Formation of sugar radicals in RNA model systems and oligomers via excitation of guanine cation radical

In previous work, we have shown that photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of DNA and its model compounds at 143 K results in the formation of neutral sugar radicals with substantial yield. In this report, we present electron spin resonance (ESR) and theoretical (DFT) evidence regarding the formation of sugar radicals after photoexcitation of guanine cation radical (G*+) in frozen aqueous solutions of one-electron-oxidized RNA model compounds (nucleosides, nucleotides and oligomers) at 143 K. Specific sugar radicals C5'*, C3'* and C1'* were identified employing derivatives of Guo deuterated at specific sites in the sugar moiety, namely, C1'-, C2'-, C3'- and C5'-. These results suggest C2'* is not formed upon photoexcitation of G*+ in one-electron-oxidized Guo and deuterated Guo derivatives. Phosphate substitution at C5'- (i.e., in 5-GMP) hinders formation of C5'* via photoexcitation at 143 K but not at 77 K. For the RNA-oligomers studied, we observe on photoexcitation of oligomer-G*+ the formation of mainly C1'* and an unidentified radical with a ca. 28 G doublet. The hyperfine coupling constants of each of the possible sugar radicals were calculated employing the DFT B3LYP/6-31G* approach for comparison to experiment. This work shows that formation of specific neutral sugar radicals occurs via photoexcitation of guanine cation radical (G*+) in RNA systems but not by photoexcitation of its N1 deprotonated species (G(-H)*). Thus, our mechanism regarding neutral sugar formation via photoexcitation of base cation radicals in DNA appears to be valid for RNA systems as well.     

Photosensitized oxidative DNA damage: from hole injection to chemical product formation and strand cleavage

Oxidatively generated damage to DNA induced by a pyrenyl photosensitizer residue (Py) covalently attached to a guanine base in the DNA sequence context 5'-d(CAT[G1Py]CG2TCCTAC) in aerated solutions was monitored from the initial one-electron transfer, or hole injection step, to the formation of chemical end-products monitored by HPLC, mass spectrometry, and high-resolution gel electrophoresis. Hole injection into the DNA was initiated by two-photon excitation of the Py residue with 355 nm laser pulses, thus producing the radical cation Py*+ and hydrated electrons; the latter are trapped by O2, thus forming the superoxide anion O2*-. The decay of the Py*+ radical is correlated with the appearance of the G*+/G(-H)* radical on microsecond time scales, and O2*- combines with guanine radicals at G1 to form alkali-labile 2,5-diamino-4H-imidazolone lesions (Iz1Py). Product formation in the modified strand is smaller by a factor of 2.4 in double-stranded than in single-stranded DNA. In double-stranded DNA, hot piperidine-mediated cleavage at G2 occurs only after G1Py, an efficient hole trap, is oxidized thus generating tandem lesions. An upper limit of hole hopping rates, khh < 5 x 103 s-1 from G1*+-Py to G2 can be estimated from the known rates of the combination reaction of the G(-H)* and O2*- radicals. The formation of Iz products in the unmodified complementary strand compared to the modified strand in the duplex is approximately 10 times smaller. The formation of tandem lesions is observed even at low levels of irradiation corresponding to "single-hit" conditions when less than approximately 10% of the oligonucleotide strands are damaged. A plausible mechanism for this observation is discussed.     

Femtosecond dynamics on 2-(2'-hydroxy-4'-diethylaminophenyl)benzothiazole: solvent polarity in the excited-state proton transfer.

