A review on point mutations via proton transfer in DNA base pairs in the absence and presence of electric fields

This is a comprehensive review that focuses on spontaneous mutations that may occur during DNA replication, the fundamental process responsible for transferring genetic information. In 1963, Löwdin postulated that these mutations are primarily a result of proton transfer reactions within the hydrogen-bonded DNA base pairs. The single and double proton transfer reactions within the base pairs result in zwitterions and rare tautomers, respectively. For persistent mutations, these products must be generated at high rates and should be thermodynamically stable. This review covers the proton transfer reactions studied experimentally and computationally. The review also examines the influence of externally applied electric fields on the thermodynamics and kinetics of proton transfer reactions within DNA base pairs, and their biological implications.

Theoretical insight into 7,8-dihydrogen-8-oxoguanine radical cation deprotonation

The pK_a values of reactive protons in 8-oxoG˙⁺ and potential energy profiles for 8-oxoG radical cation deprotonation reaction (N1–H and N7–H) were firstly calculated.

Proton Transfer and Nitro Rotation Tuned Photoisomerization of Artificial Base Pair-ZP

Recently, the successful incorporation of artificial base pairs in genetics has made a significant progress in synthetic biology. The present work reports the proton transfer and photoisomerization of unnatural base pair ZP, which is synthesized from the pyrimidine analog 6-amino-5-nitro-3-(1-β-D-2'-deoxyribo-furanosyl)-2 (1H)-pyridone (Z) and paired with its Watson-Crick complement, the purine analog 2-amino-8-(1'-β-D-2'- deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P). To explain the mechanism of proton transfer process, we constructed the relaxed potential energy surfaces (PESs) linking the different tautomers in both gas phase and solution. Our results show that the double proton transfer in the gas phase occurs in a concerted way both in S₀ and S₁ states, while the stepwise mechanism becomes more favorable in solution. The solvent effect can promote the single proton transfer, which undergoes a lower energy barrier in S₁ state due to the strengthened hydrogen bond. In contrast to the excited state ultrafast deactivation process of the natural bases, there is no conical intersection between S₀ and S₁ states along the proton transfer coordinate to activate the decay mechanism in ZP. Of particular relevance to the photophysical properties, charge-transfer character is obviously related to the nitro rotation in S₁ state. We characterized the molecular vibration effect on the electronic properties, which reveals the electronic excitation can be tuned by the rotation-induced structural distortion accompanied with the electron localization on nitro group.

The influence of base pair tautomerism on single point mutations in aqueous DNA

The relationship between base pair hydrogen bond proton transfer and the rate of spontaneous single point mutations at ambient temperatures and pressures in aqueous DNA is investigated. By using an ensemble-based multiscale computational modelling method, statistically robust rates of proton transfer for the A:T and G:C base pairs within a solvated DNA dodecamer are calculated. Several different proton transfer pathways are observed within the same base pair. It is shown that, in G:C, the double proton transfer tautomer is preferred, while the single proton transfer process is favoured in A:T. The reported range of rate coefficients for double proton transfer is consistent with recent experimental data. Notwithstanding the approximately 1000 times more common presence of single proton transfer products from A:T, observationally there is bias towards G:C to A:T mutations in a wide range of living organisms. We infer that the double proton transfer reactions between G:C base pairs have a negligible contribution towards this bias for the following reasons: (i) the maximum half-life of the G*:C* tautomer is in the range of picoseconds, which is significantly smaller than the milliseconds it takes for DNA to unwind during replication, (ii) statistically, the majority of G*:C* tautomers revert back to their canonical forms through a barrierless process, and (iii) the thermodynamic instability of the tautomers with respect to the canonical base pairs. Through similar reasoning, we also deduce that proton transfer in the A:T base pair does not contribute to single point mutations in DNA.

Solvent effect on the intermolecular proton transfer of the Watson and Crick guanine-cytosine and adenine-thymine base pairs: a polarizable continuum model study

Herein we present our results on the study of the double proton transfer (DPT) mechanism in the adenine-thymine (AT) and guanine-cytosine (GC) base pairs, both in gas phase and in solution. The latter was modeled using the polarizable continuum method (PCM) in different solvents. According to our DFT calculations, the DPT may occur for both complexes in a stepwise mechanism in condensate phase. In gas phase only the GC base pair exhibits a concerted DPT mechanism. Using the Wigner's tunneling corrections to the transition state theory we demonstrate that such corrections are important for the prediction of the rate constants of both systems in gas and in condensate phase. We also show that (i) as the polarity of the medium decreases the equilibrium constant of the DPT reaction increases in both complexes, and (ii) that the equilibrium constant in the GC complex is four orders of magnitude larger than in AT. This observation suggests that the spontaneous mutations in DNA base pairs are more probable in GC than in AT.

