RESUMEN

8-Oxoguanosine is the most common oxidatively generated base damage and pairs with complementary cytidine within duplex DNA. The 8-oxoguanosine-cytidine lesion, if not recognized and removed, not only leads to G-to-T transversion mutations but renders the base pair being more vulnerable to the ionizing radiation and singlet oxygen (1 O2 ) damage. Herein, reaction dynamics of a prototype Watson-Crick base pair [9MOG ⋅ 1MC]⋅+ , consisting of 9-methyl-8-oxoguanine radical cation (9MOG⋅+ ) and 1-methylcystosine (1MC), was examined using mass spectrometry coupled with electrospray ionization. We first detected base-pair dissociation in collisions with the Xe gas, which provided insight into intra-base pair proton transfer of 9MOG⋅+ ⋅ 1MC ← → ${{\stackrel{ {\rightarrow} } { {\leftarrow} } } }$ [9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ and subsequent non-statistical base-pair separation. We then measured the reaction of [9MOG ⋅ 1MC]⋅+ with 1 O2 , revealing the two most probable pathways, C5-O2 addition and HN7 -abstraction at 9MOG. Reactions were entangled with the two forms of 9MOG radicals and base-pair structures as well as multi-configurations between open-shell radicals and 1 O2 (that has a mixed singlet/triplet character). These were disentangled by utilizing approximately spin-projected density functional theory, coupled-cluster theory and multi-referential electronic structure modeling. The work delineated base-pair structural context effects and determined relative reactivity toward 1 O2 as [9MOG - H]⋅>9MOG⋅+ >[9MOG - HN1 ]⋅ ⋅ [1MC+HN3' ]+ ≥9MOG⋅+ ⋅ 1MC.

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RESUMEN

In DNA, guanine is the most susceptible to oxidative damage by exogenously and endogenously produced electronically excited singlet oxygen (1O2). The reaction mechanism and the product outcome strongly depend on the nucleobase ionization state and structural context. Previously, exposure of a monomeric 9-methylguanine radical cation (9MG•+, a model guanosine compound) to 1O2 was found to result in the formation of an 8-peroxide as the initial product. The present work explores the 1O2 oxidation of 9MG•+ and its dehydrogenated neutral form [9MG - H]• within a Watson-Crick base pair consisting of one-electron-oxidized 9-methylguanine-1-methylcytosine [9MG·1MC]•+. Emphasis is placed on entangling the base pair structural context and intra-base pair proton transfer with and consequences thereof on the singlet oxygenation of guanine radical species. Electrospray ionization coupled with guided-ion beam tandem mass spectrometry was used to study the formation and reaction of guanine radical species in the gas phase. The 1O2 oxidation of both 9MG•+ and [9MG - H]• is exothermic and proceeds barrierlessly either in an isolated monomer or within a base pair. Single- and multi-referential theories were tested for treating spin contaminations and multi-configurations occurring in radical-1O2 interactions, and reaction potential energy surfaces were mapped out to support experimental findings. The work provides a comprehensive profile for the singlet oxygenation of guanine radicals in different charge states and in the absence and the presence of base pairing. All results point to an 8-peroxide as the major oxidation product in the experiment, and the oxidation becomes slightly more favorable in a neutral radical form. On the basis of a variety of reaction pathways and product profiles observed in the present and previous studies, the interplay between guanine structure, base pairing, and singlet oxygenation and its biological implications are discussed.

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RESUMEN

8-Oxo-2'-deoxyguanosine (OG) is the most common DNA lesion. Notably, OG becomes more susceptible to oxidative damage than the undamaged nucleoside, forming mutagenic products in vivo. Herein the reactions of singlet O2 with the radical cations of 8-oxo-2'-deoxyguanosine (OG.+ ) and 9-methyl-8-oxoguanine (9MOG.+ ) were investigated using ion-molecule scattering mass spectrometry, from which barrierless, exothermic O2 -addition products were detected for both reaction systems. Corroborated by static reaction potential energy surface constructed using multi-reference CASPT2 theory and molecular dynamics simulated in the presence of the reactants' kinetic and internal energies, the C5-terminal O2 -addition was pinpointed as the most probable reaction pathway. By elucidating the reaction mechanism, kinetics and dynamics, and reaction products and energetics, this work constitutes the first report unraveling the synergetic damage of OG by ionizing radiation and singlet O2 .

