxidized by Br(2)(*-) at 298 K to 8-oxo-7,8-dihydro-guanine (8-oxo-G) and higher oxidation products. HPLC-EC analysis of irradiated DNA shows that the formation of 8-oxo-G could not be increased above the ratio of one 8-oxo-G to 127 +/- 6 bp regardless of dose. 8-oxo-G can be produced only at low levels because it is further oxidized to other species. These oxidation products of guanine have been extensively investigated and identified by others. Our electron spin resonance studies suggest that at 77 K 8-oxo-G is a trap for radiation-produced holes, but certain further oxidation products of 8-oxo-G (G(ox)) are found to be efficient electron traps. Gamma irradiation of oxidized DNA samples in frozen (D(2)O) aqueous ices and glassy 7 M LiBr solutions resulted in radicals formed by electron attachment to the G(ox) sites that were monitored by electron spin resonance spectroscopy (ESR) at 77 K. These ESR spectra suggest that those oxidation products of 8-oxo-G containing alpha-diketo groups account for the electron traps (G(ox)) in oxidized DNA with oxaluric acid a likely major trap. Electron transfer from DNA anion radicals to G(ox) was followed by monitoring of their ESR signals with time at 77 K. Using typical values for the tunneling constant beta estimates of the relative amount of G(ox) to base pairs were obtained. Radicals formed by UV photolysis of oxidized DNA in 8 M NaClO(4) glassy aqueous solutions were also investigated. The 8-oxo-G cation accounts for less than 10% of all the radicals observed after either gamma irradiation of oxidized DNA in frozen (D(2)O) aqueous solution or UV photolysis of oxidized DNA in 8 M NaClO(4) glassy aqueous solutions. We estimate hole transfer distances of about 7 +/- 1 bp at 1 min from G(*+) to 8-oxo-G.     

E.s.r. of free radicals in aqueous solutions of substituted pyrimidines.

Reactions of OH radicals with methyl and ethyl derivatives of uracil, cytosine and thymine in aqueous solutions have been investigated. Photolysis of H2O2 was used to generate OH radicals and the radicals on the base derivatives were spin-trapped using t-nitrosobutane and identified with the help of e.s.r. spectroscopy. Addition of OH radicals was found to take place predominantly to the C(5)--C(6) double bond of the bases. H-abstraction from the methyl group occurred in the N(1) methyl derivatives of uracil, cytosine and thymine. Radicals formed by H-abstraction from the methyl group were also detected for 3-methyluracil, thymine, 1-methylthymine and 1-ethylthymine. Introduction of a methyl or ethyl group at the N(1) position of uracil, cytosine and thymine causes an increase in the C(6) proton coupling and a decrease in the N(1) splitting for radicals formed by OH addition at the C(5) position.     

γ射线辐照嘧啶核苷水溶液的电子自旋共振（ESR）研究

亚硝基特丁烷（ＭＮＲ）为捕集剂,利用自旋捕集技术,对γ射线辐照嘧啶苷水溶液进行了ＥＳＲ研究,确定了胸苷、尿苷和胞苷可产生的自肇捕集自由基的类别,并讨论了自由基形成的机制。     

Radical formation in pyrimidine bases after X,proton and alpha-particle irradiation

Single crystals of anhydrous thymine (Ta) and cytosine monohydrate (Cm) were irradiated at room temperature using X rays, 20 MeV protons and 35 MeV alpha particles, and the relative distributions of the various radiation-induced stable radicals in the crystals were investigated. These two crystal systems were chosen because of systematic differences in their molecular packing and hydrogen-bonding network. The radicals stabilized in these systems have previously been identified and analyzed by several authors. Experimental EPR spectra could thus be reconstructed based on simulated benchmark spectra using a fitting procedure, yielding the relative amounts of the different radical species. It was found that the relative amounts of a given radical species varied with the type of radiation used, with differences being most prominent between alpha particles and protons or X rays. In Ta, an increased production of hydrogen addition or abstraction radicals was found after exposure to alpha particles. These radicals are believed to be formed predominantly from superexcited states, resulting from the higher density of ionizations along the track of the alpha particle. A corresponding reduction in radicals derived from proton transfer reactions was observed in comparison with exposure to protons or X rays. In Cm, the differences were smaller than for Ta. This is probably due to differences in the arrangement of the crystal lattice between the two systems, with Cm having an extended hydrogen-bonding network promoting fast proton transfers after ionization. Most interesting, however, was the observation that more than 50% of the radical population in Cm not could be accounted for by known radical species. The population with an unknown origin was represented with a broad singlet, having a line width of 1.5 mT and a g value of 2.0045, in the spectral reconstruction procedure.     