Detailed insights into the excited-state enol(N*)-keto(T*) intramolecular proton transfer (ESIPT) reaction in 2-(2'-hydroxy-4'-diethylaminophenyl)benzothiazole (HABT) have been investigated via steady-state and femtosecond fluorescence upconversion approaches. In cyclohexane, in contrast to the ultrafast rate of ESIPT for the parent 2-(2'-hydroxyphenyl)benzothiazole (>2.9+/-0.3 x 10(13) s(-1)), HABT undergoes a relatively slow rate (approximately 5.4+/-0.5 x 10(11) s(-1)) of ESIPT. In polar aprotic solvents competitive rate of proton transfer and rate of solvent relaxation were resolved in the early dynamics. After reaching the solvation equilibrium in the normal excited state (N(eq)*), ESIPT takes place with an appreciable barrier. The results also show N(eq)*(enol)<-->T(eq)*(keto) equilibrium, which shifts toward N(eq)* as the solvent polarity increases. Temperature-dependent relaxation dynamics further resolved a solvent-induced barrier of 2.12 kcal mol(-1) for the forward reaction in CH(2)Cl(2). The observed spectroscopy and dynamics are rationalized by a significant difference in dipole moment between N(eq)* and T(eq)*, while the dipolar vector for the enol form in the ground state (N) is in between that of N(eq)* and T(eq)*. Upon N-->N* Franck-Condon excitation, ESIPT is energetically favorable, and its rate is competitive with the solvation relaxation process. Upon reaching equilibrium configurations N(eq)* and T(eq)*, forward and/or backward ESIPT takes place with an appreciable solvent polarity induced barrier due to differences in polarization equilibrium between N(eq)* and T(eq)*.     

Polyelectrolytes in multivalent salt solutions

We study conformational and electrophoretic properties of polyelectrolytes (PEs) in tetravalent salt solutions under the action of electric fields by means of molecular dynamics simulations. Chain conformations are found to have a sensitive dependence on the salt concentration C(s). As C(s) is increased, the chains first shrink to a globular structure and subsequently re-expand above a critical concentration C(s)*. An external electric field can further alter the chain conformation. If the field strength E is larger than a critical value E*, the chains are elongated. E* is shown to be a function of C(s) by using two estimators E(I)* and E(II)* through the study of the polarization energy and the onset point of chain unfolding, respectively. The electrophoretic mobility of the chains depends strongly on C(s), and the magnitude increases significantly, accompanying the chain unfolding, when E>E(II)*. We study the condensed ion distributions modified by electric fields and discuss the connection of the modification with the change of chain morphology and mobility. Finally, E* is studied by varying the chain length N. The inflection point is used as a third estimator E(III)*. E(III)* scales as N(-0.63(4)) and N(-0.76(2)) at C(s) =0.0 and C(s)*, respectively. E(II)* follows a similar scaling law to E(III)* but a crossover appears at C(s) =C(s)* when N is small. The E(I)* estimator fails to predict the critical field, which is due to oversimplifying the critical polarization energy to the thermal energy. Our results provide valuable information to understand the electrokinetics of PE solutions at the molecular level and could be helpful in micro/nanofluidic applications.     

Effect of base sequence and deprotonation of Guanine cation radical in DNA

The deprotonation of guanine cation radical (G+*) in oligonucleotides (ODNs) was measured spectroscopically by nanosecond pulse radiolysis. The G+* in ODN, produced by oxidation with SO4-*, deprotonates to form the neutral G radical (G(-H)*). In experiments using 5-substituted cytosine-modified ODN, substitution of the cytosine C5 hydrogen by a methyl group increased the rate constant of deprotonation, whereas replacement by bromine decreased the rate constant. Kinetic solvent isotope effects on the kinetics of deoxyguanosine (dG) and ODN duplexes were examined in H2O and D2O. The rate constant of formation of G(-H)* in dG was 1.7-fold larger in H2O than D2O, whereas the rate constant in the ODN duplex was 3.8-fold larger in H2O than D2O. These results suggest that the formation of G(-H)* from G+* in the ODN corresponds to the deprotonation of the oxidized hydrogen-bridged (G+*-C) base pair by a water molecule. The characteristic absorption maxima of G+* around 400 nm were shifted to a longer wavelength in the order of G相似文献   

Isomerization pathways from the norbornadiene to the cycloheptatriene radical cation by opening a bridgehead-methylene bond: a theoretical investigation

