Hydration and stability of nucleic acid bases and base pairs

Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.     

Investigation of the tautomeric equilibrium of nucleic acid bases in aqueous solution

Relative constants of acidity and basicity of nucleic acid bases (NABs) and their tautomeric forms are calculated. The general characteristic of the effect of an aqueous solvent on the tautomeric equilibrium of NABs is formulated. It is shown that during the tautomeric transformation of NABs their acid-base properties change to the opposite ones. One of possible causes of the formation of complementary pairs with rare tautomeric forms of NABs is considered.     

Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels

The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the adenine-thymine pairs is straightforward, and tautomeric pairs are significantly less stable than the Watson-Crick pair consisting of the canonical forms. In the case of the guanine-cytosine pair, the Watson-Crick structure made by canonical forms is again the most stable. The other two structures are, however, energetically rather similar (by 5 and 6 kcal/mol), which provides a very small but non-negligible chance of detecting these structures in the DNA double helix (1:5000). Due to the fact that DNA bases and base pairs incorporated into DNA are solvated less favorably than in isolated systems, this probability represents the very upper limit. The results clearly show how precisely the canonical building blocks of DNA molecules were chosen and how well their stability is maintained.     

Some remarks about nucleic bases

The CNDO/2 method was used to compare total energies and dipolar moments for the DNA bases in their normal and tautomeric forms.The shape of the barriers between normal and tautomeric forms is also estimated for all the bases.     

Tautomeric equilibria of 5-fluorouracil anionic species in water

It has long been postulated that rare tautomeric or ionized forms of nucleic acid bases may play a role in mispair formation. Therefore, ab initio quantum chemical investigations on the tautomeric equilibrium in 5-fluorouracil (5FU) and its anions (deprotonated from N1, AN1, and from N3, AN3) and their tautomeric forms in water were performed. The effect of the water as solvent was introduced using solute-solvent clusters (four water molecules). The influence of the water molecules on the tautomeric reactions between different forms was considered by multiple proton transfer mechanisms. We show that when a water dimer is located in the reaction site between the two pairs of N-H and C═O groups, the assistive effect of the water molecules is strengthened. All calculations of the solute-water complexes were carried out at an MP2 level of theory and supplemented with correction for higher order correlation terms at CCSD(T) level, using the 6-31+G(d,p) basis set. The ab initio calculated frequencies and Raman intensities of 5FU and its anions AN1, AN3, and dianion are in good agreement with the experimental Raman frequencies in aqueous solution at different pH. In order to establish the pH-induced structural transformation in the molecule of 5FU, further (1)H, (19)F, and (13)C NMR spectra in water solution for pH = 6.9-13.8 were acquired and the chemical shift alterations were determined as a function of pH. On the basis of NMR spectroscopic data obtained for 5FU in aqueous solution at alkaline pH, we suggest the existence of a mixture of the anionic tautomeric forms predicted by our theoretical calculations.     

pi-Stacked quadruply hydrogen-bonded dimers: pi-stacking influences H-bonding

[reaction: see text] The effects of pi-stacking on the stability of multiply hydrogen-bonded systems are investigated using hybrid DFT calculations on pi-stacked quadruply H-bonded dimers of ureidopyrimidinone in its different tautomeric forms. Both the strengths of the hydrogen bonds and the relative occurrence of tautomers are influenced by pi-stacking; electrostatics and natural bond orbital analysis are used to explain these observations. Finally, these conclusions are independent of the precise nature of the multiply hydrogen-bonded systems, including the DNA base pairs.     

Investigation of the structure of and the properties of the potentially tautomeric 1,2,3,4-tetrahydro-5,7-dimethyl-6H-pyrrolo[3,4-d]pyridazine-1,4-diones in the gaseous and aqueous phases using the AM1 semi-empirical method

Potentially tautomeric 1,2,3,4-tetrahydro-5,7-dimethyl-6H-pyrrolo[3,4-d]pyridazine-1,4-diones and their fixed tautomeric forms have been studied in order to predict their tautomeric equilibrium constants and pK_a values using semi-empirical AM1 quantum-chemical calculations at the SCF level in the gas phase and in aqueous solution. Hydroxy-oxo forms were found to be more stable than dioxo and dihydroxy forms. The results obtained from the tautomeric equilibria and basicity calculations are in good agreement with experimental data.     

A study of the possible and preferred site of protonation in 7-methyl-1,5,7-triazabicyclo[4,4,0]dec-5-ene by vibrational spectroscopic methods

The normal co-ordinate analysis have been carried out for 7-methyl-1,5,7-triazabicyclo[4,4,0]dec-5-ene (MTBD) and its three possible protonated tautomeric forms. The calculations and measured infrared (IR) spectra are consistent with a tautomeric species in which the proton is attached to an imine nitrogen atom.     

