Guanine Cation Research Articles

Radical Cascade Dissociation Pathways to Unusual Nucleobase Cation Radicals.

We report unusual dissociations of protonated RNA nucleosides tagged with radical initiator groups at ribose 5'-O and furnished with a 2',3'-O-isopropylidene protecting group. The ions undergo collision-induced radical cascade dissociations starting at the radical initiator that break down the dioxolane ring and trigger the formation of nucleobase cations and cation radicals. The adenine cation radical that was formed by radical cascade dissociations was identified by MS5 UV-vis photodissociation action spectroscopy to be a higher-energy N-3-H tautomer of the canonical ionized nucleobase. The guanine cation radical was formed by radical cascade dissociations as the N-7-H tautomer. In contrast to adenosine and guanosine, radical cascade dissociations of the tagged ribocytidine ion produced protonated cytosine, whereas tagged ribothymidine showed yet different dissociations resulting in predominant thymine loss. Reaction mechanisms were suggested for the cascade dissociations that were based on Born-Oppenheimer molecular dynamics and density functional theory calculations that were used to map the relevant parts of the potential energy surfaces for adenosine, guanosine, and cytidine radical ions. The reported radical cascade dissociations represent a new, nonredox approach to nucleobase and nucleoside cation radicals that has the potential of being expanded to the generation of various oligonucleotide cation radicals.

The Absorption Spectrum of Guanine Based Radicals: a Comparative Computational Analysis

AbstractThe excited states of three radical derivatives of guanine, i. e. guanine cation (G+) and its two main deprotonated derivatives (G−H1 and G−H2), have been characterized in the Franck‐Condon region by TD‐DFT, using different functionals, CASPT2, and EOM‐EE‐CCSD calculations. In the gas phase, all the methods provide a similar description of the main spectral features, the pictures provided by TD‐DFT, with long range corrected functionals, and EOM‐EE‐CCSD being very close. Solvent effects are then taken into account by a mixed discrete‐continuum approach, including five water molecules of the first solvation shell and the Polarizable Continuum Model (PCM). The vibronic absorption line‐width has finally been simulated at the TD‐M052X level by a time dependent method within the harmonic approximation. The resulting absorption spectra are in good agreement with their experimental counterparts, providing useful indications on the use of PCM/TD‐DFT based approaches to interpret the spectra of guanine based radicals within DNA.

Tracking Photoinduced Charge Separation in DNA: from Start to Finish.

The initial studies of the dynamics of photoinduced charge separation conducted in our laboratories 20 years ago found strongly distance-dependent rate constants over short distances but failed to detect intermediates in the transport of positive charge (holes). These observations were consistent with the single-step superexchange or tunneling mechanism that had been observed for numerous donor-bridge-acceptor systems at that time. Subsequent studies found weak distance dependence for hole transport over longer distances in DNA, characteristic of incoherent hopping of either localized or delocalized holes. The introduction of synthetic DNA capped hairpin constructs possessing hole donor and acceptor chromophores (or purine bases) at opposite ends of a base-pair domain made it possible to determine the time required for transit of charge from one chromophore to the other and, in some cases, to distinguish between the transit time and the much faster initial charge injection time. These studies eliminated conventional tunneling as a viable mechanism for charge transport in DNA except at very short donor-acceptor separations; however, they did not establish the presence or nature of intermediates in the charge separation process. Recent studies in our laboratories have succeeded in identifying key intermediates as well as untangling the dynamics and efficiency of the charge separation process from start to finish. The dynamics of the initial charge injection process is dependent upon both its free energy and the stacking of the hole donor chromophore and adjacent purine base. The transport of positive charge (holes) over multiple base pairs in duplex DNA occurs most efficiently via repeating adenine bases, known as A-tracts. The transit time across an A-tract is strongly dependent upon the free energy for hole injection, whereas the efficiency of charge separation depends on the competition between charge delocalization and charge recombination in the contact radical ion pair. The guanine cation radical has been detected both by femtosecond transient absorption and by stimulated Raman spectroscopies when the guanine is located near the chromophore employed for hole injection into an A-tract. Replacement of guanine by its derivative 8-phenylethynylguanine (EG), permits tracking of hole transport across longer poly(purine) sequences as a consequence of the stronger transient absorption and stimulated Raman scattering for EG+• vs G+•. We have recently obtained evidence based on femtosecond transient absorption spectroscopy for the formation of delocalized A-polarons in A-tracts possessing four or more A-T base pairs. Similar methods have been used to track hole transport across less-common DNA structures including diblock and triblock poly(purines), locked nucleic acids, three-way junctions, and G-quadruplexes. Similar methods are have been applied to the study of photoinduced electron transport in DNA.