Three skeletal rearrangement channels for the norbornadiene (N*+) to the 1,3,5-cycloheptatriene (CHT*+) radical cation conversion, initialized by opening a bridgehead-methylene bond in N*+, are investigated using the quantum chemical B3LYP, MP2 and CCSD(T) methods in conjunction with the 6-311 +G(d,p) basis set. Two of the isomerizations proceed through the norcaradiene radical cation (NCD*+), either through a concerted path (N*+ - NCD*+), or by a stepwise mechanism via a stable intermediate (N*+ - I1 - NCD*+). At the CCSD(T)/6-311 +G(d,p)//B3LYP/6-311 +G(d,p) level, the lowest activation energy, 28.9 kcal mol(-1), is found for the concerted path whereas the stepwise path is found to be 2.3 kcal mol(-1) higher. On both pathways, NCD*+ rearranges further to CHT*+ with significantly less activation energy. The third channel proceeds from N*+ through I1 and then directly to CHT*+, with an activation energy of 37.1 kcal mol(-1). The multi-step channel reported earlier by our group, which proceeds from N*+ to CHT*+ via the quadricyclane and the bicyclo[2.2.1]hepta-2-ene-5-yl-7-ylium radical cations, is 4.6 kcal mol(-1) lower than the most favorable path of the present study. If the methylene group is substituted with C(CH3)2, however, the concerted path is estimated to be 5.6 kcal mol(-1) lower than the corresponding substituted multi-step path at the B3LYP/6-311+(d,p) level. This shows that substitution of particular positions can have dramatic effects on altering reaction barriers in the studied rearrangements. We also note that identical energies are computed for CHT*+ and NCD*+ whereas, in earlier theoretical investigations, the former was reported to be 6-17 kcal mol(-1) more stable than the latter. Finally, a bent geometry is obtained for CHT*+ with MP2/6-311 +G(d,p) in contradiction with the planar conformation reported for this cation in earlier computational studies.     

Structure of radicals from X-irradiated guanine derivatives. 2. An experimental and computational study of 9-ethylguanine single crystals

An EPR (electron paramagnetic resonance) and ENDOR (electron-nuclear double resonance) study of 9-ethylguanine crystals X-irradiated at 10 K detected evidence for three radical forms. Radical R1, characterized by three proton and two nitrogen hyperfine interactions, was identified as the product of net hydrogenation at N7 of the guanine unit. R1, which evidently formed by protonation of the primary electron addition product, exhibited an unusually distorted structure leading to net positive isotropic components of the alpha-coupling to the hydrogen attached to C8 of the guanine unit. Radical R2, characterized by two nitrogen and three proton hyperfine couplings, was identified as the primary electron loss product, *G+. Distinguishing between *G+ and its N1-deprotonated product is difficult because their couplings are so similar, and density functional theory (DFT) calculations were indispensable for doing so. The results for R2 provide the most complete ENDOR characterization of *G+ presented so far. Radical R3 exhibited a narrow EPR pattern but could not be identified. The identification of radicals R1 and R2 was supported by DFT calculations using the B3LYP/6-311+G(2df,p)//6-31+G(d,p) approach. Radical R4, detected after irradiation of the crystals at room temperature, was identified as the well-known product of net hydrogenation at C8 of the guanine component. Spectra from the room temperature irradiation contained evidence for R5, an additional radical that could not be identified. Radical concentrations from the low temperature irradiation were estimated as follows: R1, 20%; R2, 65%; R3, 15%.     

Oxidation of phenol in aqueous acid: characterization and reactions of radical cations vis-à-vis the phenoxyl radical

Aqueous sulfuric acid containing up to approximately 14 M acid (H0 > or = -7.0) was used as solvent in pulse radiolytic redox studies to characterize cationic transients of phenol (C6H5OH) and map their reactions. The primary radical yields were first measured to correlate the variation in various radical concentrations as a function of increasing acid fraction in the solvent. Compared to their respective values at pH 2, the G(Ox*) increased with almost a linear slope of approximately 0.024 micromol J(-1) for H0(-1) (or pH(-1)) up to H0 -6.0 (Ox* = *OH + SO4*-), whereas G(H*) increased with a slope of approximately 0.033 micromol J(-1) for H0(-1) (or pH(-1)) up to H0 -5.0. In the presence of > 10 M acid (H0 < -5.0), phenol was oxidized to its radical cation, C6H5OH*+, which further reacted with phenol and generated the secondary, dimeric radical cation, (C6H5OH)2*+, following an equilibrium reaction C6H5OH*+ + C6H5OH <==> (C6H5OH)2*+, with K(eq) = 315 +/- 15 M(-1). The two cationic radicals were characterized from their individual UV-vis absorption spectra and acidity. The C6H5OH*+ absorption peaks are centered at 276 and 419 nm, and it was found to be more acidic (pKa = -2.75 +/- 0.05) than (C6H5OH)2*+ (pKa = -1.98 +/- 0.02), having its major peak at 410 nm. On the other hand, in the presence of < 6.5 M acid the C6H5O* reactions followed the radical dimerization route, independent of the parent phenol concentration.     