RESUMEN

Reactions of electronically excited singlet oxygen (1O2) with the radical cations of guanine (9HG•+), 9-methylguanine (9MG•+), 2'-deoxyguanosine (dGuo•+), and guanosine (Guo•+) were studied in the gas phase by a combination of guided-ion-beam mass spectrometric measurement of product ions and cross sections as a function of collision energy (Ecol) and electronic structure calculations of the reaction potential energy surface (PES) at various levels of theory. No product could be captured in the 1O2 reaction with bare 9HG•+ or 9MG•+, because energized products decayed rapidly to reactants before being detected. To overcome this unfavorable kinetics, monohydrated 9HG•+·H2O and 9MG•+·H2O were used as reactant ions, of which the peroxide product ions were stabilized by energy relaxation via elimination of the water ligand. Reaction cross sections for 9HG•+·H2O and 9MG•+·H2O decrease with increasing Ecol, becoming negligible above 0.6 eV. This indicates that the reactions are exothermic with no barriers above reactants and the heat of formation of the products is sufficiently large to overcome their water ligand elimination energy (0.7 eV). Peroxide product ions were also detected in the 1O2 reactions with unhydrated dGuo•+ and Guo•+, in which intramolecular vibrational redistribution was able to stabilize oxidation products. 9MG•+ was utilized as a model system to explore the reaction PES for the initial 1O2 addition to the guanine radical cation. Calculations were carried out using single-reference ωB97XD, RI-MP2, and DLPNO-CCSD(T) and multireference CASSCF and CASPT2. Although the same PES profile was obtained at different levels of theory, the energies of the mixed open- and closed-shell 1O2 reactant and the open-shell reaction intermediates, transition states, and products are sensitive to the theories. By taking into account both static and dynamic electron correlations, the CASPT2 PES has provided the best agreement with the experimentally measured reaction thermodynamics and predicted 8-peroxide as the most probable initial oxidation product of the guanine radical cation.

RESUMEN

We report a kinetics and mechanistic study on the 1O2 oxidation of 9-methylguanine (9MG) and the cross-linking of the oxidized intermediate 2-amino-9-methyl-9H-purine-6,8-dione (9MOGOX) with Nα-acetyl-lysine-methyl ester (abbreviated as LysNH2) in aqueous solutions of different pH. Experimental measurements include the determination of product branching ratios and reaction kinetics using mass spectrometry and absorption spectroscopy, and the characterization of product structures by employing collision-induced dissociation. Strong pH dependence was revealed for both 9MG oxidation and the addition of nucleophiles (water and LysNH2) at the C5 position of 9MOGOX. The 1O2 oxidation rate constant of 9MG was determined to be 3.6 × 107 M-1·s-1 at pH 10.0 and 0.3 × 107 M-1·s-1 at pH 7.0, both of which were measured in the presence of 15 mM LysNH2. The ωB97XD density functional theory coupled with various basis sets and the SMD implicit solvation model was used to explore the reaction potential energy surfaces for the 1O2 oxidation of 9MG and the formation of C5-water and C5-LysNH2 adducts of 9MOGOX. Computational results have shed light on reaction pathways and product structures for the different ionization states of the reactants. The present work has confirmed that the initial 1O2 addition represents the rate-limiting step for the oxidative transformations of 9MG. All of the downstream steps are exothermic with respect to the starting reactants. The C5-cross-linking of 9MOGOX with LysNH2 significantly suppressed the formation of spiroiminodihydantoin (9MSp) resulting from the C5-water addition. The latter became dominant only at the low concentration (∼1 mM) of LysNH2.