Modulating the Catalytic Activity of Cerium Oxide Nanoparticles with the Anion of the Precursor Salt.

In this work, we tested our hypothesis that surface chemistry and antioxidant properties of cerium nanoparticles (CNPs) are affected by presence of counterions. We first employed various precursor cerium (III) (Ce(III)) salts with different counterions (acetate, nitrate, chloride, sulfate) to synthesize CNPs following the same wet chemical methodology. Electron spin resonance (ESR) studies provided evidence for the formation of radicals from counterions (e.g., NO3•2- from reduction of NO3- in CNPs synthesized from Ce(III) nitrate). Physicochemical properties of these CNPs, e.g., dispersion stability, hydrodynamic size, signature surface chemistry, SOD-mimetic activity, and oxidation potentials were found to be significantly affected by the anions of the precursor salts. CNPs synthesized from Ce(III) nitrate and Ce(III) chloride exhibited higher extent of SOD-mimetic activities. Therefore, these CNPs were studied extensively employing in-situ UV-Visible spectroelectrochemistry and changing the counterion concentrations affected the oxidation potentials of these CNPs. Thus, the physicochemical and antioxidant properties of CNPs can be modulated by anions of the precursor. Furthermore, our ESR studies present evidence of the formation of guanine cation radical (G•+) in 5'-dGMP via UV-photoionization at 77 K in the presence of CNPs synthesized from Ce(III) nitrate and chloride and CNPs act as the scavenger of radiation-produced electrons.

Direct observation of guanine radical cation deprotonation in G-quadruplex DNA.

Although numerous studies have been devoted to the charge transfer through double-stranded DNA (dsDNA), one of the major problems that hinder their potential applications in molecular electronics is the fast deprotonation of guanine cation (G(+•)) to form a neutral radical that can cause the termination of hole transfer. It is thus of critical importance to explore other DNA structures, among which G-quadruplexes are an emerging topic. By nanosecond laser flash photolysis, we report here the direct observation and findings of the unusual deprotonation behavior (loss of amino proton N2-H instead of imino proton N1-H) and slower (1-2 orders of magnitude) deprotonation rate of G(+•) within G-quadruplexes, compared to the case in the free base dG or dsDNA. Four G-quadruplexes AG3(T2AG3)3, (G4T4G4)2, (TG4T)4, and G2T2G2TGTG2T2G2 (TBA) are measured systematically to examine the relationship of deprotonation with the hydrogen-bonding surroundings. Combined with in depth kinetic isotope experiments and pKa analysis, mechanistic insights have been further achieved, showing that it should be the non-hydrogen-bonded free proton to be released during deprotonation in G-quadruplexes, which is the N2-H exposed to solvent for G bases in G-quartets or the free N1-H for G base in the loop. The slower N2-H deprotonation rate can thus ensure less interruption of the hole transfer. The unique deprotonation features observed here for G-quadruplexes open possibilities for their interesting applications as molecular electronic devices, while the elucidated mechanisms can provide illuminations for the rational design of G-quadruplex structures toward such applications and enrich the fundamental understandings of DNA radical chemistry.