Structure of radicals from X-irradiated guanine derivatives: an experimental and computational study of sodium guanosine dihydrate single crystals

In sodium guanosine dihydrate single crystals, the guanine moiety is deprotonated at N1 due to growth from high-pH (>12) solutions. Electron paramagnetic resonance (EPR) and electron-nuclear double resonance (ENDOR) studies of crystals X-irradiated at 10 K detected evidence for three radical forms. Radical R1, characterized by two proton and two nitrogen hyperfine interactions, was identified as the product of net hydrogenation at N7 of the N1-deprotonated guanine unit. R1 exhibited an unusually distorted structure leading to net positive isotropic components of the hydrogen alpha-couplings. Radical R2, characterized by one proton and one nitrogen hyperfine coupling, was identified as the primary electron-loss product. This product is equivalent to that of deprotonation at N1 by the guanine cation and represents the first ENDOR characterization of that product. Radical R3, characterized by a single hydrogen hyperfine coupling, was identified as the product of net dehydrogenation at C1' of the ribose moiety. The identification of radicals R1-R3 was supported by density functional theory (DFT) calculations on several possible structures using the B3LYP/6-311G(2df,p)//6-31G(d,p) approach. Radical R4, detected after warming the crystals to room temperature, was identified as the well-known product of net hydrogenation of C8 of the (N1-deprotonated) guanine component. Radical R1, evidently formed by protonation of the primary electron addition product, was present as roughly 60% of the total radicals detected at 10 K. Radical R2 was present as roughly 27% of the total yield, and the concentration of R3 contributed the remaining 13%. R3 is evidently the product of one-electron oxidation followed by deprotonation; thus, the balance of oxidation and reduction products is approximately equal within experimental uncertainty.     

Prototropic equilibria in DNA containing one-electron oxidized GC: intra-duplex vs. duplex to solvent deprotonation

By use of ESR and UV-vis spectral studies, this work identifies the protonation states of one-electron oxidized G:C (viz. G˙+:C, G(N1–H)˙:C(+H+), G(N1–H)˙:C, and G(N2-H)˙:C) in a DNA oligomer d[TGCGCGCA]2. Benchmark ESR and UV-vis spectra from one electron oxidized 1-Me-dGuo are employed to analyze the spectral data obtained in one-electron oxidized d[TGCGCGCA]2 at various pHs. At pH ≥7, the initial site of deprotonation of one-electron oxidized d[TGCGCGCA]2 to the surrounding solvent is found to be at N1 forming G(N1–H)˙:C at 155 K. However, upon annealing to 175 K, the site of deprotonation to the solvent shifts to an equilibrium mixture of G(N1–H)˙:C and G(N2–H)˙:C. For the first time, the presence of G(N2–H)˙:C in a ds DNA-oligomer is shown to be easily distinguished from the other prototropic forms, owing to its readily observable nitrogen hyperfine coupling (Azz(N2) = 16 G). In addition, for the oligomer in H2O, an additional 8 G N2–H proton HFCC is found. This ESR identification is supported by a UV-vis absorption at 630 nm which is characteristic for G(N2–H)˙ in model compounds and oligomers. We find that the extent of photo-conversion to the C1′ sugar radical (C1′˙) in the one-electron oxidized d[TGCGCGCA]2 allows for a clear distinction among the various G:C protonation states which can not be easily distinguished by ESR or UV-vis spectroscopies with this order for the extent of photo-conversion: G˙+:C > G(N1–H)˙:C(+H+) ? G(N1–H)˙:C. We propose that it is the G˙+:C form that undergoes deprotonation at the sugar and this requires reprotonation of G within the lifetime of exited state     