Free radicals in pyrimidines:single crystals of dihydro-6-methyl uracil irradiated and observed at 77 K.

Electron-spin-resonance measurements have been made on single crystals of dihydro-6-methyl uracil, which were irradiated by 4-0 MeV electrons at 77 K. At low temperature, four radicals have been identified. Two, the C5 and C6 hydrogen abstraction radicals, were also studied in a previous work. On exposure of U.V., the C6 abstraction radical was found to convert into the C5 abstraction radical. Annealing at room temperature reversed the process. The other radicals identified are that formed after H-atom addition to O4, and that formed after H-atom abstractions from N1, C5, and C6. The latter was not present in deuterated crystals. Both radicals were found to be unstable at intermediate temperatures. Thermoluminescence glow-curves were found to correlate to the formation and the decay of these radicals. Semi-empirical INDO MO-calculations have been performed for identification purposes.     

Electron and nuclear dynamics in many-electron atoms, molecules and chlorophyll-protein complexes: a review

It has been shown [V.A. Shuvalov, Quantum dynamics of electrons in many-electron atoms of biologically important compounds, Biochemistry (Mosc.) 68 (2003) 1333-1354; V.A. Shuvalov, Quantum dynamics of electrons in atoms of biologically important molecules, Uspekhi biologicheskoi khimii, (Pushchino) 44 (2004) 79-108] that the orbit angular momentum L of each electron in many-electron atoms is L=mVr=nPlanck's and similar to L for one-electron atom suggested by N. Bohr. It has been found that for an atom with N electrons the total electron energy equation E=-(Z(eff))(2)e(4)m/(2n(2)Planck's(2)N) is more appropriate for energy calculation than standard quantum mechanical expressions. It means that the value of L of each electron is independent of the presence of other electrons in an atom and correlates well to the properties of virtual photons emitted by the nucleus and creating a trap for electrons. The energies for elements of the 1st up to the 5th rows and their ions (total amount 240) of Mendeleev' Periodical table were calculated consistent with the experimental data (deviations in average were 5 x 10(-3)). The obtained equations can be used for electron dynamics calculations in molecules. For H(2) and H(2)(+) the interference of electron-photon orbits between the atoms determines the distances between the nuclei which are in agreement with the experimental values. The formation of resonance electron-photon orbit in molecules with the conjugated bonds, including chlorophyll-like molecules, appears to form a resonance trap for an electron with E values close to experimental data. Two mechanisms were suggested for non-barrier primary charge separation in reaction centers (RCs) of photosynthetic bacteria and green plants by using the idea of electron-photon orbit interference between the two molecules. Both mechanisms are connected to formation of the exciplexes of chlorophyll-like molecules. The first one includes some nuclear motion before exciplex formation, the second one is related to the optical transition to a charge transfer state.     

超氧自由基与嘧啶碱基及其核苷反应的ESR研究

用自旋捕集技术和ＥＳＲ方法,以ＭＮＰ为捕集剂,研究了紫外线辐照核黄素产生超氧自由基等活性氧与嘧啶碱基及其核苷的反应,确定了尿嘧啶,胞嘧啶和胸腺嘧啶及其核苷所产生的自旋加合物自由基的类别,讨论了自由基的形成机制,揭示了超氧自由基与嘧啶碱基及其核苷的反应是不是直接进行的,而是通过羟基自由基来实现的。     

Sequence and temperature dependence of the interbase hydrogen-bond breathing modes in B-DNA polymers: Comparison with low-frequency Raman peaks and their role in helix melting

We carry out temperature-dependent lattice dynamics calculations to determine the vibrational normal modes associated with the interbase H-bond breathing motion in several B-DNA copolymers at temperatures from room temperature to the melting temperatures. We take into consideration Raman selection rules and incorporate a simple empirical model of Raman susceptibility in the interbase H bonds in our calculation and compare them to Raman measurements. Our calculations are carried out using empirical force constants that are not further refined to low-frequency spectra. Our calculations show the existence of strong interbase H-bond breathing modes at frequencies and with relative oscillator strengths close to the observed Raman peaks in the range of 60–140 cm^?1 for the DNA sequences considered except for one helix. The correlation between the calculated and observed frequencies and oscillator strengths indicates that the observed Raman peaks in the frequency range are likely interbase H-bond breathing modes. We find that these modes exhibit sizable temperature as well as sequence dependence. We show the softening of these modes on approaching thermal denaturation that is also in agreement with the observed behavior in Raman and melting measurements. The sensitivity of the calculation on the empirical model of Raman susceptibility and the possible reasons for the discrepancy between a few calculated values and observations are discussed. © 1995 John Wiley & Sons, Inc.