Deprotonation Kinetics of 1-Methylguanine After One-Electron Oxidation

Among the four natural DNA bases, guanine (G) is the most sensitive to oxidation due to its lowest oxidation potential. When G base is oxidized to guanine cation radical (G(+center dot)), it will deprotonate from both the imino proton N-1-H and the amino proton N-2-H. According to the pKa values for N-1-H and N-2-H deprotonation, the main deprotonation site in G base is N-1-H which would interfere with the N-2-H deprotonation, making the kinetics of N-2-H deprotonation difficult to be measured. Herein, the N-2-H deprotonation kinetics is investigated using 1-methylguanosine (mG), where N-1-H is substituted by methyl group to avoid the N-1-H deprotonation and N-9-H is substituted by ribose to ensure enough solubility of methylguanine in water, by nanosecond transient absorption (ns-TA) spectroscopy. By 355 nm photolysis of Na2S2O8, the highly oxidizing radical SO4-center dot is generated, which will oxidize mG to mG(+center dot) instantaneously. The time-resolved absorption spectra obtained for reaction of mG with SO4-center dot exhibits transient absorptions for mG(N-2-H)(center dot) featured by absorption band at 600 nm, indicating that the mG(+center dot) deprotonation product is mG(N-2-H)(center dot) and the deprotonation site is therefore validated to be N-2-H. The mG concentration dependence of mG(N-2-H)(center dot) formation rate constant is assessed through changing the mG concentration from 0.25 mmol.L-1 to 5 mmol.L-1. The concentration dependence experiment reveals that the rate-limiting step to form mG(N-2-H)(center dot) is the bimolecular reaction of mG with SO4-center dot when mG concentration is lower than 2 mmol.L-1 and the bimolecular reaction rate constant to form mG(+center dot) is (3.7 +/- 0.1)x10(9) L.mol(-1).s(-1); when mG concentration is above 2 mmol.L-1, the rate-limiting step to form mG(N-2-H)(center dot) is the first-order mG(+center dot) deprotonation and the N-2-H deprotonation rate constant is (7.1 +/- 0.2) x 10(6) s(-1). Furthermore, the N-2-H deprotonation rate constant is measured at different temperatures varying from 278 K to 298 K. According to Arrhenius equation, the activation energy barrier for the N-2-H deprotonation is determined to be 19.9 +/- 1.0 kJ.mol(-1). These results can provide valuable kinetic information on the oxidative damage of DNA.

Calculating Hyperfine Couplings in Large Ionic Crystals Containing Hundreds of QM Atoms: Subsystem DFT Is the Key

We present an application of the linear scaling frozen density embedding (FDE) formulation of subsystem DFT to the calculation of isotropic hyperfine coupling constants (hfcc's) of atoms belonging to a guanine radical cation embedded in a guanine hydrochloride monohydrate crystal. The model systems range from an isolated guanine to a 15,000 atom QM/MM cluster where the QM region is comprised of 36 protonated guanine cations, 36 chlorine anions, and 42 water molecules. Our calculations show that the embedding effects of the surrounding crystal cannot be reproduced by small model systems nor by a pure QM/MM procedure. Instead, a large QM region is needed to fully capture the complicated nature of the embedding effects in this system. The unprecedented system size for a relativistic all-electron isotropic hfcc calculation can be approached in this work because the local nature of the electronic structure of the organic crystals considered is fully captured by the FDE approach.

Radical–Radical Interactions among Oxidized Guanine Bases Including Guanine Radical Cation and Dehydrogenated Guanine Radicals

We present here a theoretical investigation of the structural and electronic properties of di-ionized GG base pairs (G(•+)G(•+),G(-H1)(•)G(•+), and G(-H1)(•)G(-H1)(•)) consisting of the guanine cation radical (G(•+)) and/or dehydrogenated guanine radical (G(-H1)(•)) using density functional theory calculations. Different coupling modes (Watson-Crick/WC, Hoogsteen/Hoog, and minor groove/min hydrogen bonding, and π-π stacking modes) are considered. We infer that a series of G(•+)G(•+) complexes can be formed by the high-energy radiation. On the basis of density functional theory and complete active space self-consistent (CASSCF) calculations, we reveal that in the H-bonded and N-N cross-linked modes, (G(•+)G(•+))WC, (G(-H1)(•)G(-H1)(•))WC, (G(-H1)(•)G(-H1)(•))minI, and (G(-H1)(•)G(-H1)(•))minIII have the triplet ground states; (G(•+)G(•+))HoogI, (G(-H1)(•)G(•+))WC, (G(-H1)(•)G(•+))HoogI, (G(-H1)(•)G(•+))minI, (G(-H1)(•)G(•+))minII, and (G(-H1)(•)G(-H1)(•))minII possess open-shell broken-symmetry diradical-characterized singlet ground states; and (G(•+)G(•+))HoogII, (G(•+)G(•+))minI, (G(•+)G(•+))minII, (G(•+)G(•+))minIII, (G(•+)G(•+))HoHo, (G(-H1)(•)G(•+))minIII, (G(-H1)(•)G(•+))HoHo, and (G(-H1)(•)G(-H1)(•))HoHo are the closed-shell systems. For these H-bonded diradical complexes, the magnetic interactions are weak, especially in the diradical G(•+)G(•+) series and G(-H1)(•)G(-H1)(•) series. The magnetic coupling interactions of the diradical systems are controlled by intermolecular interactions (H-bond, electrostatic repulsion, and radical coupling). The radical-radical interaction in the π-π stacked di-ionized GG base pairs ((G(•+)G(•+))ππ, (G(-H1)(•)G(•+))ππ, and (G(-H1)(•)G(-H1)(•))ππ) are also considered, and the magnetic coupling interactions in these π-π stacked base pairs are large. This is the first theoretical prediction that some di-ionized GG base pairs possess diradical characters with variable degrees of ferromagnetic and antiferromagnetic characteristics, depending on the dehydrogenation characters of the bases and their interaction modes. Hopefully, this work provides some helpful information for the understanding of different structures and properties of the di-ionized GG base pairs.