1H and 13C hyperfine coupling constants of the tryptophanyl cation radical in aqueous solution from microsecond time-resolved CIDNP

Relative values of the 1H and 13C isotropic hyperfine couplings in the cationic oxidized tryptophan radical TrpH*+ in aqueous solution are determined. The data are obtained from the photo-CIDNP (chemically induced dynamic nuclear polarization) enhancements observed in the microsecond time-resolved NMR spectra of the diamagnetic products of photochemical reactions in which TrpH*+ is a transient intermediate. The method is validated using the tyrosyl neutral radical Tyr*, whose 1H and 13C hyperfine couplings have previously been determined by electron paramagnetic resonance spectroscopy. Good agreement is found with hyperfine coupling constants for TrpH*+ calculated using density functional theory methods but only if water molecules are explicitly included in the calculation.     

Isomerization and fragmentation reactions of gaseous phenylarsane radical cations and phenylarsanyl cations. A study by tandem mass spectrometry and theoretical calculations

The unimolecular reactions of radical cations and cations derived from phenylarsane, C6H5AsH2 (1) and dideutero phenylarsane, C6H5AsD2 (1-d2), were investigated by methods of tandem mass spectrometry and theoretical calculations. The mass spectrometric experiments reveal that the molecular ion of phenylarsane, 1*+, exhibits different reactivity at low and high internal excess energy. Only at low internal energy the observed fragmentations are as expected, that is the molecular ion 1*+ decomposes almost exclusively by loss of an H atom. The deuterated derivative 1-d2 with an AsD2 group eliminates selectively a D atom under these conditions. The resulting phenylarsenium ion [C6H5AsH]+, 2+, decomposes rather easily by loss of the As atom to give the benzene radical cation [C6H6]*+ and is therefore of low abundance in the 70 eV EI mass spectrum. At high internal excess energy, the ion 1*+ decomposes very differently either by elimination of an H2 molecule, or by release of the As atom, or by loss of an AsH fragment. Final products of these reactions are either the benzoarsenium ion 4*+, or the benzonium ion [C6H7]+, or the benzene radical cation, [C6H6]*+. As key-steps, these fragmentations contain reductive eliminations from the central As atom under H-H or C-H bond formation. Labeling experiments show that H/D exchange reactions precede these fragmentations and, specifically, that complete positional exchange of the H atoms in 1*+ occurs. Computations at the UMP2/6-311+G(d)//UHF/6-311+G(d) level agree best with the experimental results and suggest: (i) 1*+ rearranges (activation enthalpy of 93 kJ mol(-1)) to a distinctly more stable (DeltaH(r)(298) = -64 kJ mol(-1)) isomer 1 sigma*+ with a structure best represented as a distonic radical cation sigma complex between AsH and benzene. (ii) The six H atoms of the benzene moiety of 1 sigma*+ become equivalent by a fast ring walk of the AsH group. (iii) A reversible isomerization 1+<==>1 sigma*+ scrambles eventually all H atoms over all positions in 1*+. The distonic radical cation 1*+ is predisposed for the elimination of an As atom or an AsH fragment. The calculations are in accordance with the experimentally preferred reactions when the As atom and the AsH fragment are generated in the quartet and triplet state, respectively. Alternatively, 1*(+) undergoes a reductive elimination of H2 from the AsH2 group via a remarkably stable complex of the phenylarsandiyl radical cation, [C6H5As]*+ and an H2 molecule.     

Anisotropic ESR hyperfine interaction of electrons trapped in crystals of 1,6-hexanediol and 1,8-octanediol

Localized electrons in irradiated 1,6-hexanediol and 1,8-octanediol have been identified and studied by ESR spectroscopy at 4 K. The spectra show an anisotropic hyperfine structure with couplings less than 35 G due to at least two protons. Spectra recorded from crystals with deuterated hydroxyl groups verify that the trapping site is localized close to a hydrogen bond.     

