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.     

Study of spectral and luminescent manifestations of the aggregation of thymine chromophores in aqueous solutions of polythymidylic acid at room temperature in connection with the task of photochemical record of information on thymine

Luminescence and excitation luminescence spectra of water solutions of polythymidylic acid at room temperature were studied. Three luminescence bands at different excitation wavelengths were observed: at 338 nm, which was known earlier, and two new bands, at 320 and 350 nm. The study of excitation luminescence spectra that have not been studied earlier led us to interpret the band at 320 nm as a band of chromophores that do not interact, the band at 338 nm as a band of photochemically most active densely packed stacking dimers (absorption band exciton splitting approximately 4000 cm(-1)), and the band at 350 nm as a band of photochemically inactive big stacking aggregates (n > or = 10, exciton splitting approximately 8000 cm(-1)). Changes in optical density at 270 nm of poly-T water solutions after consecutive irradiations with UV light at 297+302 and 248 nm were studied. The causes of incomplete reversibility are discussed.     

Theoretical study of hydrophobicity and hydrophilicity of uracil and its dimers

The influence of hydrophilic and hydrophobic properties of the uracil elementary nucleic acid bases on its solubility and structure in aqueous solution was studied. Complexes of uracil with water molecules (from 1 to 14) were then calculated. The geometrical parameters of the hydrogen bridge of uracil and the changes in the frequency of valence vibrations of the bonds participating directly in hydrogen bond formation were calculated. It is shown that for the hydrogen bonds O_w?HN₁ and O_w?HN₃ the hydrogen atom can tear off, it may lead to tautomeric transformation of uracil. The results obtained having calculated the structure of uracil dimers, formed with the hydrogen bonds, in an isolated state and water solution, energy, dipole moments and the hydrogen bridge parameters made it possible to explain low solubility of uracil in water at room temperature. It is shown that water molecules with increase in their number are located mainly at one side of the plane of a pyrimidine uracil ring, that leads to the formation of stacking. Of two possible variants of stacking formation, the most profitable grouping is when a dipole moment of the formed dimer is equal to zero (anti-parallel stacking).     

Nature of the stacking of nucleic acid bases in water: a Monte Carlo simulation

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It has been found out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.     

Nature of the Stacking of Nucleic Acid Bases in Water: a Monte Carlo Simulation

Abstract

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It has been found out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.     

Effect of intramolecular interaction on the electron excitation state of nucleic acid components

A theoretical and experimental investigation of absorption and luminescence features of crystals and aggregates of nucleic acid bases were carried out. The long wavelength low intensity bands in UV-absorption nd excitation spectra, bathochromic shift of fluorescence spectra, the change of correlation between the intensity of fluorescence and phosphorescence spectra were obtained. The interpretation of these experimental results was proposed on the basis of pair interaction calculations (exciton-resonance and charge-resonance) in different conformations of cytosine dimers. The energy transfer after excitation at lambda 280 and 312 nm was investigated in nucleic acid base aggregates.     

Complexes produced by associated forms of porphyrin bound with hydrophobic-hydrophilic copolymer and transition metal ions

Properties of protonated dimeric forms of meso-tetraphenylporphine (TPP) and meso-tetra(p-aminophenyl)porphine (TAPP) bound with copolymer and also complexes produced by associated TAPP bound with copolymer, Mn2+, and Fe3+ are investigated by absorption, luminescence, and Raman spectroscopy. According to absorption spectra of protonated dimers of TPP, three dimeric forms of the porphyrin are observed in the ground state. However, selective excitation of these forms according to the fluorescence spectra reveals only two dimeric forms in the excited state. In contrast, similar selective excitation of TAPP bound with copolymer in aqueous-dioxane solution results in weak changes in the fluorescence spectra, nevertheless, there is strong interaction between porphyrin and macromolecular carboxyl groups in the ground state. In the case of the formation of the complexes between associated TAPP bound with copolymer, Mn2+ and Fe3+, a new band in the near IR region with a maximum at 840 nm is built up in the fluorescence spectrum. However, this near IR emission is completely quenched when new strong vibrational bands at approximately 1800 and 1900 cm-1 are revealed in the resonance Raman spectra of the complexes. The observed effects are explained in terms of direct participation of water molecules involved in the water-porphyrin dimeric complex in the processes of transformation of excitation energy. The involvement of water in this dimeric complex can lead to redistribution of flows of the energy degradation when transition metal ions play a role of the agent which enhances the trapping properties of the porphyrin-metal-ions complexes.     

