Why the tautomerization of the G·C Watson–Crick base pairviathe DPT does not cause point mutations during DNA replication? QM and QTAIM comprehensive analysis

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

This comprehensive review 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 in DNA 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.

Multiscale simulations reveal the role of PcrA helicase in protecting against spontaneous point mutations in DNA

Proton transfer across hydrogen bonds in DNA can produce non-canonical nucleobase dimers and is a possible source of single-point mutations when these forms mismatch under replication. Previous computational studies have revealed this process to be energetically feasible for the guanine-cytosine (GC) base pair, but the tautomeric product (G[Formula: see text]C[Formula: see text]) is short-lived. In this work we reveal, for the first time, the direct effect of the replisome enzymes on proton transfer, rectifying the shortcomings of existing models. Multi-scale quantum mechanical/molecular dynamics (QM/MM) simulations reveal the effect of the bacterial PcrA Helicase on the double proton transfer in the GC base pair. It is shown that the local protein environment drastically increases the activation and reaction energies for the double proton transfer, modifying the tautomeric equilibrium. We propose a regime in which the proton transfer is dominated by tunnelling, taking place instantaneously and without atomic rearrangement of the local environment. In this paradigm, we can reconcile the metastable nature of the tautomer and show that ensemble averaging methods obscure detail in the reaction profile. Our results highlight the importance of explicit environmental models and suggest that asparagine N624 serves a secondary function of reducing spontaneous mutations in PcrA Helicase.

Tunneling Effect in Proton Transfer: Transfer Matrix Approach

The transfer matrix (TM) method was applied to calculate the transmission probability (TP) for proton transfer reactions. The tunneling factors in the reaction rate constants were also evaluated using the TPs. To test this method, TPs for the Eckart potentials modeled as a guanine-cytosine base pair were calculated by the TM method and compared to TPs by the analytical solution. As a result, the errors in the TPs by the TM method were quite small. The tunneling factors for the guanine-thymine (G-T) and adenine-cytosine (A-C) mispair reactions were then evaluated by the TM method. A shoulder appears on each potential for these reactions [Odai, K.; Umesaki,K. J. Phys. Chem. A. 2021, 125, 8196-8204]. As a result, the shoulder for the G-T mispair reaction contributes significantly to the tunneling, while the shoulder for the A-C mispair reaction contributes little to the tunneling. These results are difficult to obtain with methods such as Wigner's tunneling factor.

Proton transfer during DNA strand separation as a source of mutagenic guanine-cytosine tautomers

Proton transfer between the DNA bases can lead to mutagenic Guanine-Cytosine tautomers. Over the past several decades, a heated debate has emerged over the biological impact of tautomeric forms. Here, we determine that the energy required for generating tautomers radically changes during the separation of double-stranded DNA. Density Functional Theory calculations indicate that the double proton transfer in Guanine-Cytosine follows a sequential, step-like mechanism where the reaction barrier increases quasi-linearly with strand separation. These results point to increased stability of the tautomer when the DNA strands unzip as they enter the helicase, effectively trapping the tautomer population. In addition, molecular dynamics simulations indicate that the relevant strand separation time is two orders of magnitude quicker than previously thought. Our results demonstrate that the unwinding of DNA by the helicase could simultaneously slow the formation but significantly enhance the stability of tautomeric base pairs and provide a feasible pathway for spontaneous DNA mutations.

Atomistic mechanisms of the tautomerization of the G·C base pairs through the proton transfer: quantum-chemical survey

This study is devoted to the investigation of the G·C*^t_O2(WC)↔G*_NH3·C*^t(WC), G·C*_O2(WC)↔G*_NH3·C*(WC) and G*·C*_O2(WC)↔G*_NH3·C(w_WC)_↓ tautomerization reactions occurring through the proton transfer, obtained at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory in gas phase under normal conditions ('WC' means base pair in Watson-Crick configuration, T=298.15 K). These reactions lead to the formation of the G*_NH3·C*^t(WC), G*_NH3·C*(WC) and G*_NH3·C(w_WC)_↓ base pairs by the participation of the G*_NH3 base with NH₃ group. Gibbs free energies of activation for these reactions are 6.43, 11.00 and 1.63 kcal·mol^-1, respectively. All of these tautomerization reactions are dipole active. Finally, we believe that these non-dissociative processes, which are tightly connected with the tautomeric transformations of the G·C base pairs, play an outstanding role in supporting of the spatial structure of the DNA and RNA molecules with various functional purposes.