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We report an experimental and computational study on the 1 O2 oxidation of gas-phase deprotonated guanine-cytosine base pair [G ⋅ C-H]- that is composed of 9HG ⋅ [C-H]- and 7HG ⋅ [C-H]- (pairing 9H- or 7H-guanine with N1-deprotonated cytosine), and 9HG ⋅ [C-H]- _PT and 7HG ⋅ [C-H]- _PT (formed by intra-base-pair proton transfer from the N1 of guanine to the N3 of [C-H]- ). The conformer-averaged reaction product ions and cross section were measured over a center-of-mass collision energy range from 0.1 to 0.5 eV using a guided-ion-beam tandem mass spectrometer. To explore conformation-specific reactivity, collision dynamics of 1 O2 with each of the four [G ⋅ C-H]- conformers was simulated at B3LYP/6-31G(d). Trajectories showed that the 1 O2 oxidation of the base pair entangles with intra-base-pair proton transfer, and prefers to occur in a collision when the base pair adopts a proton-transferred structure; trajectories also indicate that the 9HG-containing base pair favors stepwise formation of 4,8-endoperoxide of guanine, whereas the 7HG-containing base pair prefers concerted formation of guanine 5,8-endoperoxide. Using trajectory results as a guide, potential energy surfaces (PESs) along all possible reaction pathways were established using the approximately spin-projected ωB97XD/6-311++G(d,p)//B3LYP/6-311++G(d,p) method. PESs have not only rationalized trajectory findings but provided more accurate energetics and indicated that the proton-transferred base-pair conformers have lower activation barriers for oxidation than their non-proton-transferred counterparts.

RESUMEN

We compare the energies and enthalpies of inter-action of three- and seven-stranded capped polyglycine aggregates in both the pleated and rippled antiparallel and parallel ß-sheet structures as well as the collagenic (three-strand) or polyglycine II-like (seven-strand) forms using density functional theory at the B3LYP/D95(d,p) level. We present the overall interaction energies as broken down into pure H-bonding between the strands at the geometries they assume in the aggregates and the distortion energies required to achieve those geometries starting from the fully relaxed single strands. While the antiparallel sheets represent the most stable structures for both the three- and seven-strand structures, the pure H-bonding interactions are the smallest for these structures. The overall interaction energies are dominated by the energy required to distort the relaxed polyglycine strands rather than the H-bonding energies. The antiparallel ß-sheet constrained to C(s) symmetry has a lower enthalpy, but higher energy, of interaction than the fully optimized structure.

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We report DFT calculations at the B3LYP/D95(d,p) level on the gas phase, aqueous solvation and solvated energies as functions of the central psi and phi dihedral angles (in steps of 5 degrees each) of acetyl-(L)Ala-(L)Ala-(L)Ala-NH(2) (3AL) and its diastereomer, acetyl-(L)Ala-(D)Ala-(L)Ala-NH(2) (3AD). In addition to structures without internal H-bonds (C(5) interactions are neglected), many (95) structures containing internal H-bonds were completely optimized. The only minima for non-H-bonding structures in the gas phase correspond to extended beta-strands for both diastereomers. Some (but not all) structures with internal H-bonds are more stable than those without them. The energy landscapes for the solvated species show multiple minima for the non-H-bonding species and a single minimum for the H-bonding species (3(10)-helix), suggesting that the equilibrium conformational mixture in water be composed of the extended beta-strand, polyproline II, 3(10)-helix, and alpha-helix-like (with no H-bonds) conformations which are all within about 1 kcal/mol of each other. Most H-bonding structures are destabilized relative to the non-H-bonding structures in aqueous solution, but some with large dipole moments are not. The large dipole moment of the alpha-helix-like conformation leads to its increased stability in water (vs the gas phase). Significant qualitative and quantitative differences are reported for the energy landscapes of the two diastereomers when one is compared with the mirror image of the other landscape (particularly in the beta-turn region), suggesting that the differences in the energies of the unfolded peptides need to be considered when considering the stabilities of folded peptides and proteins with single amino acid mutations.

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We report completely optimized ONIOM DFT/AM1 molecular orbital calculations on several collagen-like triple helices based upon the repeating triad, ProProGly. The requirement of Gly as every third amino acid in collagen can be attributed to its enantiomorphic nature, as it behaves as a Damino acid in collagen. We, therefore, explored related collagen-like triple helices with one of the central Gly's mutated to either L or DAla; l-Ala appreciably destabilizes, while d-Ala slightly stabilizes the triple helical structure. Mutation of the same Gly to DSer, which is simply DAla with an OH in place of one of the methyl H's, induces a much greater stabilization due to an additional H-bond formed between this OH and a C=O on an adjacent peptide strand. Energies are presented for the triple helices and their component strands (both optimized and distorted to their triple helical geometries) relative to the component amino acids. The variation of relative energies with the chosen reference is delineated.

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