The effect of ionization and deprotonation of guanine on the formation of base pairs

The effect of the ionization of the guanine on the formation of base pairs is investigated using the B3LYP method with 6-31++G ∗∗ basis set. The base pairing with neutral DNA base lowers the adiabatic ionization potential of guanine, while the base pairing with protonated DNA base increases the ionization potential of guanine. The proton transfer can occur in the Watson–Crick GC and GA base pairs when an electron is lost. The effect of the deprotonation of the guanine cation on the formation of base pairs is also explored. From an energy point of view, the ionization of guanine cannot result in the Watson–Crick mispair formation, but the deprotonation from the guanine cation is in favor of the combination of the G(−H) and guanine. In the Hoogsteen base pairs, the ionization of guanine slightly affects the interaction mode, but it may result in the dissociation of the Hoogsteen base pairs if the DNA bases pairing with guanine are the protonated A, T and C. The deprotonation from guanine cation slightly affects the base pairing energies of the Hoogsteen base pairs.

Sugar radical formation by a proton coupled hole transfer in 2'-deoxyguanosine radical cation (2'-dG*+): a theoretical treatment.

Previous experimental and theoretical work has established that electronic excitation of a guanine cation radical in nucleosides or in DNA itself leads to sugar radical formation by deprotonation from the dexoxyribose sugar. In this work, we investigate a ground electronic state pathway for such sugar radical formation in a hydrated one electron oxidized 2'-deoxyguanosine (dG(*+) + 7H(2)O), using density functional theory (DFT) with the B3LYP functional and the 6-31G* basis set. We follow the stretching of the C(5')-H bond in dG(*+) to gain an understanding of the energy requirements to transfer the hole from the base to sugar ring and then to deprotonate to proton acceptor sites in solution and on the guanine ring. The geometries of reactant (dG(*+) + 7H(2)O), transition state (TS) for deprotonation of the C(5') site, and product (dG((*)C(5'), N(7)-H(+)) + 7H(2)O) were fully optimized. The zero point energy (ZPE) corrected activation energy (TS) for the proton transfer (PT) from C(5') is calculated to be 9.0 kcal/mol and is achieved by stretching the C(5')-H bond by 0.13 A from its equilibrium bond distance (1.099 A). Remarkably, this small bond stretch is sufficient to transfer the "hole" (positive charge and spin) from guanine to the C(5') site on the deoxyribose group. Beyond the TS, the proton (H(+)) spontaneously adds to water to form a hydronium ion (H(3)O(+)) as an intermediate. The proton subsequently transfers to the N(7) site of the guanine (product). The 9 kcal/mol barrier suggests slow thermal conversion of the cation radical to the sugar radical but also suggests that localized vibrational excitations would be sufficient to induce rapid sugar radical formation in DNA base cation radicals.

