On tautomerism of the cytosine molecule

Tautomerism of the cytosine molecule is discussed in connection with recent experimental matrix-isolation infrared spectroscopic measurements and recent ab initio calculations of relative stabilities of tautomers and of IR spectra for different tautomeric forms of the compound. Experimental IR spectra in the N-H and O-H stretching regions and in the C = O stretching region are presented for cytosine and for its several derivatives considered as model compounds. This experimental evidence, as well as the quantum-mechanical calculations (including both electron correlation and zero-point vibrational contributions), clearly indicate that two tautomers of cytosine, i.e. the amino-hydroxy and amino-oxo forms with the hydrogen atom at the N(1) position, exist in equilibrium when the cytosine molecule is isolated in an inert environment. The effect of the environment on the relative stabilities of several tautomers is also discussed briefly.     

Role of tautomerism in RNA biochemistry

Heterocyclic nucleic acid bases and their analogs can adopt multiple tautomeric forms due to the presence of multiple solvent-exchangeable protons. In DNA, spontaneous formation of minor tautomers has been speculated to contribute to mutagenic mispairings during DNA replication, whereas in RNA, minor tautomeric forms have been proposed to enhance the structural and functional diversity of RNA enzymes and aptamers. This review summarizes the role of tautomerism in RNA biochemistry, specifically focusing on the role of tautomerism in catalysis of small self-cleaving ribozymes and recognition of ligand analogs by riboswitches. Considering that the presence of multiple tautomers of nucleic acid bases is a rare occurrence, and that tautomers typically interconvert on a fast time scale, methods for studying rapid tautomerism in the context of nucleic acids under biologically relevant aqueous conditions are also discussed.     

Tautomeric energetics of xanthine oxidase substrates: xanthine, 2-oxo-6-methylpurine, and lumazine

The stability of the tautomers of each of the three important substrates of xanthine oxidase, xanthine, 2-oxo-6-methylpurine, and lumazine, was examined by quantum mechanical calculations. The geometries of these tautomers were optimized at the AM1, Hartree-Fock (HF/6-31G), and hybrid Hartree-Fock/density functional theory (B3LYP/6-31G(d)) levels of theory. The single point energies of some of the more stable tautomers for each of the substrates were calculated at the B3LYP/6-311 +G(2d,p) level of theory. The Conductor Polarized Continuum Model (CPCM) was used to evaluate the solvent effects on the relative stabilities of these tautomers. The calculations clearly identify the lowest energy tautomeric form for xanthine and lumazine. On the other hand, there appear to be three tautomers for 2-oxo-6-methylpurine, with only minor energetic differences in vacuo. In water, however, only one of them predominates. The lowest energy tautomers presumably represent the predominant tautomeric forms at the molybdenum center of xanthine oxidase during catalysis. Implications of these computational results are discussed in the context of enzyme catalysis.     

Electronic structure and polarizabilities of some heterocycles: I. Hydroxypyrazoles and related systems

The (hyper)polarizabilities of different tautomer forms of hydroxypyrazoles and pyrazolones have been calculated by the finite-field procedure in the MNDO approximation and the sum of states formalism in the PPP approximation, with all singly- and doubly-excited electronic configurations in the CI method. It was shown that while in the ground electronic state the values of the (hyper) polarizabilities are not essentially different, in the first excited singlet Franck-Condon state an increase of the molecular polarizabilities of some tautomers is observed. This increase is attributed to a specific change in the electronic structure of the excited state, demonstrated by the localization of the electronic transition in the different pyrazolone tautomers. The electron-donor capabilities of phenyl-substituted hydroxypyrazoles and pyrazolones are discussed.     

Watersoluble synthetic nucleic acid analogs--polyethyleneimine derivatives containing nucleic acid bases--conformation and interactionwith nucleic acids

Water soluble polyethyleneimine derivatives containing nucleic acid bases were found to interact with polynucleotides, DNA, RNA. The conformational change by formation of complex was observed by CD spectra and was discussed with the hypochromicity in UV spectra. The rates of interactions between nucleic acid bases in polymers were slow as shown by UV spectra, but the conformational changes of the polynucleotides were fast as shown by CD spectra. In the case of the uracil derivative (PEI-Hse-Ura), high value of CD spectra [theta] 2.80 = -8.0 x 10(-4) for the complex with DNA might be caused by psi type conformation of DNA.     

