Stacey D. Wetmore

Electron affinities and ionization potentials of nucleotide bases

Abstract Density-functional theory (B3LYP functional) is used to investigate the ionization potentials and electron affinities of the DNA and RNA nucleotide bases. For the first time, anions lying lower in energy than the neutral species have been calculated for both thymine and uracil (i.e., positive adiabatic electron affinities). Additionally, the calculations show that anion formation leads to significant geometrical changes to the nucleobases. This is a very important finding as previous calculations have indicated that the anions are very similar in geometry to the neutral species and reported negative valence adiabatic electron affinities.

A theoretical study of 5-halouracils: electron affinities, ionization potentials and dissociation of the related anions

Abstract The gas phase and solution electron affinities and ionization potentials of uracil, thymine and a series of 5-halouracils ( 5XU, X=F, Cl, Br ) are investigated with B3LYP. Halogen substitution has a smaller effect on the IP than the EA of U . The EAs are calculated to increase according to T U 5FU 5ClU 5BrU . The calculated barriers for the dissociation of the resulting 5XU anions to X − plus uracil-centered radicals decrease along the series 5FU − > 5ClU − > 5BrU − . The calculated trends are consistent with suggestions that 5XUs enhance the sensitivity of deoxyribonucleic acid, DNA (ribonucleic acid, RNA) to ionizing radiation and that 5BrU leads to the greatest enhancement.

Noncovalent Interactions Involving Histidine: The Effect of Charge on π-π Stacking and T-Shaped Interactions with the DNA Nucleobases

Detailed (gas-phase) MP2/6-31G*(0.25) potential energy surface scans and CCSD(T) energy calculations at the complete basis set (CBS) limit were used to analyze the (face-to-face) stacking and (edge-to-face) T-shaped interactions between histidine (modeled as imidazole) and the DNA nucleobases. For the first time, a variety of relative monomer arrangements between both neutral and protonated histidine and the natural nucleobases were considered to determine the effects of charge on the optimum dimer geometry and binding strength. Our results reveal that protonation of histidine changes the preferred relative orientations of the monomers and propose that these geometric differences may be combined with experimental crystal structures to assess the protonation state of histidine in different environments. It is also found that protonation affects the nucleobase binding preference, as well as the magnitude of the stacking and T-shaped interactions. Indeed, the maximum possible stacking and T-shaped interactions involving the neutral histidine range between approximately 20 and 45 kJ mol(-1), while this range increases to 40-105 kJ mol(-1) upon protonation, which represents an up to 330% enhancement. Although an increase in the interaction energies upon protonation of histidine is expected, the present work provides a measure of the magnitude of this enhancement in the gas phase and reveals that the amplification is almost entirely due to larger electrostatic contributions. The relative strengthening of different classifications of dimers upon protonation leads to stronger T-shaped interactions than stacking energies for protonated histidine, while the stacking and T-shaped interactions involving neutral histidine are of comparable magnitude. Thus, there is a significant difference in the nature of the pi(cation)-pi interactions involving protonated histidine and the pi-pi interactions involving neutral histidine. The calculated strengths of the interactions studied in the present work suggest that both neutral and cationic histidine contacts will provide significant stabilization to DNA-protein complexes. Although solvation effects will decrease the magnitude of the reported interactions, our results are applicable to a variety of low-polarity, biologically-relevant environments such as nonpolar enzyme active sites. Therefore, our calculations suggest that these interactions may also be important for many biological processes. The proposed significance of these interactions is supported by the large number of histidine-nucleobase contacts that appear in experimental crystal structures. The highly accurate (MP2/6-31G*(0.25)) preferred structures and (CCSD(T)/CBS) binding strengths reported in the present work can be used as benchmarks to analyze the performance of existing, or to develop new, molecular mechanics force fields for use in large-scale molecular dynamics (MD) studies of DNA-protein complexes.

DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

Four hundred twenty-eight high-resolution DNA–protein complexes were chosen for a bioinformatics study. Although 164 crystal structures (38% of those searched) contained no interactions, 574 discrete π–contacts between the aromatic amino acids and the DNA nucleobases or deoxyribose were identified using strict criteria, including visual inspection. The abundance and structure of the interactions were determined by unequivocally classifying the contacts as either π–π stacking, π–π T-shaped or sugar–π contacts. Three hundred forty-four nucleobase–amino acid π–π contacts (60% of all interactions identified) were identified in 175 of the crystal structures searched. Unprecedented in the literature, 230 DNA–protein sugar–π contacts (40% of all interactions identified) were identified in 137 crystal structures, which involve C–H···π and/or lone–pair···π interactions, contain any amino acid and can be classified according to sugar atoms involved. Both π–π and sugar–π interactions display a range of relative monomer orientations and therefore interaction energies (up to –50 (–70) kJ mol−1 for neutral (charged) interactions as determined using quantum chemical calculations). In general, DNA–protein π-interactions are more prevalent than perhaps currently accepted and the role of such interactions in many biological processes may yet to be uncovered.

Evidence for Stabilization of DNA/RNA-Protein Complexes Arising from Nucleobase-Amino Acid Stacking and T-Shaped Interactions.

The stacking and T-shaped interactions between the natural DNA or RNA nucleobases (adenine, cytosine, guanine, thymine, uracil) and all aromatic amino acids (histidine, phenylalanine, tyrosine, tryptophan) were investigated using ab initio quantum mechanical calculations. We characterized the potential energy surface of nucleobase-amino acid dimers using the MP2/6-31G*(0.25) method. The stabilization energies in dimers with the strongest interactions were further examined at the CCSD(T)/CBS level of theory. Results at the highest level of theory possible for these systems indicate that both stacking and T-shaped interactions are very close in magnitude to biologically relevant hydrogen bonds. Additionally, T-shaped interactions are as strong, if not stronger, than the corresponding stacking interactions. Our systematic consideration of the interaction energies in 485 possible combinations of monomers shows that a variety of these contacts are essential when considering the role of aromatic amino acids in the binding of proteins to DNA or RNA. This work also illustrates how our calculated binding strengths can be used by biochemists to estimate the magnitude of these noncovalent interactions in a variety of DNA/RNA-protein active sites.

Effects of Ionizing Radiation on Crystalline Cytosine Monohydrate.

Possible radical reaction products observed when subjecting monohydrate crystals of the DNA base cytosineto ionizing radiation are characterized and analyzed by means of density functional theory. Comparison ismade with data from a recently published detailed ESR and ENDOR study by Sagstuen et al. (Sagstuen, E.;Hole, E. O.; Nelson, W. H.; Close, D. M. J. Phys. Chem. 1992, 96, 8269), as well as earlier studies onmethylcytosine and cytidine monophosphates. For cytosine monohydrate it is found, when comparing computedand measured radical hyperfine coupling constants, that products other than those initially assumed are possiblybeing formed. Instead of the original model that irradiation leads to the net reaction of dehydrogenation atthe N1 position of one cytosine molecule and hydrogenation at the N3 position of a second cytosine, wepresent an alternative mechanism where water is involved in the process. This alternative mechanism leadsto the formation of N3 hydrogenation and C5 hydroxylation net products, as the main reactions. Not only dothe hyperfine couplings provide a better match for the latter but they are also energetically favored over thefirst mechanism.

Theoretical Investigation of Adenine Radicals Generated in Irradiated DNA Components.

Density functional theory is used to investigate various hydrogenated, dehydrogenated, and hydroxylated radicals formed upon irradiation of adenine. The relative energies, geometries, and hyperfine coupling constants of possible radicals are discussed. Th

Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking.