Model Calculations of Radiation-Induced Damage in 1-Methyluracil:9-Ethyladenine

Detailed EPR and ENDOR experiments on the cocrystalline complex of 1-methyluracil:9-Ethyladenine (MUEA) have revealed that the major radiation-induced products observed at 10 K on MU are: MUEA1, a radical formed by net hydrogen abstraction from the N1-CH₃ methyl group, MUEA2, the MU radical anion, and MUEA3, the C5 H-addition radical. The following four products were observed on the adenine moiety at 10 K, MUEA4, the N3 protonated adenine anion, MUEA5, the native adenine cation, MUEA6, the amino deprotonated adenine cation, and MUEA7, the C8 H-addition radical formed by net H-addition to C8 of the adenine base. The geometries, energetics, and hyperfine properties of all possible radicals of MU and EA, the native anions and cations, as well as radicals formed via net hydrogen atom abstraction (deprotonated cations) or addition (protonated anions) were investigated theoretically. All systems were optimized using the hybrid Hartree–Fock–density functional theory functional B3LYP, in conjunction with the 6-31G(d,p) basis set of Pople and co-workers. Calculations of the anisotropic hyperfine couplings for all the radicals observed in MUEA are presented and are shown to compare favorably with the experimentally measured hyperfine couplings. The calculated ionizations potentials indicate that EA would be the preferred oxidation site. In MUEA, both the adenine cation and its N4-deprotonated derivative were observed. The calculated electron affinities indicate that MU would be the preferred reduction site. In MUEA radical, MUEA2 is a uracil reduction product, however the protonation state of this radical could not be determined experimentally. Calculations suggest that MUEA2 is actually the C4=O protonated anion.     

EPR studies of amine radical cations. Part 2. Thermal and photo-induced rearrangements of propargylamine and allylamine radical cations in low-temperature freon matrices

Matrix EPR studies and quantum chemical calculations have been used to characterize the consecutive H-atom shifts undergone by the nitrogen-centered parent radical cations of propargylamine (1b*+) and allylamine (5*+) on thermal or photoinduced activation. The radical cation rearrangements of these unsaturated parent amines occur initially by a 1,2 H-atom shift from C1 to C2 with pi-bond formation at the positively charged nitrogen; this is followed by a consecutive reaction involving a second H-atom shift from C2 to C3. Thus, exposure to red light (lambda > 650 nm) converts 1b*+ to the vinyl-type distonic radical cation 2*+ which in turn is transformed on further photolysis with blue-green light (lambda approximately 400-600 nm) to the allene-type heteroallylic radical cation 3*+. Calculations show that the energy ordering is 1b*+ > 2*+ > 3*+, so that the consecutive H-atom shifts are driven by the formation of more stable isomers. Similarly, the parent radical cation of allylamine 5*+ undergoes a spontaneous 1,2-hydrogen atom shift from C1 to C2 at 77 K with a t1/2 of approximately 1 h to yield the distonic alkyl-type iminopropyl radical cation 6*+; this thermal reaction is attributed largely to quantum tunneling, and the rate is enhanced on concomitant photobleaching with visible light. Subsequent exposure to UV light (lambda approximately 350-400 nm) converts 6*+ by a 2,3 H-shift to the 1-aminopropene radical cation 7*+, which is confirmed to be the lowest-energy isomer derived from the ionization of either allylamine or cyclopropylamine. Although the parent radical cations of N, N-dimethylallylamine (9*+) and N-methylallylamine (11*+) are both stabilized by the electron-donating character of the methyl group(s), the photobleaching of 9*+ leads to the remarkable formation of the cyclic 1-methylpyrrolidine radical cation 10*+. The first step of this transformation now involves the migration of a hydrogen atom to C2 of the allyl group from one of the methyl groups (rather than from C1); the reaction is then completed by the cyclization of the generated MeN + (=CH2) CH2CH2CH2* distonic radical cation, possibly in a concerted overall process. In contrast to the ubiquitous H-atom transfer from carbon to nitrogen that occurs in the parent radical cations of saturated amines, the alternate rearrangements of either 1b*+ or 5*+ to an ammonium-type radical cation by a hypothetical H-atom shift from C1 to the ionized NH2 group are not observed. This is in line with calculations showing that the thermal barrier for this transformation is much higher (approximately 120 kJ mol-1) than those for the conversion of 1b*+ --> 2*+ and 5*+--> 6*+ (approximately 40-60 kJ mol-1).     

