Tautomerism of nucleic acid bases and the effect of molecular interactions on tautomeric equilibria

Autocatalysis in Formose Reaction and Formation of RNA Nucleosides

Understanding of the abiotic formation of nucleosides under geochemical conditions is currently a major scientific challenge. In this study, free radical pathways for formation of RNA nucleosides with canonical nucleobases are proposed for the first time. The pathways proceed with relatively low energy barriers for the formation of ribose as well as all RNA nucleosides. The formose reaction proceeds either with or without Ca²⁺ and CaOH⁺ cations. An autocalytic cycle for the formation of both glycolaldehyde and glyceraldehyde is identified when Ca²⁺ or CaOH⁺ cations are involved in the reaction. The results suggest that Ca²⁺ cations are not involved in the formation of ribose from glyceraldehyde. In addition, these pathways lead to the formation of dihydroxyacetone and d-erythrose. Calculated results show that the glycosidic bond can be formed abiotically between the d-ribose and the nucleobase, where d-ribose forms a cyclic free radical that subsequently reacts with the neutral nucleobase. Involvement of proper nucleobase tautomer is important for the formation of RNA nucleosides. Our approaches provide a solution for the long-standing question of how the glycosidic bond is formed under the abiotic conditions with low energy barriers. The pathways for formation of the sugars without a catalyst are relevant to the formation of sugars in interstellar clouds. On the other hand, the autocalysis in the formose reaction followed by the formation of the nucleosides is appropriate for the abiotic synthesis taking place in the presence of water in the early Earth environment. The Ca²⁺ and CaOH⁺ cations appear to be the first nonenzymatic catalytic systems for formation of biomolecules.

The Role of Proton Transfer on Mutations

Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.

Gas-phase tautomers of protonated 1-methylcytosine. Preparation, energetics, and dissociation mechanisms

Tautomers of 1-methylcytosine that are protonated at N-3 (1+) and C-5 (2+) have been specifically synthesized in the gas phase and characterized by tandem mass spectrometry and quantum chemical calculations. Ion 1+ is the most stable tautomer in aqueous and methanol solution and is likely to be formed by electrospray ionization of 1-methylcytosine and transferred in the gas phase. Gas-phase protonation of 1-methylcytosine produces a mixture of 1+ and the O-2-protonated tautomer (3+), which are nearly isoenergetic. Dissociative ionization of 6-ethyl-5,6-dihydro-1-methylcytosine selectively forms isomer 2+. Upon collisional activation, ions 1+ and 3+ dissociate by loss of ammonia and [C,H,N,O], whose mechanisms have been established by deuterium labeling and ab initio calculations. The main dissociations of 2+ following collisional activation are losses of CH2=C=NH and HN=C=O. The mechanisms of these dissociations have been elucidated by deuterium labeling and theoretical calculations.

Charges of phosphate groups. A role in stabilization of 2'-deoxyribonucleotides. A DFT investigation

We have analyzed the relative stabilities and Gibbs tautomeric free energy for tautomeric transitions of neutral 2'-deoxyribonucleotides and its mono- and di-protonated forms. Geometry optimizations of these nucleic acid constituents have been performed at the DFT/B3LYP level using the standard 6-31G(d) basis set. The prediction of relative stabilities, Gibbs tautomeric free energy has been made at the B3LYP/6-311++G(d,p)//B3LYP/6-31G(d) level of theory. For each nucleoside four major conformers, i.e., north/anti, north/syn, south/anti, and south/syn have been taken into consideration. We have found the substantial effect of the uncompensated charge on the relative stability of 2'-deoxyribonucleotides. In particular, when the charge of 2'-deoxyribonucleotide anions is completely compensated by protons, the syn conformations have been found to be the global minima due to stabilization provided by intramolecular hydrogen bonds. However, the negative charge that appears due to the successive removal of the protons from the phosphate group destabilizes these syn conformations and stabilizes preferably the south/anti conformations (except of 2'-deoxyguanosine phosphate). Only 2'-deoxyribonucleotides, possessing south/anti and north/anti orientations, containing guanine and cytosine can contribute significantly to the rate of spontaneous point mutations due to the formation of biologically relevant amounts of 'rare' tautomers. However, we found strong influence of uncompensated negative charge for 2'-deoxyribonucleotides which possess syn conformations. Finally we have found that the proton transfer could result in the spontaneous change of 2'-deoxyribonucleotides conformations. We conclude that this phenomenon could be considered as a new way for the stabilization of 'rare' isomers for such DNA bases as cytosine and thymine.