Proton transfer in guanine-cytosine base pair analogues studied by NMR spectroscopy and PIMD simulations

It has been hypothesised that proton tunnelling between paired nucleobases significantly enhances the formation of rare tautomeric forms and hence leads to errors in DNA replication. Here, we study nuclear quantum effects (NQEs) using deuterium isotope-induced changes of nitrogen NMR chemical shifts in a model base pair consisting of two tautomers of isocytosine, which form hydrogen-bonded dimers in the same way as the guanine-cytosine base pair. Isotope effects in NMR are consequences of NQEs, because ro-vibrational averaging of different isotopologues gives rise to different magnetic shielding of the nuclei. The experimental deuterium-induced chemical shift changes are compared with those calculated by a combination of path integral molecular dynamics (PIMD) simulations with DFT calculations of nuclear shielding. These calculations can directly link the observable isotope-induced shifts with NQEs. A comparison of the deuterium-induced changes of 15N chemical shifts with those predicted by PIMD simulations shows that inter-base proton transfer reactions do not take place in this system. We demonstrate, however, that NMR isotope shifts provide a unique possibility to study NQEs and to evaluate the accuracy of the computational methods used for modelling quantum effects in molecules. Calculations based on the PBE functional from the general-gradient-approximation family provided significantly worse predictions of deuterium isotope shifts than those with the hybrid B3LYP functional.

Quantum mechanical studies on the existence of AC mismatches through prototopic tautomerization pathway in adenine and cytosine recognition

The gas phase studies on the electronic stabilities and thermochemical properties of metastable AC mismatches have been performed and the results are analyzed to explain the features of experimentally available AC mismatches. The hydrogen bonding patterns observed in these mismatches are relevant to the formation of stable AC mismatches. In these AC pairs, the H migration mechanism to generate other tautomeric forms is not observed, which shows the compatibility of H bonding capacity of the sites involved in H bonds. The presence of hydrogen bond type –N[Formula: see text]H–N– may contribute to better AC pairing, hence cisA1-1cisC2, transA2-cisC1 and transA1-1cisC2 are found to be more favorable pairs compared to other AC pairs.

Influence of Coupling and Embedding Schemes on QM Size Convergence in QM/MM Approaches for the Example of a Proton Transfer in DNA

The influence of embedding and coupling schemes on the convergence of the QM size in the QM/MM approach is investigated for the transfer of a proton in a DNA base pair. We find that the embedding scheme (mechanical or electrostatic) has a much greater impact on the convergence behavior than the coupling scheme (additive QM/MM or subtractive ONIOM). To achieve size convergence, QM regions with up to 6000 atoms are necessary for pure QM or mechanical embedding. In contrast, electrostatic embedding converges faster: for the example of the transfer of a proton between DNA base pairs, we recommend including at least five base pairs and 5 Å of solvent (including counterions) into the QM region, i.e., a total of 1150 atoms.

Exposing the G-quadruplex to electric fields: the role played by telomeres in the propagation of DNA errors

We use quantum calculations to assess the impact of external electric fields on the stability of G-quadruplex, a key structure in telomere functionality.

A novel conception for spontaneous transversions caused by homo-pyrimidine DNA mismatches: a QM/QTAIM highlight

We have firstly shown that the T·T(w) and C·C(w) DNA mismatches with wobble (w) geometry stay in slow tautomeric equilibrium with short T·T*(WC) and C·C*(WC) Watson-Crick (WC) mispairs. These non-dissociative tautomeric rearrangements are controlled by the plane-symmetric, highly stable, highly polar and zwitterionic transition states. The obtained results allow us to understand in what way the T·T(w) and C·C(w) mismatches acquire enzymatically competent T·T*(WC) and C·C*(WC) conformations directly in the hydrophobic recognition pocket of a high-fidelity DNA-polymerase, thereby producing thermodynamically non-equilibrium spontaneous transversions. The simplest numerical estimation of the frequency ratio of the TT to CC spontaneous transversions satisfactorily agrees with experimental data.