Quantum and classical effects in DNA point mutations: Watson-Crick tautomerism in AT and GC base pairs

Proton transfer along the hydrogen bonds of DNA can lead to the creation of short-lived, but biologically relevant point mutations that can further lead to gene mutation and, potentially, cancer. In this work, the energy landscape of the canonical A-T and G-C base pairs (standard, amino-keto) to tautomeric A*-T* and G*-C* (non-standard, imino-enol) Watson-Crick DNA base pairs is modelled with density functional theory and machine-learning nudge-elastic band methods. We calculate the energy barriers and tunnelling rates of hydrogen transfer between and within each base monomer (A, T, G and C). We show that the role of tunnelling in A-T tautomerisation is statistically unlikely due to the presence of a small reverse reaction barrier. On the contrary, the thermal populations of the G*-C* point mutation could be non-trivial and propagate through the replisome. For the direct intramolecular transfer, the reaction is hindered by a substantial energy barrier. However, our calculations indicate that tautomeric bases in their monomeric form have remarkably long lifetimes.

The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair

The Watson-Crick base pair proton transfer tautomers would be widely considered as a source of spontaneous mutations in DNA replication if not for their short lifetimes and thermodynamic instability. This work investigates the effects external electric fields have on the stability of the guanine-cytosine proton transfer tautomers within a realistic strand of aqueous DNA using a combination of ensemble-based classical molecular dynamics (MD) coupled to quantum mechanics/molecular mechanics (QM/MM). Performing an ensemble of calculations accounts for the stochastic aspects of the simulations while allowing for easier identification of systematic errors. The methodology applied in this work has previously been shown to estimate base pair proton transfer rate coefficients that are in good agreement with recent experimental data. A range of electric fields in the order of 104 to 109 V m-1 is investigated based on their real-life medicinal applications which include gene therapy and cancer treatments. The MD trajectories confirm that electric fields up to 1.00 × 109 V m-1 have a negligible influence on the structure of the base pairs within DNA. The QM/MM results show that the application of large external electric fields (1.00 × 109 V m-1) parallel to the hydrogen bonds increases the thermodynamic population of the tautomers by up to one order of magnitude; moreover, the lifetimes of the tautomers remain insignificant when compared to the timescale of DNA replication.

Novel mechanisms of the conformational transformations of the biologically important G·C nucleobase pairs in Watson–Crick, Hoogsteen and wobble configurations via the mutual rotations of the bases around the intermolecular H-bonds: a QM/QTAIM study

It was established conformational transformations of the G·C nucleobase pairs, occurring via the mutual rotation of the G and C bases around the intermolecular H-bonds.

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.

A Quantum-Mechanical Looking Behind the Scene of the Classic G·C Nucleobase Pairs Tautomerization