Recognition tunneling measurement of the conductance of DNA bases embedded in self-assembled monolayers

The DNA bases interact strongly with gold electrodes, complicating efforts to measure the tunneling conductance through hydrogen-bonded Watson Crick base pairs. When bases are embedded in a self-assembled alkane-thiol monolayer to minimize these interactions, new features appear in the tunneling data. These new features track the predictions of density-functional calculations quite well, suggesting that they reflect tunnel conductance through hydrogen-bonded base pairs.     

Investigation of the structure of and the properties of the potentially tautomeric 1,2,3,4-tetrahydro-5,7-dimethyl-6H-pyrrolo[3,4-d]pyridazine-1,4-diones in the gaseous and aqueous phases using the AM1 semi-empirical method

Potentially tautomeric 1,2,3,4-tetrahydro-5,7-dimethyl-6H-pyrrolo[3,4-d]pyridazine-1,4-diones and their fixed tautomeric forms have been studied in order to predict their tautomeric equilibrium constants and pK_a values using semi-empirical AM1 quantum-chemical calculations at the SCF level in the gas phase and in aqueous solution. Hydroxy-oxo forms were found to be more stable than dioxo and dihydroxy forms. The results obtained from the tautomeric equilibria and basicity calculations are in good agreement with experimental data.     

Vibrational dynamics of DNA. I. Vibrational basis modes and couplings

Carrying out density functional theory calculations of four DNA bases, base derivatives, Watson-Crick (WC) base pairs, and multiple-layer base pair stacks, we studied vibrational dynamics of delocalized modes with frequency ranging from 1400 to 1800 cm(-1). These modes have been found to be highly sensitive to structure fluctuation and base pair conformation of DNA. By identifying eight fundamental basis modes, it is shown that the normal modes of base pairs and multilayer base pair stacks can be described by linear combinations of these vibrational basis modes. By using the Hessian matrix reconstruction method, vibrational coupling constants between the basis modes are determined for WC base pairs and multilayer systems and are found to be most strongly affected by the hydrogen bonding interaction between bases. It is also found that the propeller twist and buckle motions do not strongly affect vibrational couplings and basis mode frequencies. Numerically simulated IR spectra of guanine-cytosine and adenine-thymine bases pairs as well as of multilayer base pair stacks are presented and described in terms of coupled basis modes. It turns out that, due to the small interlayer base-base vibrational interactions, the IR absorption spectrum of multilayer base pair system does not strongly depend on the number of base pairs.     

Thin‐Film Properties of DNA and RNA Bases: A Combined Experimental and Theoretical Study

The structures of the DNA and RNA bases cytosine, uracil, and thymine in thin films with a nominal film thickness of about 20 nm are studied by using X‐ray photoemission spectroscopy (XPS) and Fourier‐transform infrared spectroscopy. The molecules are evaporated in situ from powder on a gold foil. The experimental results indicate that cytosine is composed of two energetically close tautomeric forms, whereas uracil and thymine exist in only one tautomeric form. Additionally, quantum chemical calculations are performed to complement the experimental results. The relative energies of the tautomeric forms of cytosine, uracil, and thymine are calculated using Hartree–Fock (HF), density functional theory (DFT), and post‐HF methods. Furthermore, the assignment of the XPS spectra is supported by using simple model considerations employing Koopmans ionization energies and Mulliken net atomic charges.     

Replication Experiments with Nucleotide Base Analogues

The principles governing the replication fidelity of genomes are not fully understood yet. Watson and Crick's base-pairing principle for matched deoxyribonucleotide (DNA) bases can explain why the guanine–cytosine and adenine-thymine base pairs are approximately one hundred times more stable thermodynamically than mismatched combinations. In vitro, DNA polymerases reduce the number of mismatched base pairs to about 10^?6 per Watson–Crick base pair. Replication fidelity can further be enhanced to a mutation probability of 10^?10or less in vivo if optimal conditions for DNA synthesis are provided by polymerase–assisting proteins and DNA-repairing enzymes. The precise reasons for the formation of mismatched base pairs (mispairs), which are responsible for a substantial part of DNA mutations, are still in debate. Although it is agreed that a template-directed “reading” of the hydrogen-substitution pattern in the heterocyclic bases is crucial for proper base pairing during DNA synthesis, it is not clear which type of “misreading” leads to mispairs. Misreading may be due to a non-Watson–Crick base pairing as well as to a change in the hydrogen-substitution pattern, leading to Watson-Crick-like mispairs. The surprising discovery of the selective and quantitative DNA-polymerase-catalyzed formation of a pyridine-pyrimidine base pair (involving a nucleotide base analogue) indicated that rare tautomeric forms in template DNA strands can lead to Watson-Crick-like mispairings that are hardly recognized by the polymerase's proofreading activity. This reveals new pathways for substitution mutations (replication-dependent DNA point mutations) and suggests a new type of mutagen in vivo.     

A TDDFT study of the excited states of DNA bases and their assemblies

We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional. Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and pi-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.     