Probing the N(5)-H bond of the isoalloxazine moiety of flavin radicals by X- and W-band pulsed electron-nuclear double resonance.

An X- (9.7 GHz and W-band (94 GHz) pulsed electron-nuclear double resonance (ENDOR) study of the flavin cofactor of Escherichia coli DNA photolyase in its neutral radical form is presented. Through proton and deuteron ENDOR measurements at T = 80 K, we detect and characterize the full anisotropy of the hyperfine coupling (hfc) tensor of the proton or deuteron bound to N(5) of the isoalloxazine ring. Scaling of the anisotropic proton hfc components by multiplication with the quotient of the magnetogyric ratio of a deuteron and a proton, chiD/chiH, reveals subtle differences compared to the respective deuteron couplings obtained by 95-GHz deuterium ENDOR spectroscopy on an H-->D buffer-exchanged sample. These differences can be attributed to the different lengths of N(5)-H and N(5)-D bonds arising from the different masses of protons and deuterons. From the R(-3) dependence of the dipolar hyperfine splitting, we estimated that the N(5)-D bond is about 2.5% shorter than the respective N(5)-H bond. That such subtle bond-length differences can be resolved by pulsed ENDOR spectroscopy suggests that this method may be favorably used to probe the geometry of hydrogen bonds between the H(5) of the paramagnetic flavin and the protein backbone. Such information is only obtained with difficulty by other types of spectroscopy.     

Radical cations from dicyclopropylidenemethane and its octamethyl derivative

The radical cations of dicyclopropylidenemethane (2) and its octamethyl derivative (2-Me8) are prone to rearrangements into those of (2-methylallylidene)cyclopropane (2a) and its octamethyl derivative (2a-Me8), respectively, by opening one three-membered ring. In contrast to the radical cations of bicyclopropylidene (1) and its octamethyl derivative (1-Me8), 2*+ and 2-Me8*+ are stable to opening of the second ring, because in this case the resulting species would be a non-Kekulé hydrocarbon with a quartet ground state. Similarly to 1, octamethyl substitution in 2 promotes the tendency to rearrangement. Thus, ESR and ENDOR studies indicate that the primary radical cation 2*+, which is formed upon gamma-irradiation of 2 in a CFCl3 matrix at 77 K, does not rearrange up to 150 K. On the other hand, when 2-Me8 is treated in the same way, only the rearranged radical cation 2a-Me8*+ can be observed and characterized by its ESR and ENDOR spectra. Nevertheless, the existence of the two "missing" species, 2a*+ and 2-Me8*+, is revealed by other methods. According to UV and IR studies, X irradiation of 2 in an Ar matrix leads directly to the ring-opened radical cation 2a*+. Moreover, magnetic field effects on the decay of fluorescence, which appears upon recombination of the radical anion of p-terphenyl with a radical cation generated from 2-Me8 in liquid octane, strongly suggest that 2-Me8*+ (and not 2a-Me8*+) is formed initially. From the temperature dependence of the decay, the activation energy of the ring-opening process 2-Me8*+ --> 2a-Me8*+ is estimated. The radical cations 2a*+ and 2a-Me8*+ are formally distonic with the spin residing in the allylic moiety and the charge accommodated on the central carbon atom of the allene pi-system. The intact cyclopropylidenemethylidene moiety assumes a "bisected" conformation, thus favoring an optimal interaction with the positively charged center on the pi-system.     

Oxidation of guanine in G, GG, and GGG sequence contexts by aromatic pyrenyl radical cations and carbonate radical anions: relationship between kinetics and distribution of alkali-labile lesions