For the first time, at the MP2/6-311++G(2df,pd)//B3LYP/6-311++G(d,p) level of theory, a comprehensive quantum-mechanical investigation of the physico-chemical mechanism of the tautomeric wobblization of the four biologically-important G·C nucleobase pairs by the participation of the monomers in rare, in particular mutagenic, tautomeric forms (marked with an asterisk) was provided. These novel tautomeric transformations (wobblization or shifting of the bases within the pair) are intrinsically inherent properties of the G·C nucleobase pairs. In this study, we have obtained intriguing results, lying far beyond the existing representations. Thus, it was shown that Löwdin's G*·C*(WC) base pair does not tautomerize according to the wobblization mechanism. Tautomeric wobblization of the G*·C*(rWC) (relative Gibbs free energy ΔG = 0.00/relative electronic energy ΔE = 0.00 kcal·mol-1) ("r"-means the configuration of the base pair in reverse position; "WC"-the classic Watson-Crick configuration) and G*t·C*(H) (ΔG = -0.19/ΔE = 0.29 kcal·mol-1) ("H"-Hoogsteen configuration;"t" denotes the O6H hydroxyl group in the trans position) base pairs are preceded by the stages of the base pairs tautomerization by the single proton transfer (SPT). It was established that the G*t·C*(rH) (ΔG = 2.21/ΔE = 2.81 kcal·mol-1) base pair can be wobbled through two different pathways via the traditional one-stage mechanism through the TSs, which are tight G+·C- ion pairs, stabilized by the participation of only two intermolecular H-bonds. It was found out that the G·C base pair is most likely incorporated into the DNA/RNA double helix with parallel strands in the G*·C*(rWC), G·C*(rwwc), and G*·C(rwwc) ("w"-wobble configuration of the pair) tautomeric forms, which are in rapid tautomeric equilibrium with each other. It was proven that the G*·C*(rWC) nucleobase pair is also in rapid tautomeric equilibrium with the eight tautomeric forms of the so-called Levitt base pair. It was revealed that a few cases of tautomerization via the DPT of the nucleobase pairs by the participation of the C8H group of the guanine had occurred. The biological role of the obtained results was also made apparent.

A quantum chemical view of the interaction of RNA nucleobases and base pairs with the side chains of polar amino acids

Hydrogen bonding between amino acids and nucleobases is important for RNA-protein recognition. As a first step toward understanding the physicochemical features of these contacts, the present work employs density functional theory calculations to critically analyze the intrinsic structures and strength of all theoretically possible model hydrogen-bonded complexes involving RNA nucleobase edges and polar amino acid side chains. Our geometry optimizations uncover a number of unique complexes that involve variable hydrogen-bonding characteristics, including conventional donor-acceptor interactions, bifurcated interactions and single hydrogen-bonded contacts. Further, significant strength of these complexes in the gas phase (-27 kJ mol^-1 to -226 kJ mol^-1) and solvent phase (-19 kJ mol^-1 to -78 kJ mol^-1) points toward the ability of associated contacts to provide stability to RNA-protein complexes. More importantly, for the first time, our study uncovers the features of complexes involving protonated nucleobases, as well as those involving the weakly polar cysteine side chain, and thereby highlights their potential importance in biological processes that involve RNA-protein interactions. Additional analysis on select base pair-amino acid complexes uncovers the ability of amino acid side chain to simultaneously interact with both nucleobases of the base pair, and highlights the greater strength of such interactions compared to base-amino acid interactions. Overall, our analysis provides a basic physicochemical framework for understanding the molecular basis of nucleic acid-protein interactions. Further, our quantum chemical data can be used to design better algorithms for automated search of these contacts at the RNA-protein interface.Communicated by Ramaswamy H. Sarma.

Intramolecular tautomerization of the quercetin molecule due to the proton transfer: QM computational study

Quercetin molecule (3, 3', 4', 5, 7-pentahydroxyflavone, C15H10O7) is an important flavonoid compound of natural origin, consisting of two aromatic A and B rings linked through the C ring with endocyclic oxygen atom and five hydroxyl groups attached to the 3, 3', 4', 5 and 7 positions. This molecule is found in many foods and plants, and is known to have a wide range of therapeutic properties, like an anti-oxidant, anti-toxic, anti-inflammatory etc. In this study for the first time we have revealed and investigated the pathways of the tautomeric transformations for the most stable conformers of the isolated quercetin molecule (Brovarets' & Hovorun, 2019) via the intramolecular proton transfer. Energetic, structural, dynamical and polar characteristics of these transitions, in particular relative Gibbs free and electronic energies, characteristics of the intramolecular specific interactions-H-bonds and attractive van der Waals contacts, have been analysed in details. It was demonstrated that the most probable process among all investigated is the proton transfer from the O3H hydroxyl group of the C ring to the C2' carbon atom of the C2'H group of the B ring along the intramolecular O3H…C2' H-bond with the further formation of the C2'H2 group. It was established that the proton transfer from the hydroxyl groups to the carbon atoms of the neighboring CH groups is assisted at the transition states by the strong intramolecular HCH…O H-bond (~28.5 kcal∙mol-1). The least probable path of the proton transfer-from the C8H group to the endocyclic O1 oxygen atom-causes the decyclization of the C ring in some cases. It is shortly discussed the biological importance of the obtained results.