Can DNA-binding proteins of replisome tautomerize nucleotide bases? Ab initio model study

Ab initio quantum-chemical study of specific point contacts of replisome proteins with DNA modeled by acetic acid with canonical and mutagenic tautomers of DNA bases methylated at the glycosidic nitrogen atoms was performed in vacuo and continuum with a low dielectric constant (??～?4) corresponding to a hydrophobic interface of protein-nucleic acid interaction. All tautomerized complexes were found to be dynamically unstable, because the electronic energies of their back-reaction barriers do not exceed zero-point vibrational energies associated with the vibrational modes whose harmonic vibrational frequencies become imaginary in the transition states of the tautomerization reaction. Additionally, based on the physicochemical arguments, it was demonstrated that the effects of biomolecular environment cannot ensure dynamic stabilization. This result allows suggesting that hypothetically generated by DNA-binding proteins of replisome rare tautomers will have no impact on the total spontaneous mutation due to the low reverse barrier allowing a quick return to the canonical form.     

Nucleic acid-metal interactions: V. The effect of silver(I) on the structures of A- and B-DNA forms

The interaction of silver(I) with DNA has been studied with uv LD in aqueous solution and in a humid anisotropic poly(vinyl alcohol) host (B-DNA) and also in 80% ethanolic solution (A-DNA). Addition of silver ions has a pronounced effect on the dichroic spectra of DNA, indicating that the DNA structure is significantly altered. By correlation with calculated reduced LD spectra, using intensities and moments of the corresponding electronic transitions of the DNA bases, the experimental spectra of DNA at high silver content may be interpreted in terms of tilt and roll angles of the bases in the double helix. In ethanolic A-DNA solution there is a pronounced decrease in the orientation by flow of DNA, suggesting that the complexation of DNA to silver may be accompanied by the formation of compact tertiary structures.     

The interactions of square platinum(II) complexes with guanine and adenine: a quantum-chemical ab initio study of metalated tautomeric forms

The influence of binding of square planar platinum complexes on tautomeric equilibria of the DNA bases guanine and adenine was investigated using the density functional B3LYP method. Neutral trans-dichloro(amine)-, +1 charged chloro(diamine)-, and +2 charged triamine-platinum(II) species were chosen for coordination to bases. Only the N₇ interaction site of the bases was considered. The calculations demonstrate that the neutral platinum adduct does not change the tautomeric equilibria of the bases. Furthermore, N₇ binding of the neutral Pt adduct moderately reduces the probability of protonation of the N₁ position of adenine. Larger effects can be observed for +1 and mainly +2 adducts, but these can be rationalized by electrostatic effects. Since the electrostatic effects are expected to be efficiently compensated for by a charged backbone of DNA and counterions in a polar solvent, no dramatic increase in mispair formation is predicted for Pt(II) adducts, which is in agreement with experiment. The interaction energies between Pt adducts and the nucleobases were also evaluated. These interaction energies range from ca. 210 kJ/mol for neutral adducts, interacting with both bases and their tautomers, up to 500 kJ/mol for the +2 charged adducts, interacting with the keto-guanine tautomer and the anti-imino-adenine tautomer. The surprisingly large interaction energy for the latter structure is due to the strong H-bond between the NH₃ ligand group of the metal adduct and the N₆ nitrogen atom of the base. Received: 6 July 1999 / Accepted: 7 December 1999     

Structure and redox properties of radicals derived from one-electron oxidised methylxanthines

The repair of the one electron oxidised form of a xanthine derivative by another xanthine derivative was studied by reacting aqueous binary mixtures of xanthine derivatives with sulphate radical anion (SO(4)( -)) and following the concentration of both compounds as a function of time. The relative behaviour observed enabled the establishment of a qualitative order of antioxidant capacities for the several xanthines studied in acidic and neutral media. The same order was confirmed quantitatively by measuring the reduction potentials of the xanthines by cyclic voltammetry. Theoretical DFT calculations were used to calculate the relative stabilities of the tautomers of each xanthine neutral radical. It was also demonstrated that the deprotonation of a xanthine radical cation never occurs from N1, unless no other possibility is available. At high pH values, it was possible to obtain the ESR spectra of the radical anions derived from 1-methylxanthine, 3-methylxanthine and xanthosine. The theoretical calculations also enabled the assignment of the ESR hyperfine coupling constants of the spectra of these radical anions. The coupling constants calculated are in good agreement with the experimental values.     