Oxidatively generated DNA damage induced by the aromatic radical cation of the pyrene derivative 7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene (BPT), and by carbonate radicals anions, was monitored from the initial one-electron transfer, or hole injection step, to the formation of hot alkali-labile chemical end-products monitored by gel electrophoresis. The fractions of BPT molecules bound to double-stranded 20-35-mer oligonucleotides with noncontiguous guanines G and grouped as contiguous GG and GGG sequences were determined by a fluorescence quenching method. Utilizing intense nanosecond 355 nm Nd:YAG laser pulses, the DNA-bound BPT molecules were photoionized to BPT*+ radicals by a consecutive two-photon ionization mechanism. The BPT*+ radicals thus generated within the duplexes selectively oxidize guanine by intraduplex electron-transfer reactions, and the rate constants of these reactions follow the trend 5'-..GGG.. > 5'-..GG.. > 5'-..G... In the case of CO3*- radicals, the oxidation of guanine occurs by intermolecular collision pathways, and the bimolecular rate constants are independent of base sequence context. However, the distributions of the end-products generated by CO3*- radicals, as well as by BPT*+, are base sequence context-dependent and are greater than those in isolated guanines at the 5'-G in 5'-...GG... sequences, and the first two 5'- guanines in the 5'-..GGG sequences. These results help to clarify the conditions that lead to a similar or different base sequence dependence of the initial hole injection step and the final distribution of oxidized, alkali-labile guanine products. In the case of the intermolecular one-electron oxidant CO3*-, the rate constant of hole injection is similar for contiguous and isolated guanines, but the subsequent equilibration of holes by hopping favors trapping and product formation at contiguous guanines, and the sequence dependence of these two phenomena are not correlated. In contrast, in the case of the DNA-bound oxidant BPT*+, the hole injection rate constants, as well as hole equilibration, exhibit a similar dependence on base sequence context, and are thus correlated to one another.     

EPR and ENDOR study of radiation-induced radical formation in purines: sodium inosine crystals X-irradiated at 10 K

X-irradiated single crystals of sodium inosine (Na(+)*Inosine(-)*2.5H(2)O), in which the hypoxanthine base is present as the N1-deprotonated anion, were investigated using K-band (24 GHz) electron paramagnetic resonance (EPR), electron-nuclear double resonance (ENDOR), and ENDOR induced EPR (EIE) techniques at 10 K. At least five different radicals were present immediately after irradiation at 10 K. R1, which decayed upon warming the crystals to 50 K, was identified as the electron-loss product of the parent N1-deprotonated hypoxanthine base. Hyperfine couplings to HC8 and HC2 were fully characterized with ENDOR spectroscopy, and the identification was supported by DFT calculations. R2, which also decayed on warming to 50 K, exhibited nearly equal couplings to HC2 and HC8. Taken in combination with an extensive set of DFT calculations, the experimental results indicate that R2 is the (doubly negative) product of electron-gain by the initially anionic N1-deprotonated hypoxanthine parent. R3, which exhibited hyperfine coupling only to HC8 could not be identified. R4, which persisted on annealing to 260 K, exhibited one large alpha-proton hyperfine coupling which was fully characterized by ENDOR. Based on DFT calculations and the experimental data, R4 was identified as the product of net H-abstraction from C5'. The remaining HC5' was the source of the measured alpha-proton coupling. R5, present at low temperature and the only observable radical after warming the crystals to room temperature, was identified as the C8-H addition radical. The alpha-coupling to HC2 and beta-couplings to the pair of C8 methlyene protons were fully characterized by ENDOR.     

The electronic structure of the flavin cofactor in DNA photolyase.

Density functional theory is used to calculate the electronic structure of the neutral flavin radical, FADH(*), formed in the light-induced electron-transfer reaction of DNA repair in cis,syn-cyclobutane pyrimidine dimer photolyases. Using the hybrid B3LYP functional together with the double-zeta basis set EPR-II, (1)H, (13)C, (15)N, and (17)O isotropic and anisotropic hyperfine couplings are calculated and explained by reference to the electron densities of the highest occupied molecular orbital and of the unpaired spin distribution on the radical. Comparison of calculated and experimental hyperfine couplings obtained from EPR and ENDOR/TRIPLE resonance leads to a refined structure for the FAD cofactor in Escherichia coli DNA photolyase. Hydrogen bonding at N3H, O4, and N5H results in significant changes in the unpaired spin density distribution and hyperfine coupling constants. The calculated electronic structure of FADH(*) provides evidence for a superexchange-mediated electron transfer between the cyclobutane pyrimidine dimer lesion and the 7,8-dimethyl isoalloxazine moiety of the flavin cofactor via the adenine moiety.