Tautomerism in nucleic acid bases and base pairs: a brief overview

Tautomeric equilibrium and spectroscopic properties of 8-azaguanine revealed by quantum chemistry methods

8-azaguanine is a triazolopyrimidine nucleobase analog possessing potent antibacterial and antitumor activities, and it has been implicated as a lead molecule in cancer and malaria therapy. Its intrinsic fluorescence properties can be utilized for monitoring its interactions with biological polymers like proteins or nucleic acids. In order to better understand these interactions, it is important to know the tautomeric equilibrium of this compound. In this work, the tautomeric equilibrium of all natural neutral and anionic compound forms (except highly improbable imino-enol tautomers) as well as their methyl derivatives and ribosides was revealed by quantum chemistry methods. It was shown that, as expected, tautomers protonated at positions 1 and 9 dominate neutral forms both in gas phase and in aqueous solution. 8-azaguanines methylated at any position of the triazole ring are protonated at position 1. The computed vertical absorption and emission energies are in very good agreement with the experimental data. They confirm the validity of the assumption that replacing the proton with the methyl group does not significantly change the positions of absorption and fluorescence peaks.

DFT Meets Wave-Function Composite Methods for Characterizing Cytosine Tautomers in the Gas Phase

A general strategy for the accurate computation of structural and spectroscopic properties of biomolecule building blocks in the gas phase has been further improved and validated with a special reference to tautomeric equilibria. The main improvements concern the use of the cc-pVTZ-F12 basis set in both DFT and CCSD(T)-F12 computations, the inclusion of core-valence correlation in geometry optimizations by double hybrid functionals, and the use of the cc-pVQZ-F12 basis set for complete basis set extrapolation at the MP2-F12 level. The resulting model chemistry is applied to the challenging problem of cytosine tautomers in the gas phase. The results are in remarkable agreement with experiment concerning both rotational and vibrational spectroscopic parameters and permit their unbiased interpretation in terms of structural and thermochemical features. Together with the intrinsic interest of the studied molecule, the accuracy of the results obtained at reasonable cost without any empirical parameter suggests that the proposed composite method can be profitably employed for accurate investigations of other molecular bricks of life.

Tautomerism and Rotamerism of Favipiravir and Halogenated Analogues in Solution and in the Solid State

Favipiravir is an important selective antiviral against RNA-based viruses, and currently, it is being repurposed as a potential drug for the treatment of COVID-19. This type of chemical system presents different carboxamide-rotameric and hydroxyl-tautomeric states, which could be essential for interpreting its selective antiviral activity. Herein, the tautomeric 3-hydroxypyrazine/3-pyrazinone pair of favipiravir and its 6-substituted analogues, 6-Cl, 6-Br, 6-I, and 6-H, were fully investigated in solution and in the solid state through ultraviolet-visible, 1H nuclear magnetic resonance, infrared spectroscopy, and X-ray diffraction techniques. Also, a study of the gas phase was performed using density functional theory calculations. In general, the keto-enol balance in these 3-hydroxy-2-pyrazinecarboxamides is finely modulated by external and internal electrical variations via changes in solvent polarity or by replacement of substituents at position 6. The enol tautomer was prevalent in an apolar environment, whereas an increase in the level of the keto tautomer was favored by an increase in solvent polarity and, even moreso, with a strong hydrogen-donor solvent. Keto tautomerization was favored either in solution or in the solid state with a decrease in 6-substituent electronegativity as follows: H ≫ I ≈ Br > Cl ≥ F. Specific rotameric states based on carboxamide, "cisoide" and "transoide", were identified for the enol and keto tautomer, respectively; their rotamerism is dependent on the tautomerism and not the aggregation state.

Complementary base pair interactions between different rare tautomers of the second-generation artificial genetic alphabets

The functionality of a semisynthetic DNA in the biological environment will depend on the base pair nature of its complementary base pairs. To understand this, base pair interactions between complementary bases of recently proposed eight second-generation artificial nucleobases are studied herein by considering their rare tautomeric conformations and a dispersion-corrected density functional theoretic method. It is found that the binding energies of two hydrogen-bonded complementary base pairs are more negative than those of the three hydrogen-bonded base pairs. However, as the former base pairs are endothermic, the semisynthetic duplex DNA would involve the latter base pairs.