Novel Tautomerisation Mechanisms of the Biologically Important Conformers of the Reverse Löwdin, Hoogsteen, and Reverse Hoogsteen G*·C* DNA Base Pairs via Proton Transfer: A Quantum-Mechanical Survey

For the first time, in this study with the use of QM/QTAIM methods we have exhaustively investigated the tautomerization of the biologically-important conformers of the G*·C* DNA base pair-reverse Löwdin G*·C*(rWC), Hoogsteen G*'·C*(H), and reverse Hoogsteen G*'·C*(rH) DNA base pairs-via the single (SPT) or double (DPT) proton transfer along the neighboring intermolecular H-bonds. These tautomeric reactions finally lead to the formation of the novel G· C O 2 * (rWC), G N 2 * · C(rWC), G*'N2·C(rWC), G N 7 * · C(H), and G*'N7·C(rH) DNA base mispairs. Gibbs free energies of activation for these reactions are within the range 3.64-31.65 kcal·mol-1 in vacuum under normal conditions. All TSs are planar structures (Cs symmetry) with a single exception-the essentially non-planar transition state TSG*·C*(rWC)↔G+·C-(rWC) (C1 symmetry). Analysis of the kinetic parameters of the considered tautomerization reactions indicates that in reality only the reverse Hoogsteen G*'·C*(rH) base pair undergoes tautomerization. However, the population of its tautomerised state G*'N7·C(rH) amounts to an insignificant value-2.3·10-17. So, the G*·C*(rWC), G*'·C*(H), and G*'·C*(rH) base pairs possess a permanent tautomeric status, which does not depend on proton mobility along the neighboring H-bonds. The investigated tautomerization processes were analyzed in details by applying the author's unique methodology-sweeps of the main physical and chemical parameters along the intrinsic reaction coordinate (IRC). In general, the obtained data demonstrate the tautomeric mobility and diversity of the G*·C* DNA base pair.

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.

Unexpected Routes of the Mutagenic Tautomerization of the T Nucleobase in the Classical A·T DNA Base Pairs: A QM/QTAIM Comprehensive View

In this paper using quantum-mechanical (QM) calculations in combination with Bader's quantum theory of "Atoms in Molecules" (QTAIM) in the continuum with ε = 1, we have theoretically demonstrated for the first time that revealed recently highly-energetic conformers of the classical A·T DNA base pairs - Watson-Crick [A·T(wWC)], reverse Watson-Crick [A·T(wrWC)], Hoogsteen [A·T(wH)] and reverse Hoogsteen [A·T(wrH)] - act as intermediates of the intrapair mutagenic tautomerization of the T nucleobase owing to the novel tautomerisation pathways: A·T(wWC)↔A·T*(w⊥ WC); A·T(wrWC)↔A·T O 2 * (w⊥ rWC); A·T(wH)↔A·T*(w⊥ H); A·T(wrH)↔A·T O 2 * (w⊥ rH). All of them occur via the transition states as tight ion pairs (A+, protonated by the N6H2 amino group)·(T-, deprotonated by the N3H group) with quasi-orthogonal geometry, which are stabilized by the participation of the strong (A)N6+H···O4-/O2-(T) and (A)N6+H···N3-(T) H-bonds. Established tautomerizations proceed through a two-step mechanism of the protons moving in the opposite directions along the intermolecular H-bonds. Initially, proton moves from the N3H imino group of T to the N6H2 amino group of A and then subsequently from the protonated N6+H3 amino group of A to the O4/O2 oxygen atom of T, leading to the products - A·T*(w⊥ WC), A·T O 2 * (w⊥ rWC), A·T*(w⊥ H), and A·T O 2 * (w⊥ rH), which are substantially non-planar, conformationally-labile complexes. These mispairs are stabilized by the participation of the (A)N6H/N6H'···N3(T) and (T)O2H/O4H···N6(A) H-bonds, for which the pyramidalized amino group of A is their donor and acceptor. The Gibbs free energy of activation of these mutagenic tautomerizations lies in the range of 27.8-29.8 kcal·mol-1 at T = 298.15 K in the continuum with ε = 1.