Electronic spectra for nitrosyl(protoporphyrin IX dimethyl ester)iron(II) and its complexes with nitrogenous bases as model systems for nitrosylhemoproteins

Soret and visible absorption spectra for nitrosyl(protoporphyrin IX dimethyl ester)iron(II) (Fe(PPIXDME)(NO] and its complexes with nitrogenous bases (imidazoles, pyridines, aliphatic amines, and cyclic secondary amines) as model systems for nitrosylhemoproteins have been measured in various solvents. As the solvent polarity increases, the Soret and visible absorption bands for the five-coordinate Fe(PPIXDME) (NO) were shifted to shorter wavelengths. Accompanying the coordination of a nitrogenous base to the vacant axial position of Fe(PPIXDME)(NO), the Soret band becomes sharp and the band maximum is shifted to longer wavelengths. The band positions for the six-coordinate Fe(PPIXDME)(NO)(Base) complex are not sensitive to the pi-bonding ability of the axial ligand trans to NO group. The electronic spectra of five-coordinate Fe(PPIXDME)(NO) and six-coordinate Fe(PPIXDME)(NO)(Base) complexes are interpreted in relation to the structural information. The comparison of the spectra for model systems with those for nitrosylhemoproteins is discussed.     

Synthesis and properties of oligonucleotides containing 2''-deoxynebularine and 2''-deoxyxanthosine.

The preparation of synthetic oligonucleotides containing 2'-deoxynebularine (dN) and 2'-deoxyxanthosine (dX) is described. The thermal stabilities of duplexes containing dX, dN, and 2'-deoxyinosine (dI) base-paired with the four natural bases have been measured. Xanthine base pairs have stabilities at pH 5.5 that are similar to those of dI-containing duplexes at neutral pH. When xanthine is paired with adenine or cytosine an unusual stabilization of the duplex structure is observed at acid pH. Incorporation of base mispairs opposite template xanthine sites were measured using Drosophila DNA polymerase alpha. The relative nucleoside incorporation rates are in the order: T greater than C much greater than A approximately equal to G. These rates do not correlate with relative thermodynamic stabilities of base mispairs with xanthine obtained from Tm measurements: T greater than G greater than A approximately equal to C. We suggest that DNA polymerase misinsertion rates are greatest when the base mispair can be formed in accordance with Watson-Crick as opposed to other base pairing geometries even though other geometries, e.g. wobble, may result in a more stable final DNA product.     

DFT and MP2 study of low barrier proton transfer in hydrazide schiff base tautomers via water bridges and in the gas

MP2 and DFT studies were performed on the tautomers of N′-ethylideneacetohydrazide in different environments including gas phase, continuum solvent and microhydrated environment. The ground electronic state structures of the tautomers were optimized at the MP2 and B3LYP levels of theory using 6-311++G(d,p), separately. The optimized geometries of the transition states of different tautomerism processes, which occur through the proton transfer (PT) reaction, were determined using the QST3 approach at the same levels of theory. The same stability order as T1Z〉 T1E〉 T2ZE〉 T2ZZ〉 T2EE〉 T2EZ〉 T6〉 T4E was found for the tautomers in the gas phase, continuum solvent and microhydrated environment for both B3LYP and MP2 levels of theory. In addition, the variations of the Gibbs free energies of tautomeric processes, the activation Gibbs free energies of the forward and reverse tautomeric processes with the polarity of the solvent (in continuum solvent model) and the number of water molecules (in microhydrated environment) were investigated. It was found that the reverse tautomeric process is more favorable in all considered environments thermodynamically and kinetically. In addition, it was shown that the rate constants of the reverse and forward considered tautomeric processes decrease with the solvent polarity in the continuum solvent model and the process becomes more difficult than the gas phase. The opposite trend is seen in the microhydrated environment.     