Prebiotic Synthesis and Isomerization in Interstellar Analog Ice: Glycinal, Acetamide, and Their Enol Tautomers

Glycinal (HCOCH₂ NH₂ ) and acetamide (CH₃ CONH₂ ) are simple molecular building blocks of biomolecules in prebiotic chemistry, though their origin on early Earth and formation in interstellar media remain a mystery. These molecules are formed with their tautomers in low temperature interstellar model ices upon interaction with simulated galactic cosmic rays. Glycinal and acetamide are accessed via barrierless radical-radical reactions of vinoxy (⋅CH₂ CHO) and acetyl (⋅C(O)CH₃ ), and then undergo keto-enol tautomerization. Exploiting tunable photoionization reflectron time-of-flight mass spectroscopy and photoionization efficiency (PIE) curves, these results demonstrate fundamental reaction pathways for the formation of complex organics through non-equilibrium ice reactions in cold molecular cloud environments. These molecules demonstrate an unconventional starting point for abiotic synthesis of organics relevant to contemporary biomolecules like polypeptides and cell membranes in deep space.

Charge Transfer and Electron Production in Proton Collisions with Uracil: A Classical and Semiclassical Study

Cross sections for charge transfer and ionization in proton-uracil collisions are studied, for collision energies 0.05<E<2500 keV, using two computational models. At low energies, below 20 keV, the charge transfer total cross section is calculated employing a semiclassical close-coupling expansion in terms of the electronic functions of the supermolecule (H-uracil)+. At energies above 20 keV, a classical-trajectory Monte Carlo method is employed. The cross sections for charge transfer at low energies have not been previously reported and have high values of the order of 40 Å2, and, at the highest energies of the present calculation, they show good agreement with the previous results. The classical-trajectory Monte Carlo calculation provides a charge transfer and electron production cross section in reasonable agreement with the available experiments. The individual molecular orbital contributions to the total electron production and charge transfer cross sections are analyzed in terms of their energies; this permits the extension of the results to other molecular targets, provided the values of the corresponding orbital energies are known.

Rare Tautomers of Artificially Expanded Genetic Letters and their Effects on the Base pair Stabilities

To expand the existing genetic letters, it is necessary to design robust nucleotides that can function naturally in living cells. Therefore, it is desirable to examine the roles of recently proposed second-generation artificially expanded genetic letters in producing stable duplex DNA. Here, a reliable dispersion-corrected density functional theory method is used to understand the electronic structures and properties of different rare tautomers of proposed expanded genetic letters and their effects on the base pair stabilities in the duplex DNA. It is found that the rare tautomers are not only stable in the aqueous medium but can also base pair with natural bases to produce stable mispairs. Except for J and V, all the artificial genetic letters are found to produce mispairs that are about 1-7 kcal/mol more stable than their complementary counterparts. They are also appreciably more stable than the naturally occurring G:C, A:T, and G:T pairs. The higher base pair stabilities are found to be mainly because of the polarity of monomers and attractive electrostatic interactions.

Unitary structure of palindromes in DNA

We investigate the quantum behavior encountered in palindromes within DNA structure. In particular, we reveal the unitary structure of usual palindromic sequences found in genomic DNAs of all living organisms, using the Schwinger's approach. We clearly demonstrate the role played by palindromic configurations with special emphasis on physical symmetries, in particular subsymmetries of unitary structure. We unveil the prominence of unitary structure in palindromic sequences in the sense that vitally significant information endowed within DNA could be transformed unchangeably in the process of transcription. We introduce a new symmetry relation, namely purine-purine or pyrimidine-pyrimidine symmetries (p-symmetry) in addition to the already known symmetry relation of purine-pyrimidine symmetries (pp-symmetry) given by Chargaff's rule. Therefore, important vital functions of a living organisms are protected by means of these symmetric features. It is understood that higher order palindromic sequences could be generated in terms of the basis of the highest prime numbers that make up the palindrome sequence number. We propose that violation of this unitary structure of palindromic sequences by means of our proposed symmetries leads to a mutation in DNA, which could offer a new perspective in the scientific studies on the origin and cause of mutation.