Human DNMT1 transition state structure

Human DNA methyltransferase 1 (DNMT1) maintains the epigenetic state of DNA by replicating CpG methylation signatures from parent to daughter strands, producing heritable methylation patterns through cell divisions. The proposed catalytic mechanism of DNMT1 involves nucleophilic attack of Cys(1226) to cytosine (Cyt) C6, methyl transfer from S-adenosyl-l-methionine (SAM) to Cyt C5, and proton abstraction from C5 to form methylated CpG in DNA. Here, we report the subangstrom geometric and electrostatic structure of the major transition state (TS) of the reaction catalyzed by human DNMT1. Experimental kinetic isotope effects were used to guide quantum mechanical calculations to solve the TS structure. Methyl transfer occurs after Cys(1226) attack to Cyt C6, and the methyl transfer step is chemically rate-limiting for DNMT1. Electrostatic potential maps were compared for the TS and ground states, providing the electronic basis for interactions between the protein and reactants at the TS. Understanding the TS of DNMT1 demonstrates the possibility of using similar analysis to gain subangstrom geometric insight into the complex reactions of epigenetic modifications.

Mutagenic effects induced by the attack of NO2 radical to the guanine-cytosine base pair

We investigate the attack of the nitrogen dioxide radical (NO^•₂) to the guanine—cytosine (GC) base pair and the subsequent tautomeric reactions able to induce mutations, by means of density functional theory (DFT) calculations. The conducted simulations allow us to identify the most reactive sites of the GC base pair. Indeed, the computed relative energies demonstrate that the addition of the NO^•₂ radical to the C8 position of the guanine base forms to the most stable adduct. Although the initial adducts might evolve to non-canonical structures via inter-base hydrogen bonds rearrangements, the probability for the proton exchange to occur lies in the same range as that observed for undamaged DNA. As a result, tautomeric errors in NO₂-attacked DNA arises at the same rate as in canonical DNA, with no macroscopic impact on the overall stability of DNA. The potential mutagenic effects of the GC–NO^•₂ radical adducts likely involve side reactions, e.g., the GC deprotonation to the solvent, rather than proton exchange between guanine and cytosine basis.

New structural hypostases of the A·T and G·C Watson–Crick DNA base pairs caused by their mutagenic tautomerisation in a wobble manner: a QM/QTAIM prediction

Our investigation reveals the hitherto unknown ability of the canonical Watson–Crick DNA base pairs to switch into wobble mismatches with mutagenic tautomers, clarifying the nature of genome instability.

DNA spontaneous mutation and its role in the evolution of GC-content: assessing the impact of the genetic sequence

We use theoretical tools to investigate the possible role played by a DNA sequence in the base pair tautomerization phenomena.

Assessing the importance of proton transfer reactions in DNA

Although engineered by millions of years of evolution, the cellular machinery is not flawless, and errors regularly appear during DNA replication. The subsequent alteration of the stored genetic message results in a mutation and might be the starting point of important health disorders. The question therefore is what causes DNA mutations? All living organisms are constantly exposed to a number of external agents such as free radicals and to radiation, which may lead to induced mutations. There are also mutations happening without invoking the action of any exogenous element, the so-called spontaneous mutations. The former can be partially controlled by avoiding exposure to high-risk environments, while the latter are more intriguing because their origin is unclear and difficult to determine. As noted by Watson and Crick when they first discovered the DNA structure, the correct replication of DNA rests on the assumption that the base pairs remain in their most stable, canonical form. However, protons along the interbase hydrogen-bond network are not static entities. They can in fact interchange their positions in DNA bases through proton transfer (PT) reactions before strands unwind, giving rise to noncanonical structures defined as rare tautomers. The importance of these rare tautomers was also cleverly anticipated by Watson and Crick and some years later claimed by Löwdin to be a source of spontaneous mutations. In Watson and Crick's words: "It would be of interest to know the precise difference in free energy between the various tautomeric forms under physiological conditions." Unfortunately, rare tautomeric forms are very difficult to detect, so no direct and accurate free energy measure has been discerned. In contrast, theoretical chemistry is making good progress toward the quantification of PT reactions in DNA and their biological consequences. This Account touches upon the theoretical studies devoted to appraising the importance of rare tautomers as promoters of spontaneous mutations. We focus in particular on the crucial role played by the biological environment on DNA stability. It has now been demonstrated that valuable macroscopic predictions require not only highly accurate theories but also refined chemical models. Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations performed on short but complete DNA sequence fragments emerge in this context as the most adequate tools. In addition, these methods can be used to quantify the effect of different external agents on the PT tautomeric equilibria and, eventually, to conveniently handle them. This is the case for the possible alteration of the naturally observed mutation rate by exposure to intense electric fields. Theoretical predictions envision in this respect promising applications of ultrashort electric pulses in medicine to selectively modify the mutated/canonical ratio in DNA.