T-shaped geometries and interaction energies between select DNA nucleobases (adenine or 3-methyladenine) and all aromatic amino acids (histidine, phenylalanine, tyrosine, or tryptophan) were examined using BSSE-corrected MP2/6-31G*(0.25) potential energy surface scans, which determined the preferred nucleobase (face)-amino acid (edge) and nucleobase (edge)-amino acid (face) interactions. The energies of dimers with the strongest interactions were further studied at the CCSD(T)/CBS level of theory, which suggests that the T-shaped interactions in adenine dimers are very strong (up to -35 kJ mol(-1)). Nucleobase methylation to form a cationic damaged base (3-methyladenine) plays a large role in the relative monomer orientations and magnitude of the interactions, which increase by 17-125%. Most importantly, this study is the first to compare the stacking and T-shaped interactions between all aromatic amino acids and select (natural and damaged) DNA nucleobases where the differences between stacking and T-shaped interactions at the CCSD(T)/CBS level are small. Therefore, our results indicate that T-shaped interactions cannot be ignored when studying biological processes, and this manuscript discusses the importance of these interactions in the context of DNA repair.

Density functional theory investigation of hyperfine coupling constants in peroxyl radicals

The geometries and 17O hyperfine coupling constants in several peroxyl radicals have been determined through the use of density functional theory. Becke’s three-parameter hybrid exchange functional (B3) together with the correlation functional of Lee, Yang, and Parr (LYP) in combination with a variety of basis sets was used to study basis set effects. Subsequently, the effects of different gradient-correlated functionals were also examined. Results comparable to experimental values are obtained for all of the alkyl peroxyl radicals at the B3LYP level with IGLO-III or s-shell decontracted IGLO-III, 6-311G(d,p), 6-311+G(2df,p), and the augmented correlation-consistent polarized-valence triple-zeta basis set of D. E. Woon and T. H. Dunning [J. Chem. Phys. 98, 1358 (1993)], R. E. Kendall, T. H. Dunning, and R. J. Harrison [J. Chem. Phys. 96, 6796 (1992)], and T. H. Dunning [J. Chem. Phys. 90, 1007 (1989)]. Calculations imply that the spin density ratio between the inner and outer oxygens is 0.3:0.7, supportin...

Modeling the Chemical Step Utilized by Human Alkyladenine DNA Glycosylase: A Concerted Mechanism Aids in Selectively Excising Damaged Purines

Human alkyladenine DNA glycosylase (AAG) initiates the repair of a wide variety of (neutral or cationic) alkylated and deaminated purines by flipping damaged nucleotides out of the DNA helix and catalyzing the hydrolytic N-glycosidic bond cleavage. Unfortunately, the limited number of studies on the catalytic pathway has left many unanswered questions about the hydrolysis mechanism. Therefore, detailed ONIOM(M06-2X/6-31G(d):AMBER) reaction potential energy surface scans are used to gain the first atomistic perspective of the repair pathway used by AAG. The lowest barrier for neutral 1,N(6)-ethenoadenine (εA) and cationic N(3)-methyladenine (3MeA) excision corresponds to a concerted (A(N)D(N)) mechanism, where our calculated ΔG(‡) = 87.3 kJ mol(-1) for εA cleavage is consistent with recent kinetic data. The use of a concerted mechanism supports previous speculations that AAG uses a nonspecific strategy to excise both neutral (εA) and cationic (3MeA) lesions. We find that AAG uses nonspecific active site DNA-protein π-π interactions to catalyze the removal of inherently more difficult to excise neutral lesions, and strongly bind to cationic lesions, which comes at the expense of raising the excision barrier for cationic substrates. Although proton transfer from the recently proposed general acid (protein-bound water) to neutral substrates does not occur, hydrogen-bond donation lowers the catalytic barrier, which clarifies the role of a general acid in the excision of neutral lesions. Finally, our work shows that the natural base adenine (A) is further inserted into the AAG active site than the damaged substrates, which results in the loss of a hydrogen bond with Y127 and misaligns the general base (E125) and water nucleophile to lead to poor nucleophile activation. Therefore, our work proposes how AAG discriminates against the natural purines in the chemical step and may also explain why some damaged pyrimidines are bound but are not excised by this enzyme.