Application of capillary gas chromatography-mass spectrometry to chemical characterization of radiation-induced base damage of DNA: implications for assessing DNA repair processes

The application of capillary gas chromatography-mass spectrometry (GC-MS) to the chemical characterization of radiation-induced base products of calf thymus DNA is presented. Samples of calf thymus DNA irradiated in N2O-saturated aqueous solution were hydrolyzed with HCOOH, trimethylsilylated, and subjected to GC-MS analysis using a fused-silica capillary column. Hydrolysis conditions suitable for the simultaneous analysis of the radiation-induced products of all four DNA bases in a single run were determined. The trimethylsilyl derivatives of these products had excellent GC properties and easily interpretable mass spectra; an intense molecular ion (M+.) and a characteristic (M-CH3)+ ion were observed. The complementary use of t-butyldimethylsilyl derivatives was also demonstrated. These derivatives provided an intense characteristic (M-57)+ ion, which appeared as either the base peak or the second most intense ion in the spectra. All mass spectra obtained are discussed. Because of the excellent resolving power of capillary GC and the accurate high-sensitivity identification by MS, the capillary GC-MS is suggested as a very suitable technique for identification of altered bases removed from DNA by base excision-repair enzymes such as DNA glycosylases and, thus, as very useful for an understanding of the base excision-repair of DNA.     

Luminescence of stable stacking aggregates of adenine and uracil in water

Luminescence and excitation spectra of the highly luminescent stacking dimers of adenine and uracil in water solutions are studied. By the luminescence excitation spectra, it is shown that the stacking aggregates of adenine and uracil are formed with participation of rare forms of monomers: adenine N7H tautomers, and uracil in uncommon hydration states, e.g. lacking H-bonds with water. The temperature dependence of luminescence intensity of monomers and stacking dimers of uracil shows that stacking dimers do not dissociate even at 85°C, just as described earlier for adenine and adenosine. Stable stacking aggregates of nucleic bases are the likely precursors of RNA molecules in chemical evolution. This hypothesis is supported by new data on their heat stability.     

Cisplatin adducts in DNA: distortion and recognition

 cis-Diamminedichloroplatinum (II) (cisplatin) and derivatives are very successful anticancer chemotherapeutic agents. They crosslink cellular DNA, forming bifunctional adducts with the N7 of guanine bases. In this review, recent structures of cisplatin adducts are summarised, and the significance for the recognition of DNA structure by proteins is discussed. Two new structures of intrastrand GpG adducts have been presented, showing a significant kinking of the helix axis and a novel hybrid A-B helical geometry. The relevance of this structure to the recognition of HMG-box and related proteins is discussed. A new structure of a cross-strand cisplatin adduct reveals a major disruption of the local DNA structure. The basepairs containing the modified guanine bases are broken, with extrusion of the cytosine bases into the solvent. The backbone reverses direction locally, with the result that the platinum adduct is located in what is the minor groove of the DNA overall. The extrusion of single bases out of the helix is strongly reminiscent of the effect of certain methylases on their DNA targets. Received: 30 January 1996 / Accepted: 21 February 1996     

Infrared and electron paramagnetic resonance study of nitrosyl(protoporphyrin IX dimethyl ester)iron(II) and its complexes with nitrogenous bases as model systems for nitrosylhemoproteins: effect of solvent polarity

Infrared and electron paramagnetic resonance spectra of nitrosyl(protoporphyrin IX dimethyl ester)iron(II)(Fe(PPDME)(NO)) and its complexes with nitrogenous bases (N bases) such as imidazoles, pyridines, aliphatic amines, and anilines have been measured in various solvents. At room temperature, giso, Aiso, and nu NO values of five-coordinate Fe(PPDME)(NO) decreased with an increase in solvent polarity parameter ET, indicating the interaction between the solvent and the vacant axial coordination position. It has been found that the nu NO value of six-coordinate species is very sensitive to the solvent polarity, while the giso value is less sensitive. The solvent effect on the equilibrium constants, which are evaluated from the intensity change of the NO stretching band for five- and six-coordinate species, is discussed.     