CP/MAS spectroscopy in the determination of the tautomeric forms of gossypol, its Schiff bases and hydrazones in the solid state

New Schiff bases and new hydrazones were synthesized and studied by (13)C and (15)N CP/MAS spectroscopy and by (1)H--(1)H COSY, (1)H--(13)C HMBC, (1)H--(13)C HSQC, (1)H--(15)N HMQC and (1)H--(15)N HSQC correlations. The CP/MAS investigation of gossypol has demonstrated that in the solid state it exists exclusively in the aldehyde-aldehyde tautomeric form. In contrast, CP/MAS studies of hydrazones and Schiff bases reveal that these compounds occur in the solid state in the N-imine-N-imine and enamine-enamine tautomeric forms, respectively. It is shown that the (13)C resonances of C-6, C-7 and C-11 carbon atoms are suitable for distinguishing between the tautomeric forms of aza-derivatives of gossypol in the solid state. Furthermore, we have proved that the (15)N CP/MAS spectra can be used to identify these tautomeric forms.     

Tautomerism of xanthine and alloxanthine: A model for substrate recognition by xanthine oxidase

Summary Tautomerism of neutral xanthine and alloxanthine has been examined both in the gas phase and in aqueous solution. The tautomeric preference in the gas phase has been studied by means of semiempirical and ab initio quantum-mechanical computations with inclusion of correlation effects at the Møller-Plesset level, and from density-functional calculations. The influence of solvent on the relative stability between tautomers has been estimated from self-consistent reaction field calculations performed with different models. The results provide a detailed picture of tautomerism for these biologically relevant purine bases. The functional implications in the recognition by xanthine oxidase are analyzed from inspection of the interaction patterns of the most stable tautomeric forms. A model for the recognition of these purine derivatives in the enzyme binding site is discussed.     

Syntheses and structural studies of Schiff bases involving hydrogen bonds

New Schiff bases have been prepared by reacting 3-hydroxy-4-pyridine- carboxaldehyde with various amines. NMR spectroscopic methods provided clear evidence that the Schiff bases exist in the solid state and in solution as hydroxyimino tautomers with the E-configuration. A study of the stabilities of the tautomeric forms and the different conformers has been carried out using density functional calculations at the B3LYP/6-31G** level.     

Benzoderivatives of nucleic acid bases as modified DNA building blocks

The tautomeric properties of benzoderivatives of the canonical nucleic acid bases have been studied by using different computational approaches. Attention has been paid to the impact of the benzene group in altering the tautomeric preferences of the canonical bases both in the gas phase and in aqueous solution. To this end, relative solvation free energies of the tautomers determined from Self-Consistent Reaction Field continuum calculations and Monte Carlo-Free Energy Perturbation are combined with gas-phase tautomerization free energies determined from quantum mechanical calculations. The results provide a detailed picture of the tautomeric preferences of the benzoderivatives of nucleic acid bases. This information is used to examine the recognition properties of the preferred tautomers of the benzo-fused derivatives, paying particular attention to the ability to form Watson-Crick hydrogen-bonding and stacking interactions as well as to the hydrophobic nature of the modified bases. The implications of present results on the potential use of benzo-fused bases as potential building blocks in modified DNA duplexes are examined.     

Tautomerism of pyrimidines and purines in the gas phase and in low-temperature matrices,and some biological implications

Infrared spectra in the NH, OH, and C?O stretching regions are reviewed for various methylated and halogenated 2(4)-oxopyrimidines and uracils, as well as other nucleic acid derivatives, in the vapor phase and in low-temperature matrices. The 2-oxopyrimidines are predominantly in the enol form both in the vapor phase and in low-temperature matrices. By contrast, the 4-oxopyrimidines exhibit comparable populations of the keto and enol forms, with K_T ≈ 1–2, and a difference in chemical binding energy between the two forms in the gaseous phase of the order of 1–2 kcal/mol. The observed tautomeric equilibria in the gas phase point to the need for a drastic revision of interpretations of theoretical methods, and simultaneously provide the appropriate quantitative data necessary for testing the results of quantum mechanical calculations. In sharp contrast to other heterocyclic systems, several of the bases found in natural nucleic acids were found to exist predominantly in the keto or amino forms, as in the solution phase. In particular, uracils exist predominantly in the keto form. This has made possible, for this class of compounds, to evaluate the heats of sublimation and vaporization, and to relate these data to hydrogen bonding and stacking interactions in the condensed phases. Examples are presented of base analogs which do exhibit appreciable tautomerism in solution. Some biological implications of the foregoing are presented in relation to the types of heterocyclic bases found in natural nucleic acids, and to concepts of spontaneous and induced mutagenesis.     

Electronic Structures and Spectra of the Bases and Base Pairs of Nucleic Acids

The present paper covers electronic structures and spectra of the bases and the base pairs of nucleic acids calculated by using the INDO/S method. For free bases we give the energy levels of ground states and transition energies of low-lying excited states and discuss the band characters. The results indicate that the calculated spectra are in good agreement with experimental values. On the other hand, our calculations for A-T and G-C pairs are very beneficial to understanding hydrogen bond properties of these pairs.