Coupling between hydrogen atoms transfer and stacking interaction in adenine-thymine/guanine-cytosine complexes: a theoretical study

Four different complexes of two base pairs, an adenine-thymine and a guanine-cytosine one, have been studied in order to understand the modifications induced by the staking interaction between the two base pairs on the hydrogen atoms transfers between the bases in either base pair. The inclusion of these two kinds of interactions allows us to clarify if some properties, as the mechanism of hydrogen transfer, is exclusively a local effect of a base pair or can be modified by a more long-range interaction between the base pairs. The results on these four complexes are compared with those of the monomeric systems, the A-T and G-C base pair, and with those of the A-T and G-C dimers. The specificity of each complex and of each hydrogen bond has been analyzed.

DPT tautomerisation of the wobble guanine·thymine DNA base mispair is not mutagenic: QM and QTAIM arguments

We have shown for the first time, connecting QM methods with QTAIM analysis and using the methodology of the sweeps of the energetical, electron-topological and geometrical parameters, that the tautomerisation of the wobble guanine·thymine (wG·T) DNA base mispair into the wG(*)·T(*) base mispair induced by the double proton transfer (DPT), which undergoes a concerted asynchronous pathway, is not mutagenic. The wG·T → wG(*)·T(*) DPT tautomerisation does not result in the transition of the G base into its mutagenic tautomeric form G(*) able to mispair with the T base within the Watson-Crick base pairing scheme. This observation is explained by the so-called quantum protection of the wG·T DNA base mispair from its mutagenic tautomerisation - the dynamical non-stability of the tautomerised wG(*)·T(*) base mispair and significantly negative value of the Gibbs free energy of activation for the reverse reaction of the wG·T → wG(*)·T(*) DPT tautomerisation.

Is the DPT tautomerization of the long A·G Watson-Crick DNA base mispair a source of the adenine and guanine mutagenic tautomers? A QM and QTAIM response to the biologically important question

Herein, we first address the question posed in the title by establishing the tautomerization trajectory via the double proton transfer of the adenine·guanine (A·G) DNA base mispair formed by the canonical tautomers of the A and G bases into the A*·G* DNA base mispair, involving mutagenic tautomers, with the use of the quantum-mechanical calculations and quantum theory of atoms in molecules (QTAIM). It was detected that the A·G ↔ A*·G* tautomerization proceeds through the asynchronous concerted mechanism. It was revealed that the A·G base mispair is stabilized by the N6H···O6 (5.68) and N1H···N1 (6.51) hydrogen bonds (H-bonds) and the N2H···HC2 dihydrogen bond (DH-bond) (0.68 kcal·mol(-1) ), whereas the A*·G* base mispair-by the O6H···N6 (10.88), N1H···N1 (7.01) and C2H···N2 H-bonds (0.42 kcal·mol(-1) ). The N2H···HC2 DH-bond smoothly and without bifurcation transforms into the C2H···N2 H-bond at the IRC = -10.07 Bohr in the course of the A·G ↔ A*·G* tautomerization. Using the sweeps of the energies of the intermolecular H-bonds, it was observed that the N6H···O6 H-bond is anticooperative to the two others-N1H···N1 and N2H···HC2 in the A·G base mispair, while the latters are significantly cooperative, mutually strengthening each other. In opposite, all three O6H···N6, N1H···N1, and C2H···N2 H-bonds are cooperative in the A*·G* base mispair. All in all, we established the dynamical instability of the А*·G* base mispair with a short lifetime (4.83·10(-14) s), enabling it not to be deemed feasible source of the A* and G* mutagenic tautomers of the DNA bases. The small lifetime of the А*·G* base mispair is predetermined by the negative value of the Gibbs free energy for the A*·G* → A·G transition. Moreover, all of the six low-frequency intermolecular vibrations cannot develop during this lifetime that additionally confirms the aforementioned results. Thus, the A*·G* base mispair cannot be considered as a source of the mutagenic tautomers of the DNA bases, as the A·G base mispair dissociates during DNA replication exceptionally into the A and G monomers in the canonical tautomeric form.

Selecting DFT methods for use in optimizations of enzyme active sites: applications to ONIOM treatments of DNA glycosylases