Novel pathway for mutagenic tautomerization of classical А∙Т DNA base pairs via sequential proton transfer through quasi-orthogonal transition states: A QM/QTAIM investigation

In this paper we have theoretically predicted a novel pathway for the mutagenic tautomerization of the classical A∙T DNA base pairs in the free state, the Watson-Crick A·Т(WC), reverse Watson-Crick A·Т(rWC), Hoogsteen A·Т(H) and reverse Hoogsteen A·Т(rH) pairs, via sequential proton transfer accompanied by a significant change in the mutual orientation of the bases. Quantum-mechanical (QM) calculations were performed at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level in vacuum phase, along with Bader's quantum theory of Atoms in Molecules (QTAIM). These processes involve transition states (TSs) with quasi-orthogonal structures (symmetry C1), which are highly polar, tight ion pairs (A-, N6H2-deprotonated)∙(T+, O4/O2-protonated). Gibbs free energies of activation for the A∙T(WC) / A∙T(rWC) ↔ A*∙Т(rwWC) / A*∙Т(wWC) tautomeric transitions (~43.5 kcal∙mol-1) are lower than for the A∙T(H) / A∙T(rH) ↔ A*N7∙Т(rwH) / A*N7∙Т(wH) tautomerisations (~53.0 kcal∙mol-1) (rare tautomers are marked by an asterisk; w-wobble configured tautomerisation products). The (T)N3+H⋯N1-(A), (T)O4+H⋯N1-(A) / (T)N3+H⋯N1-(A) and (T)O2+H⋯N1-(A) H-bonds are found in the transition states TSA-·T+A·T(WC)↔A*·T(rwWC) / TSA-·T+A·T(rWC)↔A*·T(wWC). However, in the transition state TSA-·T+A·Т(H)↔A*N7·T(rwH) / TSA-·T+A·Т(rH)↔A*N7·T(wH), the (T)N3+H⋯N7-(A), (T)O4+H⋯N7-(A) / (T)N3+H⋯N7-(A) and (T)O2+H⋯N7-(A) H-bonds are supplemented by the attractive (T)O4+/O2+⋯N6-(A) van der Waals contacts. It was demonstrated that the products of the tautomerization of the classical A∙T DNA base pairs-A*∙Т(rwWC), A*N7∙Т(rwH) and A*N7∙Т(wH) (symmetry Cs)-further transform via double proton transfer into the energetically favorable wobble A∙T*(rwWC), A∙T*(rwH) and A∙T*O2(wH) base mispairs (symmetry Cs).

Formic acid catalyzed isomerization of protonated cytosine: a lower barrier reaction for tautomer production of potential biological importance

Tautomerism in nucleotide bases is one of the possible mechanisms of DNA mutation. In spite of numerous studies on the structure and energy of protonated cytosine tautomers, little information is available on the process of their intra- and intermolecular tautomerizations. The catalytic ability of H₂O, HCOOH, and the HCOOHH₂O group to facilitate the tautomerism of the Cyt2t⁺ to CytN3⁺ isomer has been studied. It is shown that the activation free energies of tautomerism in the gas phase are 161.17, 58.96, 26.06, and 15.69 kJ mol^-1, respectively, when the reaction is carried out in the absence and presence of H₂O, HCOOH, or the HCOOHH₂O group. The formation of a doubly hydrogen bonded transition state is central to lowering the activation free energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of intramolecular tautomerization, the isomerization of the Cyt2t⁺ to CytN3⁺ isomer remains unfavorable, and the HCOOH and HCOOHH₂O group mediated mechanisms are still more favorable. Meanwhile, conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants. The rate constant with Wigner tunneling correction for direct tautomerization is obviously smaller than that of HCOOH-mediated tautomerization, which is the most plausible mechanism. Finally, another important finding is that the product complex (CytN3⁺HCOOH) is in the rapid tautomeric equilibrium with the reaction complex (Cyt2t⁺HCOOH) (τ_99.9% = 3.84 × 10^-12 s), which is implemented by the mechanism of the concerted synchronous double proton transfer. Its lifetime of the formed CytN3⁺HCOOH complex (τ = 8.33 × 10^-9 s) is almost one order of magnitude larger than the time required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication (several ns), which is further dissociated into the CytN3⁺ and HCOOH monomers. The results of the present study demonstrate the feasibility of acid catalysis for DNA base isomerization reactions that would otherwise be forbidden.