Double-proton transfer in adenine-thymine and guanine-cytosine base pairs. A post-Hartree-Fock ab initio study

The results of a comprehensive study on the double-proton transfer in Adenine-Thymine (AT) and Guanine-Cytosine (GC) base pairs at room temperature in gas phase and with the inclusion of environmental effects are obtained. The double-proton-transfer process has been investigated in the AT and GC base pairs at the B3LYP/6-31G(d) and MP2/6-31G(d) levels of theory. It has been predicted that the hydrogen-bonded bases possess nonplanar geometries due to sp3 hybridization of nitrogen atoms and because of the soft intermolecular vibrations in the molecular complexes. An analysis of the energetic parameters of the local minima suggests that rare AT base pair conformation is not populated due to the shallowness of this minimum, which completely disappears from the Gibbs free energy surface. The stabilization of canonic or rare forms of the DNA bases by water molecules and metal cations has been predicted by calculating the optimal configuration of charges (using differential product/transition state stabilization approach) followed by calculations of the interactions between the base pair and a water/sodium cation.

Quantum chemistry predicted correlations between geometric isomerism (conformation) of -OH and =NH substituents and typical group frequencies of nucleic acid bases: cytosine

Results of a search for correlations between typical group mode frequencies and conformation of -OH and =NH substituents is reported. The study is based on quantum chemical data (HF/6-31G (d, p) and MP2 (full)/6-31G (d, p) approximations) of 13 isomers of cytosine. It is closely related to investigations of stability and energetics of all isomers of the more common nucleic acid bases, which revealed correlations between conformation (geometric isomerism) of OH and =NH substituents on the one hand and conversion energies, relaxation of internal structural parameters, electric field gradients, etc. on the other hand. In the majority of cases alteration of conformation of these substituents is accompanied by systematic frequency shifts of stretching, in-plane and out-of-plane bending (torsional) modes conventionally assigned to such groups and by alteration of quantum chemically predicted estimates of harmonic valence force constants and structural parameters dominating the mode frequencies. For identification of group modes 'fractional' mass (other than 'natural' mass) isotope shifts of frequency and normal vectors proved useful. Likewise, estimation of effects of force constant and structural parameter alterations on frequency shifts by first order perturbation theory of the FG problem of partial structures contributed valuable insight into the origin of the shifts.

Electron impact ionization mass spectrometry and intramolecular cyclization in 2-substituted pyrimidin-4(3H)-ones

Electron impact ionization mass spectrometry indicates that the behavior of W-unsubstituted pyrirnidin-4-ones with CH2-R type substitution at C-2 differs from homologs that are N-substituted and/or 2-aryl- or 2-methyl-substituted. A dominant intramolecular cycliza-tion was found to occur between 3ZV (in agreement with the predominance of the 3NH tautomers) and the ortho positions of the aryl moiety in compounds with a CH2-aryl substitution at C-2. Theoretical calculations with an AMI SCFR method on 2-, 6-, and 2, 6-disubstituted pyrimidin-4-ones support the mass spectrometric observations.

Structure and conformation of N4-hydroxycytosine and N4-hydroxy-5-fluorocytosine. A theoretical ab initio study

Optimal molecular geometries and molecular energies were obtained for N4-hydroxycytosine and its 5-fluoro congener with the use of the theoretical ab initio quantum mechanical calculations within the Self Consistent Field method corrected for the electron correlation effects by the second-order Many Body Perturbation Theory (SCF + MBPT(2)). The 6-31G Gaussian basis set was employed. Several tautomeric and rotameric forms were considered. For N4-hydroxycytosine and N4-hydroxy-5-fluorocytosine the imino tautomer (in the conformation syn relatively to the N3-nitrogen atom) appeared to be the most stable form. The imino tautomer of N4-hydroxy-cytosine in the anti rotameric form is by 12.8 kJ mol-1 less stable than the imino-syn form. The 5-fluoro substituent raises the energy difference between the syn and anti rotamers up to 38.5 kJ mol-1. The potential energy barrier for the syn-anti rotation in the imino form of N4-hydroxycytosine is estimated to be about 180 kJ/mol. The results presented in this paper suggest that the syn-imino and anti-imino forms can be treated as two structural isomers that do not interconvert at temperatures relevant to biochemical conditions. The theoretical results also show that the amino tautomeric forms do not compete with the imino forms in the gas-phase and in non-polar and weakly-polar environment. In a polar environment (e.g., in aqueous solutions), however, one may expect an increased population of the amino forms. Qualitatively, the results of the present study agree well with the available experimental and theoretical data for N4-hydroxycytosine and some of its derivatives. The implications of the present study are discussed in relation to the molecular mechanisms of mutagenesis caused by NH2OH and of enzyme (thymidylate synthase) inhibition by N4-hydroxydeoxycytidine monophosphate.