Impact of the Characteristics of Quantum Chemical Databases on Machine Learning Prediction of Tautomerization Energies

An essential aspect for adequate predictions of chemical properties by machine learning models is the database used for training them. However, studies that analyze how the content and structure of the databases used for training impact the prediction quality are scarce. In this work, we analyze and quantify the relationships learned by a machine learning model (Neural Network) trained on five different reference databases (QM9, PC9, ANI-1E, ANI-1, and ANI-1x) to predict tautomerization energies from molecules in Tautobase. For this, characteristics such as the number of heavy atoms in a molecule, number of atoms of a given element, bond composition, or initial geometry on the quality of the predictions are considered. The results indicate that training on a chemically diverse database is crucial for obtaining good results and also that conformational sampling can partly compensate for limited coverage of chemical diversity. The overall best-performing reference database (ANI-1x) performs on average by 1 kcal/mol better than PC9, which, however, contains about 2 orders of magnitude fewer reference structures. On the other hand, PC9 is chemically more diverse by a factor of ∼5 as quantified by the number of atom-in-molecule-based fragments (amons) it contains compared with the ANI family of databases. A quantitative measure for deficiencies is the Kullback-Leibler divergence between reference and target distributions. It is explicitly demonstrated that when certain types of bonds need to be covered in the target database (Tautobase) but are undersampled in the reference databases, the resulting predictions are poor. Examples of this include the poor performance of all databases analyzed to predict C(sp²)-C(sp²) double bonds close to heteroatoms and azoles containing N-N and N-O bonds. Analysis of the results with a Tree MAP algorithm provides deeper understanding of specific deficiencies in predicting tautomerization energies by the reference datasets due to inadequate coverage of chemical space. Capitalizing on this information can be used to either improve existing databases or generate new databases of sufficient diversity for a range of machine learning (ML) applications in chemistry.

Guanine Tautomerism in Ionic Complexes with Ag+ Investigated by IRMPD Spectroscopy and Mass Spectrometry

In this paper, we present the IRMPD spectra of three ionic complexes between guanine (G) and silver (Ag⁺): [GAg-H₂O]⁺, [GAgG]⁺ produced in the electrospray ionization source of the mass spectrometer, and [GAg]⁺ produced by collision induced dissociation of the [GAgG]⁺ complex. On the basis of the comparison of theoretically calculated IR spectra, we show that there are two isomers of each complex containing two different keto-amino (KA) tautomers of G (GKA(1,9) and GKA(1,7)). The observed isomers are the most stable structures in aqueous solution, and their experimentally estimated relative populations are in better agreement with the calculated relative populations in solution than in the gas phase, both at 298 K. We concluded that these observations suggest that GKA(1,9) and GKA(1,7) coexist in solution according to previous theoretical reports (Colominas, C.; et al. J. Am. Chem. Soc. 1996, 118, 6811). We were unable to find any evidence of the presence of the GEA(9), GKA(3,7), GKA(3,9), or GKA(7,9), whose relative stabilities in solution are strongly dependent on the theoretical method used to account for the solvent effect (Hanus, M.; et al. J. Am. Chem. Soc. 2003, 125, 7678).

On the Track of the Missing tRNA Genes: A Source of Non-Canonical Functions?

Cellular tRNAs appear today as a diverse population of informative macromolecules with conserved general elements ensuring essential common functions and different and distinctive features securing specific interactions and activities. Their differential expression and the variety of post-transcriptional modifications they are subject to, lead to the existence of complex repertoires of tRNA populations adjusted to defined cellular states. Despite the tRNA-coding genes redundancy in prokaryote and eukaryote genomes, it is surprising to note the absence of genes coding specific translational-active isoacceptors throughout the phylogeny. Through the analysis of different releases of tRNA databases, this review aims to provide a general summary about those “missing tRNA genes.” This absence refers to both tRNAs that are not encoded in the genome, as well as others that show critical sequence variations that would prevent their activity as canonical translation adaptor molecules. Notably, while a group of genes are universally missing, others are absent in particular kingdoms. Functional information available allows to hypothesize that the exclusion of isodecoding molecules would be linked to: 1) reduce ambiguities of signals that define the specificity of the interactions in which the tRNAs are involved; 2) ensure the adaptation of the translational apparatus to the cellular state; 3) divert particular tRNA variants from ribosomal protein synthesis to other cellular functions. This leads to consider the “missing tRNA genes” as a source of putative non-canonical tRNA functions and to broaden the concept of adapter molecules in ribosomal-dependent protein synthesis.