Direct Observation of the Hole Protonation State and Hole Localization Site in DNA-Oligomers

In this work, it is shown that the incorporation of an 8-deuteroguanine (G*) moiety in DNA-oligomers allows for direct determination at 77 K of (i) the location of holes (i.e., the radical site) within dsDNA at specific base sites, even within stacks of G, as well as (ii) the protonation state of the hole at that site. These findings are based on our work and demonstrate that selective deuteration at C-8 on a guanine moiety in dGuo results in an ESR signal from the guanine cation radical (G**(+)) which is easily distinguishable from that of the undeuterated guanine cation radical (G*(+)). G**(+) is also found to be easily distinguishable from its conjugate base, the N1-deprotonated radical, G*(-H)*. Our ESR results clearly establish that at 77 K (i) one-electron oxidized guanine in double stranded DNA-oligomers exists as the deprotonated neutral radical G(-H)* as a result of facile proton transfer to the hydrogen bonded cytosine and (ii) the hole is preferentially located at the 5'-end in several ds DNA-oligomers with a GGG sequence.

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<GG<GGG-containing ODNs. In contrast, the spectra of G(-H)* were not affected by the sequence and were essentially similar to that of free dG. These results suggest that the positive charge in G+* in ODN is delocalized over the extended pi orbitals of DNA base. The rate constant of the deprotonation was altered by the sequence of ODNs, where bases adjacent to guanine are important factors for deprotonation.

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.

Sugar Radicals Formed by Photoexcitation of Guanine Cation Radical in Oligonucleotides

This work presents evidence that photoexcitation of guanine cation radical (G+*) in dGpdG and DNA-oligonucleotides TGT, TGGT, TGGGT, TTGTT, TTGGTT, TTGGTTGGTT, AGA, and AGGGA in frozen glassy aqueous solutions at low temperatures leads to hole transfer to the sugar phosphate backbone and results in high yields of deoxyribose radicals. In this series of oligonucleotides, we find that G+* on photoexcitation at 143 K leads to the formation of predominantly C5'* and C1'* with small amounts of C3'*. Photoconversion yields of G+* to sugar radicals in oligonucleotides decreased as the overall chain length increased. However, for high molecular weight dsDNA (salmon testes) in frozen aqueous solutions, substantial conversion of G+* to C1'* (only) sugar radical is still found (ca. 50%). Within the cohort of sugar radicals formed, we find a relative increase in the formation of C1'* with length of the oligonucleotide, along with decreases in C3'* and C5'*. For dsDNA in frozen solutions, only the formation of C1'* is found via photoexcitation of G+*, without a significant temperature dependence (77-180 K). Long wavelength visible light (>540 nm) is observed to be about as effective as light under 540 nm for photoconversion of G+* to sugar radicals for short oligonucleotides but gradually loses effectiveness with chain length. This wavelength dependence is attributed to base-to-base hole transfer for wavelengths >540 nm. Base-to-sugar hole transfer is suggested to dominate under 540 nm. These results may have implications for a number of investigations of hole transfer through DNA in which DNA holes are subjected to continuous visible illumination.

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.

The guanine cation radical: investigation of deprotonation states by ESR and DFT.

This work reports ESR studies that identify the favored site of deprotonation of the guanine cation radical (G*+) in an aqueous medium at 77 K. Using ESR and UV-visible spectroscopy, one-electron oxidized guanine is investigated in frozen aqueous D2O solutions of 2'-deoxyguanosine (dGuo) at low temperatures at various pHs at which the guanine cation radical, G*+ (pH 3-5), singly deprotonated species, G(-H)* (pH 7-9), and doubly deprotonated species, G(-2H)*- (pH > 11), are found. C-8-deuteration of dGuo to give 8-D-dGuo removes the major proton hyperfine coupling at C-8. This isolates the anisotropic nitrogen couplings for each of the three species and aids our analyses. These anisotropic nitrogen couplings were assigned to specific nitrogen sites by use of 15N-substituted derivatives at N1, N2, and N3 atoms in dGuo. Both ESR and UV-visible spectra are reported for each of the species: G*+, G(-H)*, and G(-2H)*-. The experimental anisotropic ESR hyperfine couplings are compared to those obtained from DFT calculations for the various tautomers of G(-H)*. Using the B3LYP/6-31G(d) method, the geometries and energies of G*+ and its singly deprotonated state in its two tautomeric forms, G(N1-H)* and G(N2-H)*, were investigated. In a nonhydrated state, G(N2-H)* is found to be more stable than G(N1-H)*, but on hydration with seven water molecules G(N1-H)* is found to be more stable than G(N2-H)*. The theoretically calculated hyperfine coupling constants (HFCCs) of G*+, G(N1-H)*, and G(-2H)*- match the experimentally observed HFCCs best on hydration with seven or more waters. For G(-2H)*-, the hyperfine coupling constant (HFCC) at the exocyclic nitrogen atom (N2) is especially sensitive to the number of hydrating water molecules; good agreement with experiment is not obtained until nine or 10 waters of hydration are included.