Luminescence of stable stacking aggregates of adenine and uracil in water

Luminescence and excitation spectra of the highly luminescent stacking dimers of adenine and uracil in water solutions are studied. By the luminescence excitation spectra method it is shown that the stacking aggregates of adenine and uracil are formed with participation of rare forms of monomer molecules: N7H tautomers of adenine and the uracil molecules in rare forms of hydratation, for example molecules without H-bonds with water. The study of temperature dependence of luminescence intensity of monomers and stacking dimers of uracil has shown that stacking dimers do not dissociate even at 85 degrees C similarly as described earlier for adenine and adenosine. Stable stacking aggregates of nucleic bases are most likely to be the precursors of RNA molecules in chemical evolution. This hypothesis is supported by new data on their stability.     

Quantum chemical investigation of intramolecular thione-thiol tautomerism of 1,2,4-triazole-3-thione and its disubstituted derivatives

The one step intramolecular thione-thiol tautomerism of 1,2,4-triazole-3-thione and its disubstituted derivatives has been studied through the use of electronic structure methods. Due to the absence of experimental data for the parent molecule of 1,2,4-triazole-3-thione the structure and energetics of aforementioned tautomers were derived using various basis sets and levels including HF, B3LYP, and MP2 methods. The gas phase results show that in all different levels of theory the most stable tautomer is the thione form. It has also been revealed that B3LYP/6-31G(d,p) level is quite well suited and reliable to investigate these kinds of tautomerism. To account the influence of substituents on the mentioned tautomerization, the tautomerism and conformational properties as well as vibrational analysis of 20 halophenyl and isopyridyl derivatives were investigated using B3LYP/6-31G(d,p) calculations. In all cases the calculations indicate that substituents have no considerable effects on relative stabilities and energy barriers for the thione-thiol proton transfer and the thione forms are the predominant species in the gas phase. In order to figure out the relative stabilities of the species involved in the tautomerism, geometrical and natural bond orbital (NBO) analyses have been employed. It has also been shown that the computed vibrational frequencies of tautomers with different scaling factors could be used to interpret the vibrational frequencies in IR spectrum of similar species.     

Potential of mean force calculations of the stacking-unstacking process in single-stranded deoxyribodinucleoside monophosphates.

The free energy of the stacking-unstacking process of deoxyribodinucleoside monophosphates in aqueous solution has been investigated by potential of mean force calculations along a reaction coordinate, defined by the distance between the glycosidic nitrogen atoms of the bases. The stacking-unstacking process of a ribodinucleoside monophosphate was observed to be well characterized by this coordinate, which has the advantage that it allows for a dynamical backbone and flexible bases. All 16 naturally occurring DNA dimers composed of the adenine, cytosine, guanine, or thymine bases in both the 5' and the 3' positions were studied. From the free-energy profiles we observed the deepest minima for the stacked states of the purine-purine dimers, but good stacking was also observed for the purine-pyrimidine and pyrimidine-purine dimers. Substantial stacking ability was found for the dimers composed of a thymine base and a purine base and also for the deoxythymidylyl-3',5'-deoxythymidine dimer. Very poor stacking was observed for the dCpdC dimer. Conformational properties and solvent accessibility are discussed for the stacked and unstacked dimers. The potential of mean force profiles of the stacking-unstacking process for the DNA dimers are compared with the RNA dimers.     

First-principles study of Carbz-PAHTDDT dye sensitizer and two Carbz-derived dyes for dye sensitized solar cells

Dimers of cytosine and its N¹-methylated counterpart were investigated in gas-phase and in various solvents including chloroform, dimethylsulfoxide, and water. The studies were performed at DFT/M06-2X/6-31+G(d,p) level of theory. Relative stabilities of tautomers of cytosine solvated explicitly by a small number of solvent molecules were evaluated. Further solvation effect calculations for homodimers were carried out with conductor-like polarizable continuum model (CPCM). H-NMR shifts and IR frequencies for optimized structures were calculated and compared with available experimental data.