The influence of Cu+ binding to hypoxanthine on stabilization of mismatches involving hypoxanthine and DNA bases: a DFT study

In the present work, the influence of Cu⁺ binding to N3- and N7-positions of hypoxanthine on energetic, geometrical and topological properties of hypoxanthine-guanine, hypoxanthine-adenine, hypoxanthine-cytosine, hypoxanthine-thymine and hypoxanthine-hypoxanthine mismatches is theoretically investigated. The calculations, in gas phase, are performed at B3LYP/6-311++G(3df,3pd) level of theory. Unlike the other mispairs, Cu⁺ binding to N3-position of hypoxanthine causes the proton transfer process from enol form of hypoxanthine to imino forms of adenine and cytosine. This process also occurs in all mismatches having enol form of hypoxanthine when Cu⁺ binds to N7-position of hypoxanthine. The mismatches are stabilized by hydrogen bonds. The influence of Cu⁺ on hydrogen bonds is also examined by atoms in molecules (AIM) and natural bond orbital (NBO) analyses. Communicated by Ramaswamy H. Sarma.

Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs

For the first time novel high-energy conformers-A·T(wWC) (5.36), A·T(wrWC) (5.97), A·T(wH) (5.78), and A·T(wrH) (ΔG = 5.82 kcal·mol-1) (See Graphical Abstract) were revealed for each of the four biologically important A·T DNA base pairs - Watson-Crick A·T(WC), reverse Watson-Crick A·T(rWC), Hoogsteen A·T(H) and reverse Hoogsteen A·T(rH) at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of quantum-mechanical theory in the continuum with ε = 4 under normal conditions. Each of these conformers possesses substantially non-planar wobble (w) structure and is stabilized by the participation of the two anti-parallel N6H/N6H'…O4/O2 and N3H…N6 H-bonds, involving the pyramidalized amino group of the A DNA base as an acceptor and a donor of the H-bonding. The transition states - TSA·T(WC)↔A·T(wWC), TSA·T(rWC)↔A·T(wrWC), TSA·T(H)↔A·T(wH), and TSA·T(rH)↔A·T(wrH), controlling the dipole-active transformations of the conformers from the main plane-symmetric state into the high-energy, significantly non-planar state and vice versa, were localized. They also possess wobble structures similarly to the high-energy conformers and are stabilized by the participation of the N6H/N6H'…O4/O2 and N3H…N6 H-bonds. Discovered conformers of the A·T DNA base pairs are dynamically stable short-lived structures [lifetime τ = (1.4-3.9) ps]. Their possible biological significance and future perspectives have been briefly discussed.

Physico-chemical profiles of the wobble ↔ Watson-Crick G*·2AP(w) ↔ G·2AP(WC) and A·2AP(w) ↔ A*·2AP(WC) tautomerisations: a QM/QTAIM comprehensive survey

This study is intended to clarify in detail the tautomeric transformations of the wobble (w) G*·2AP(w) and A·2AP(w) nucleobase mispairs involving 2-aminopurine (2AP) into the Watson-Crick (WC) G·2AP(WC) and A*·2AP(WC) base mispairs (asterisks denote mutagenic tautomers of the DNA bases), respectively, by quantum-mechanical methods and Bader's Quantum Theory of Atoms in Molecules. Our previously reported methodology has been used, which allows the evolution of the physico-chemical parameters to be tracked along the entire internal reaction coordinate (IRC), not exclusively in the stationary states of these reactions. These biologically important G*·2AP(w) ↔ G·2AP(WC) and A·2AP(w) ↔ A*·2AP(WC) w ↔ WC tautomerisations, which are involved in mutagenic tautomerically-conformational pathways, determine the origin of the transitions and transversions induced by 2AP. In addition, it is established that they proceed through planar, highly stable, zwitterionic transition states and they exhibit similar physico-chemical profiles and stages of sequential intrapair proton transfer, followed by spatial rearrangement of the nucleobases relative to each other within the base pairs. These w ↔ WC tautomerisations occur non-dissociatively and are accompanied by a significant alteration in geometry (from wobble to Watson-Crick and vice versa) and redistribution of the specific intermolecular interactions, which can be divided into 10 patterns including AHB H-bonds and loosened A-H-B covalent bridges along the IRC of tautomerisation. Based on the redistribution of the geometrical and electron-topological parameters of the intrapair hydrogen bonds, exactly 9 key points have been allocated to characterize the evolution of these reactions.