Intermolecular orientations of adenosine-5-monophosphate in aqueous solution as studied by fast fourier ytsndgotm 1H Nmr spectroscopy

Proton magnetic resonance spectra of 5′AMP were taken in the concentration range of 0.001–2.2M. The concentration profiles of all the nonexchangeable protons were determined. The data for 5′AMP was compared to those of adenine, adenosine, and poly(A). Theoretically computed isoshielding lines of the adenine moiety were used to qualitatively predict a preferred stacking geometry of 5′AMP in aqueous solution. It is concluded that 5′AMP at pH 8 forms multistacked aggregates at high concentration levels and that a preferred orientation is such that the bases are aligned face to back with considerable, though less than 100%, base overlap; and that the ribose moieties of adjacent molecules are near one another with the phosphate groups well separated. Mn(II) ion binding studies show that the stacks are not restricted to one unique orientation type. Specific evidence is given showing that base-stacking orientations in the solid state may in some cases be considerably different from that in aqueous solution, due in part to numerous hydrogen bonding differences, and this is shown to be the case for base-stacked adenosine. In the case of 5′AMP the stacking orientations between the solid and liquid states are also different, except in this comparison the solid-state structure carries a positive charge.     

Relationship between absorption and fluorescence excitation spectra of psoralens and coumarins and their concentration

The shape of absorption spectra is changed and their maxima are red shifted with an increase of furocoumarin (psoralen, 8-methoxypsoralen and angelicin) concentration. Fluorescence excitation spectra of psoralen, 7-methoxycoumarin and 7-hydroxy-4-methylocumarin do not depend on the concentration in solutions. They are similar or coincident with absorption spectra of the most concentrated solutions. One may conclude the existence of different forms of furocoumarin and coumarin aggregates in solution. From the coincidence or similarity of fluorescence excitation spectra and absorption spectra in the most concentrated solutions it may be proposed that only the aggregated forms of psoralens and coumarins (the dimers or associates of higher order) are able to emit fluorescence.     

A study of the spectral and luminescence manifestations of the aggregation of thymine chromophores in polythymidylic acid aqueous solutions at room temperature in the context of photochemical information recording using thymine

The luminescence and excitation spectra of polythymidylic acid aqueous solutions at room temperature were studied. In addition to the previously described band at 338 nm, two new bands at 320 and 350 nm were recorded at various excitation wavelengths. An examination of the excitation spectra that had not been studied previously, as well as their comparison with the differential absorption spectra previously recorded during photodimerization, allowed us to interpret the band at 320 nm as the band of noninteracting chromophores; the band at 338 nm as the band of the most photochemically active, densely packed stacking dimmers (exciton splitting of absorption band of ～4000 cm^?1); and the band at 350 nm as the band of photochemically inactive large stacking aggregates (n ≥ 10, exciton splitting of ～8000 cm^?1). The changes in the optical density of the polythymidylic acid aqueous solution at γ = 270 nm after successive irradiation of the solution with light at 279 + 302 and 248 nm were studied. The reasons for their incomplete reversibility are discussed.     

Migration of electron excitation energy in mixed associates of chlorophyll and its derivatives]

The intracomplex migration is investigated of electron excitation energy between molecules which are a part of a mixed associate. Weakly fluorescent and nonfluorescent associates of chlorophyll and its analogues as well as of bacteriochlorophyll and neoxanthine have been used as donors and acceptors. The migration of excitation energy with variation of quantum yield of donor emission from 5-10(-3) to less than or equal to 10(-4) and also with very weak overlapping of luminescence and absorption spectra for the pair D leads to A is experimentally discovered by luminescence excitation spectra of mixed pigment aggregates. A specific disturbing action of Pd and Cu ions on chlorophyll a luminescence with formation of mixed complexes of chlorophyll with Pd-pheophytin a and Cu-pheophytin b is observed. The presence of Pd and Cu ions in the structure of the mixed complexes gives rise to a considerable reduction of chlorophyll apparently due to increasing intersystem crossing probability in the chlorophyll molecule. The probability of intracomplex energy migration in systems under investigation amounts to approximately 10(12) sec-1 according to the obtained estimations. The probable mechanism of energy migration in mixed associates is discussed. The obtained results may be used for elucidation of a possible role of the mixed aggregates and effective intracomplex migration of excitation energy in photosynthetic apparatus of green plants.     