When using a hybrid methodology to treat an enzymatic reaction, many factors contribute to selecting the method for the high-level region, which can be complicated by the presence of dispersion-driven interactions such as π–π stacking. In addition, the proper treatment of the reaction center often requires a large number of heavy atoms to be included in the high-level region, precluding the use of ab initio methods such as MP2 as well as large basis sets, in the optimization step. In the present work, popular DFT methods were tested to identify an appropriate functional for treating the high-level region in ONIOM optimizations of reactions catalyzed by nonmetalloenzymes. Eight different DFT methods (B3LYP, B97-2, MPW1K, MPWB1K, BB1K, B1B95, M06-2X, and ωB97X-D) in combination with four double-ζ quality Pople basis sets were tested for their ability to optimize noncovalent interactions (hydrogen bonding and π–π) and characterize reactions (proton transfer, SN2 hydrolysis, and unimolecular cleavage). Although the primary focus of this study is accurate structure determination, energetics were also examined at both the optimization level of theory, and with triple-ζ quality basis set and select (M06-2X or ωB97X-D) methods. If dispersion-driven interactions exist within the active site, then MPWB1K/6-31G(d,p) or M06-2X/6-31+G(d,p) are recommended for the optimization step with subsequent triple-ζ quality single-point energies. However, since dispersion-corrected functionals (M06-2X and ωB97X-D) generally require diffuse functions to yield appropriate geometries, the possible size of the high-level region is greatly limited with these methods. In contrast, if the model is large enough to recover steric constraints on π–π interactions, then B3LYP with a small basis set performs comparatively well for the optimization step and is significantly less computationally expensive. Interestingly, the functionals that afford the best geometries often do not yield the best energetics, which emphasizes the importance of structural benchmark studies.

Theoretical investigation of the coupling between hydrogen-atom transfer and stacking interaction in adenine-thymine dimers

Three different dimers of the adenine-thymine (A-T) base pair are studied to point out the changes of important properties (structure, atomic charge, energy and so on) induced by coupling between the movement of the atoms in the hydrogen bonds and the stacking interaction. The comparison of these results with those for the A-T monomer system explains the role of the stacking interaction in the hydrogen-atom transfer in this biologically important base pair. The results support the idea that this coupling depends on the exact dimer considered and is different for the N-N and N-O hydrogen bonds. In particular, the correlation between the hydrogen transfer and the stacking interaction is more relevant for the N-N bridge than for the N-O one. Also, the two different mechanisms of two-hydrogen transfer (step by step and concerted) can be modified by the stacking interaction between the base pairs.

Gas-phase hydration thermochemistry of sodiated and potassiated nucleic acid bases

Hydration reactions of sodiated and potassiated nucleic acid bases (uracil, thymine, cytosine, and adenine) produced by electrospray have been studied in a gas phase using the pulsed ion-beam high-pressure mass spectrometer. The thermochemical properties, ΔH(o)(n), ΔS(o)(n), and ΔG(o)(n), for the hydrated systems were obtained from hydration equilibrium measurement. The structural aspects of the hydrated complexes are discussed in conjunction with available literature data. The correlation between water binding energies in the hydrated complexes and the corresponding metal ion affinities of nucleobases suggests that a significant (if not dominant) amount of the canonical structure of cytosine undergoes tautomerization during electrospray ionization, and the thermochemical values for cationized cytosine probably correspond to a mixture of tautomeric complexes.

Hydrogen bond dynamics in crystalline β-9-anthracene carboxylic acid--a combined crystallographic and spectroscopic study

We compare results from single crystal X-ray diffraction and FTIR spectroscopy to elucidate the nature of hydrogen bonding in β-9-anthracene carboxylic acid (β-9AC, C(15)H(10)O(2)). The crystallographic studies indicate a disorder for the protons in the cyclic hydrogen bond. This disorder allows the determination of the energy difference between two proton sites along the hydrogen bond. The temperature dependent Fourier transform infrared spectroscopy (FTIR) underpins the crystallographic results. The combination of both methods allows the estimation of a one-dimensional potential curve describing the OH-stretching motion. The dynamical properties of the proton transfer along the hydrogen bond are extracted from this potential. The work presented here has profound implication on future studies of photochemical dynamics of crystalline β-9AC, which can deliver a deeper understanding of the mechanism of photochemical driven molecular machines and the optical and electronic properties of molecular organic semiconductors.

Improved DFT description of intrastrand cross-link formation by inclusion of London dispersion corrections

The formation of covalent linkages between two vicinal nucleotides has been proved experimentally to constitute a particularly deleterious class of DNA lesions. These tandem lesions by essence present a competitive chemistry. The density functional theory with dispersion (DFT-D) method is shown to dramatically improve the theoretical description of the formation of a prototypical intrastrand cross-link, when compared to pure or hybrid GGA functionals which strongly deviate from the π-π self-stacking mode, as dinucleotides are artificially stabilized by the formation of unrealistic intramolecular hydrogen bonds (HBs). Inclusion of London dispersion correction restores a more realistic picture of the reactant structure and also of geometries and energies along the reaction profile. This paves the way toward a robust insilico screening of intrastrand cross-link DNA defects.