Theoretical study of mechanisms for the hydrolytic deamination of cytosine via steered molecular dynamic simulations

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations. Two pathways were considered to explain the mechanism of this process, where the water molecule attacks the C–N bond to give an intermediate (an amino–hydroxy–oxo structure in the A-path, and a hydroxy–oxo in the B-path) as the determinant step of reaction. Stationary structures along both energy profiles were analyzed at molecular dynamics level, obtaining states with higher free energies than those from electronic calculations in the gas phase and in solution described as a continuous medium. From the results obtained, the more complex A-pathway, with five steps, was kinetically the most favorable (with an endergonic reaction energy of 7.41 kcal mol⁻¹, a high barrier of 67.53 kcal mol⁻¹, and a small velocity constant k₂ = 1.80 × 10⁻³⁷ s⁻¹), concluding that the uracil base can participate in a spontaneous genetic mutation since the uracil–ammonia complex has a long lifetime of 6.10 × 10²⁷ s. This process turns out exergonic and faster when carried out in gas phase simulation or electronic calculation with a continuous medium, due to the disappearance of explicit water molecules that can compete with the assistant molecule.

Gibbs free energy profiles of the cytosine deamination assisted by a water molecule in a discrete aqueous medium were obtained by the application of Steered Molecular Dynamic (SMD) simulations.

The A·T(rWC)/A·T(H)/A·T(rH) ↔ A·T*(rwWC)/A·T*(wH)/A·T*(rwH) mutagenic tautomerization via sequential proton transfer: a QM/QTAIM study

In this study for the first time we have revealed by QM and QTAIM calculations at the MP2/aug-cc-pVDZ//B3LYP/6-311++G(d,p) level of QM theory the novel routes of the mutagenic tautomerization of three biologically important A·T DNA base pairs – reverse Watson–Crick A·T(rWC), Hoogsteen A·T(H) and reverse Hoogsteen A·T(rH) – followed by their rebuilding into the wobble (w) A·T*(rw_WC), A·T*(w_H) and A·T*(rw_H) base mispairs by the participation of the mutagenic tautomers of the DNA bases (denoted by asterisk) and vice versa, thus complementing the physico-chemical property of the canonical A·T(WC) Watson–Crick DNA base pair reported earlier (Brovarets' et al., RSC Adv., 2015, 5, 99594–99605). These non-dissociative tautomeric transformations in the classical A·T(rWC), A·T(H) and A·T(rH) DNA base pairs proceed similarly to the canonical A·T(WC) DNA base pair via the intrapair sequential proton transfer with shifting towards major or minor grooves of DNA followed by further double proton transfer along the intermolecular H-bonds and are controlled by the plane symmetric and highly stable transition states – tight ion pairs formed by the A⁺ nucleobase, protonated by the N1/N7 nitrogen atoms, and T⁻ nucleobase, deprotonated by the N3H imino group. Comparison of the estimated populations of the tautomerised states (10⁻²¹ to 10⁻¹⁴) with similar characteristics for the canonical A·T(WC) DNA base pair (10⁻⁸ to 10⁻⁷) leads authors to the conclusion, that only a base pair with WC architecture can be a building block of the DNA macromolecule as a genetic material, which is able for the evolutionary self-development. Among all four classical DNA base pairs, only A·T(WC) DNA base pair can ensure the proper rate of the spontaneous point errors of replication in DNA.

We discovered tautomeric wobbling of the classical A·T DNA base pairs. This data evidence, that only a base pair with Watson–Crick architecture can be a building block of the DNA macromolecule as a genetic material, which is able for the evolutionary self-development.