Computational estimation of the acidities of purines and indoles

Purines and related compounds are central ingredients in the genetic code and form the structural framework for many drugs and other bioactive compounds. A key feature of these compounds is their acidity, as expressed by their pK_a values. For a proper understanding of the behaviors of these compounds, it is important to have a theoretical means for estimating their acidities. Here we present a quantum-chemical quantitative structure-activity relationship (QSAR) study of these compounds aimed at estimating the aqueous pK_a values of purines and related compounds based on the energy differences in solution ΔE(H₂O) between the parent compounds and their dissociation products. This method was applied to both the cation → neutral (pK_a1) and neutral → anion (pK_a2) dissociations of the compounds. Computations were performed using density functional theory at the B3LYP/6-31 + G** level with the SM8 aqueous solvent model. Good-quality QSAR regression equations were obtained for both dissociations using the ΔE(H₂O) descriptor. These equations were applied to estimate missing pK_a values for compounds in this category, and should also be applicable to the acidities of other related heterocyclic compounds.

DNA Polymerase λ Active Site Favors a Mutagenic Mispair between the Enol Form of Deoxyguanosine Triphosphate Substrate and the Keto Form of Thymidine Template: A Free Energy Perturbation Study

Human DNA polymerase λ is an intermediate fidelity member of the X family, which plays a role in DNA repair. Recent X-ray diffraction structures of a ternary complex of a loop-deletion mutant of polymerase λ, a deoxyguanosine triphosphate analogue, and a gapped DNA show that guanine and thymine form a mutagenic mispair with an unexpected Watson-Crick-like geometry rather than a wobble geometry. Hence, there is an intriguing possibility that either thymine in the DNA or guanine in the deoxyguanosine triphosphate analogue may spend a substantial fraction of time in a deprotonated or enol form (both are minor species in aqueous solution) in the active site of the polymerase λ mutant. The experiments do not determine particular forms of the nucleobases that contribute to this mutagenic mispair. Thus, we investigate the thermodynamics of formation of various mispairs between guanine and thymine in the ternary complex at a neutral pH using classical molecular dynamics simulations and the free energy perturbation method. Our free energy calculations, as well as a comparison of the experimental and computed structures of mispairs, indicate that the Watson-Crick-like mispair between the enol tautomer of guanine and the keto tautomer of thymine is dominant. The wobble mispair between the keto forms of guanine and thymine and the Watson-Crick-like mispair between the keto tautomer of guanine and the enol tautomer of thymine are less prevalent, and mispairs that involve deprotonated guanine or thymine are thermodynamically unlikely. These findings are consistent with the experiment and relevant for understanding mechanisms of spontaneous mutagenesis.

Watson-Crick-like pairs in CCUG repeats: evidence for tautomeric shifts or protonation

RNA transcripts that include expanded CCUG repeats are associated with myotonic dystrophy type 2. Crystal structures of two CCUG-containing oligomers show that the RNA strands associate into slipped duplexes that contain noncanonical C-U pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual Watson-Crick-like pairing. The overhanging ends of the duplexes interact forming U-U pairs, which also show tautomerism. Duplexes consisting of CCUG repeats are thermodynamically less stable than the trinucleotide repeats involved in the TRED genetic disorders, but introducing LNA residues increases their stability and raises the melting temperature of the studied oligomers by ∼10°C, allowing detailed crystallographic studies. Quantum mechanical calculations were performed to test the possibility of the tautomeric transitions or protonation within the noncanonical pairs. The results indicate that tautomeric or ionic shifts of nucleobases can manifest themselves in biological systems, supplementing the canonical "rules of engagement."