Photo-induced Hole Transfer from Base to Sugar in DNA: Relationship to Primary Radiation Damage

This work presents the hypothesis that photo-excitation of G.+ in DNA and model systems results in the same electronic states expected from direct ionization of the sugar phosphate backbone and that these states lead to specific sugar radicals on the DNA sugar phosphate backbone. As evidence we show that visible photo-excitation of guanine cation radicals (G.+) in the dinucleoside phosphate TpdG results in high yields (about 85%) of deoxyribose sugar radicals at the C1' and C3' sites. Further, we have calculated transition energies of hole transfer from G.+ in TpdG using time-dependent density functional theory (TD-DFT) at the B3LYP/6-31G(d) level in gas phase as well as in a solvated environment. These calculations clearly predict that visible excitation of G.+ in TpdG causes transitions from only inner-shell filled molecular orbitals (MOs) to the singly occupied molecular orbital (SOMO) that effectively result in hole transfer from guanine either to the sugar phosphate backbone or to the adjacent base, thymine. The hole transfer is followed by rapid deprotonation from the sugar to form C1' and C3' radicals. These experimental and theoretical results are in agreement with our previously published experimental and theoretical results that photo-excitation of G.+ results in high yields of deoxyribose sugar radicals in DNA, guanine deoxyribonucleosides and deoxyribonucleotides. Photo-excitation of G.+ therefore provides a convenient method to produce and study sugar radicals that are expected to be formed in gamma-irradiated DNA systems unencumbered by the many other pathways involved in direct ionization.

Base Sequence Effects on Transport in DNA

Given the success of the polaron model based on solvation in accounting for the width of a hole polaron on an all-adenine (A) sequence on DNA, we extend the calculations to other sequences. We find excellent agreement with the free energy differences measured by Lewis et al. (J. Am. Chem. Soc. 2000, 122, 12037-12038) between a guanine (G) cation and a pair of bases, GG, or a triple of bases, GGG, in all cases surrounded by As, by treating AGGA and AGGGA as solvated polarons. There is additional support for hole polaron formation in DNA from experiments in which oxidative damage due to injected holes is investigated in sequences involving Gs and As. Theory and comparison with transport measurements on repeated sequences involving multiple thymines (Ts) or combinations such as ATs or GCs, where C is cytosine, led to the suggestion that the basic sequences in these cases must be polarons whose wave functions have substantial amplitudes on both chains in a duplex. The size of an electron polaron in DNA is predicted to be similar to that of a hole polaron, approximately 4 or 5 bases. Although experiments have shown that polaron hopping is the dominant mode of charge transport in DNA with repeated sequences such as AGGA, further investigations, particularly of temperature dependence of site energies and transfer integrals, are needed to determine to what extent hole transport takes place by polaron hopping for arbitrary DNA sequences.

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.

Direct experimental observation of the low ionization potentials of guanine in free oligonucleotides by using photoelectron spectroscopy.

Photodetachment photoelectron spectroscopy is used to probe the electronic structure of mono-, di-, and trinucleotide anions in the gas phase. A weak and well defined threshold band was observed in the photoelectron spectrum of 2'-deoxyguanosine 5'-monophosphate at a much lower ionization energy than the other three mononucleotides. Density function theory calculations revealed that this unique spectral feature is caused by electron-detachment from a pi orbital of the guanine base on 2'-deoxyguanosine 5'-monophosphate, whereas the lowest ionization channel for the other three mononucleotides takes place from the phosphate group. This low-energy feature was shown to be a "fingerprint" in all the spectra of dinucleotides and trinucleotides that contain the guanine base. The current experiment provides direct spectroscopic evidence that the guanine base is the site with the lowest ionization potential in oligonucleotides and DNA and is consistent with the fact that guanine is most susceptible to oxidation to give the guanine cation in DNA damage.