Surfactant micelles containing protoporphyrin IX as models of primitive photocatalytic systems: a spectral study

Micelles of various surfactants containing protoporphyrin IX (PPIX) have been studied as models of primitive membrane-like photocatalytic systems. Spectral characteristics (absorption spectra, fluorescence emission and excitation spectra, fluorescence quantum yields and lifetimes) have been measured to indicate specific interactions of PPIX molecules with the micelles. Two types of PPIX aggregates are probably formed in water: non-fluorescent clusters corresponding to the absorption peak at 642-648 nm and fluorescent friable dimers with strong solute-solvent interactions corresponding to the absorption peak at 618 nm. The aggregates are solubilized by the micelles, which results in an increase of the fluorescence quantum yield (and thus in the increase of the PPIX sensitizing ability). Solubilization of PPIX molecules by SDS-micelles is enhanced by the partial neutralization of the negative surface charge of the micelles. Neutral Triton X-100 micelles solubilize PPIX much better than SDS particles; however, some of the clusters formed in the bulk aqueous phase of the detergent-water system remain aggregated in the crown of the micelle. The positively charged CTAB micelles have been shown to provide the best solubilization of PPIX accompanied by the highest increase of its emitting activity. The results are discussed in terms of the possible role of PPIX-containing membraneous systems in primitive photosynthesis.     

Calculation of spectra of absorption and circular dichroism of Rhodopseudomonas acidophila light harvesting complexes based on roentgen structural data

Absorption and circular dichroism spectra of two forms of the peripheral light-harvesting complex from photosynthetic purple bacteria Rhodopseudomonas acidophila were calculated. Calculations were carried out on the basis of exciton theory for circular aggregates of bacteriochlorophyll molecules and X-ray data for these forms of the complex. It was shown that theoretical spectra fit well experimental ones at the same values of excitation energy, homogeneous and inhomogeneous broadening, and bandwidth for all bacteriochlorophyll molecules of complexes. To approximate the circular dichroism spectra of complexes, it was necessary to change the orientations and the values of the moments of transition of Qy molecules relative to their orientation determined on the basis of X-ray structure analysis data.     

Fluorescence Analysis of 7-Aminoactinomycin–Telomeric Oligonucleotide d[AGGG(TTAGGG)<Subscript>3</Subscript>] Complexes

Interactions of 7-aminoactinomycin D (a fluorescent analogue of actinomycin D, an anticancer antibiotic) and two structural forms of the model guanine-rich telomeric oligonucleotide d[AGGG(TTAGGG)₃] have been studied. We have shown that 7-aminoactinomycin D induces fluorescence in two G-quadruplex structures formed with the presence of potassium or sodium ions. The enthalpy of the interaction between the phenoxasone chromophore of the antibiotic and the telomeric oligonucleotide as determined by analysis of excitation spectra is 5.5 kcal/mol. This value differs little from those obtained for complexes with guanine, adenine, or thymine aggregates (6–7 kcal/mol). In the oligonucleotide, the antibiotic is located within dynamic cavities. Therefore, 7-aminoactinomycin D is not released from telomeric structures to the aqueous phase spontaneously or even by photoexcitation, but it is easily released from the surface of aggregates of the respective nucleobases. The entropy term of the interaction energy calculated as a difference between the total energy determined from the binding constant and the enthalpy determined from excitation spectra constitutes approximately 30% for the telomeric oligonucleotide and is virtually null in interactions with nucleobase aggregates.     

Mechanism of ultraviolet-induced mutagenesis: the coding properties of ultraviolet-irradiated poly(dC) replicated by E. coli DNA polymerase I.

We have identified three lesions rather than cyclobutane dimers which alter the properties of UV-irradiated poly(dC) as a template for E.coli DNA polymerase I, and have characterised these lesions with respect to their coding properties, rates of formation and decay, and their sensitivity to uracil DNA glycosylase. Our results lead us to conclude that these lesions are (1) cytosine hydrates, which code for cytosine and to a lesser extent thymine, (2) uracil hydrates, which code for adenine and are not sensitive to uracil DNA glycosylase, and (3) uracils, which code for adenine and are removed by uracil DNA glycosylase.     