A QM/QTAIM research under the magnifying glass of the DPT tautomerisation of the wobble mispairs involving 2-aminopurine

In this study, a comprehensive survey of the changes of the physico-chemical parameters at each point of the IRC for the biologically important T·2AP*(w) ↔ T*·2AP(w) and G·2AP*(w) ↔ G*·2AP(w) DPT tautomerisation reactions involved in the point mutations (transitions and transversions) induced by 2-aminopurine (2AP) in DNA is provided.

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.

Tautomeric transition between wobble A·C DNA base mispair and Watson-Crick-like A·C* mismatch: microstructural mechanism and biological significance

Here, we use MP2/DFT quantum-chemical methods combined with Quantum Theory of Atoms in Molecules to study the tautomeric transition between wobble A·C(w) mismatch and Watson-Crick-like A·C*(WC) base mispair, proceeding non-dissociatively via sequential proton transfer between bases through the planar, highly stable and zwitterionic TS(A∙C-)(A∙C(W)<-->A∙C&(WC)) transition state joined by the participation of (A)N6(+)H∙∙∙N4(-)(C), (A)N1(+)H∙∙∙N4(-)(C) and (A)C2(+)H∙∙∙N3(-)(C) H-bonds. Notably, the A·C(w) ↔ A·C*(WC) tautomerization reaction is accompanied by 10 unique patterns of the specific intermolecular interactions that consistently replace each other. Our data suggest that biologically significant A·C(w) → A·C*(WC) tautomerization is a kinetically controlled pathway for formation of the enzymatically competent Watson-Crick-like A·C*(WC) DNA base mispair in the essentially hydrophobic recognition pocket of the high-fidelity DNA-polymerase, responsible for the occurrence of spontaneous point AC/CA incorporation errors during DNA biosynthesis.

Theoretical study of enzymatically catalyzed tautomerization of carbon acids in aqueous solution: quantum calculations and steered molecular dynamics simulations

The thermodynamics and kinetics of enzymatically assisted reactions of carbon acids were studied theoretically in this work. Quantum electronic (QE) structure calculations and steered molecular dynamics (SMD) simulations were carried out. Three 3-butenal tautomerization reactions that proceed from the β,γ-unsaturated reactant (R) to the α,β-unsaturated carbon acid product (P) and occur in two elementary steps through an intermediate (I) were studied, ignoring or including the surrounding aqueous medium in the calculations. The Gibbs free energies of activation of the R ⇆ I enolization and I ⇆ P ketonization steps were found to decrease considerably when residues simulating enzymes were introduced into these processes. Although the processes became slightly more favorable thermodynamically when the solution was included in the simulations, they became less favorable kinetically. The results from SMD simulations of these reactions were qualitatively consistent with the values we obtained using QE as well as those found by other authors in similar studies. Our simulations also allowed us to perform a detailed study of these reactions in solution.

Gas-phase acidity and dynamics of the protonation processes of carbidopa and levodopa. A QM/QD study

The present work details, our efforts to investigate and compare the acid-base properties of levodopa (LD) and carbidopa (CD), a drug combination being used in the treatment of Parkinson's disease. Protonation and deprotonation were examined for all possible sites in the two drugs. Proton affinity and proton detachment enthalpies were computed at the B3LYP/6-311++G** level of theory. Results of the present work reveal that CD is more basic and can abstract protons in solution much more efficiently than LD. Furthermore, at all deportation sites considered, CD is more acidic than LD. DFT-based ADMP, dynamic simulations have been performed to explore the dynamics of the protonation processes in LD and CD. Thus, while the dynamics of the protonation process of LD is very straightforward leading to the formation of the corresponding cation, the protonation process in CD is very complex involving a major geometry change and rearrangement. Results of the present work reveal that the active species in acid medium is not CD in its normal geometry but a carbonyl hydrazine form instead. The presence of the carbonyl group β to the hydrazine group may very well underlie its enhanced activity which allows it to bind to the active site of the DDC enzyme. The relative stabilities of various water-water-CD complexes have been computed and compared.