Fluorometric determination of adenine and its derivatives by reaction with glyoxal hydrate trimer

A fluorometric determination of adenine has been devised. It was found that adenine gives strong fluorescence when reacting with glyoxal hydrate trimer in an acidic medium. The maximum wavelengths of excitation and emission spectra were 328 and 382 mμ, respectively. This reaction was successfully applied to determination of 0.2–1.0 or 2.0–10.0 mμmoles of adenine and its derivatives, in which the hydrogen atom at position 9 is substituted with ribose or substituted ribose. Other nucleic acid bases, guanine, uracil, thymine, and cytosine, did not interfere with this fluorometric determination of adenine.     

The physical basis of nucleic acid base stacking in water

It has been argued that the stacking of adenyl groups in water must be driven primarily by electrostatic interactions, based upon NMR data showing stacking for two adenyl groups joined by a 3-atom linker but not for two naphthyl groups joined by the same linker. In contrast, theoretical work has suggested that adenine stacking is driven primarily by nonelectrostatic forces, and that electrostatic interactions actually produce a net repulsion between adenines stacking in water. The present study provides evidence that the experimental data for the 3-atom-linked bis-adenyl and bis-naphthyl compounds are consistent with the theory indicating that nonelectrostatic interactions drive adenine stacking. First, a theoretical conformational analysis is found to reproduce the observed ranking of the stacking tendencies of the compounds studied experimentally. A geometric analysis identifies two possible reasons, other than stronger electrostatic interactions, why the 3-atom-linked bis-adenyl compounds should stack more than the bis-naphthyl compounds. First, stacked naphthyl groups tend to lie further apart than stacked adenyl groups, based upon both quantum calculations and crystal structures. This may prevent the bis-naphthyl compound from stacking as extensively as the bis-adenyl compound. Second, geometric analysis shows that more stacked conformations are sterically accessible to the bis-adenyl compound than to the bis-naphthyl compound because the linker is attached to the sides of the adenyl groups, but to the ends of the naphthyl groups. Finally, ab initio quantum mechanics calculations and energy decompositions for relevant conformations of adenine and naphthalene dimers support the view that stacking in these compounds is driven primarily by nonelectrostatic interactions. The present analysis illustrates the importance of considering all aspects of a molecular system when interpreting experimental data, and the value of computer models as an adjunct to chemical intuition.     

Effect of protein side chain amide group on the hydrogen-bond equilibrium in nucleobases studied by infrared and 13C-NMR spectroscopy

Infrared spectra of 1:1 hydrogen-bonded complexes formed by derivatives of adenine and model molecules bearing the protein side chain amide group have been measured in chloroform solution. From the temperature dependence of hydrogen-bond formation, thermodynamic data on these complexes are determined. On the basis of these data, it is shown that the complexes consist of cyclic heterodimers, those that use the adenine N(1)H bond being favoured. Similarly infrared and 13C-NMR spectroscopy reveals that uracil-amide cyclic heterodimers formed through the uracil 4-carbonyl group are predominant. All of these results predict that Watson-Crick hydrogen bonds in adenine-uracil base-pairs may be opened to some extent, as proved in this work. The possible biological importance of these observations is also discussed.     

A proton magnetic resonance study of the interaction of adenylyl (3' is greater than 5') adenosine with polyuridylic acid

The interaction of adenylyl (3′ → 5′) adenosine (ApA) with polyuridylic acid in D₂O solution at neutral pD has been studied by high resolution proton magnetic, resonance spectroscopy. At temperatures above ～32°C, no evidence was obtained for the interaction of ApA with poly U. Below this temperature, a rigid triple-stranded complex involving a stoichiometry of 1 adenine to 2 uracil bases is formed, presumably via specific adenine–uracil base-pairing and cooperative base stacking of the adenine bases in a manner similar to that previously reported for the adenosine–poly U complex.     

Luminescence of thymine aqueous solutions at the room temperature

The distinguishing features of luminescence of aqueous thymine solutions at room temperature (a broadening of luminescence spectra as compared with low-temperature spectra and differences between excitation and absorption spectra) are discussed. It is shown that these features are due to bimolecular photochemical reactions that lead to the formation of photoproducts (at the first stages, photoadducts) with a comparatively high luminescence ability.