Thermal perturbation differential spectra of ribonucleic acids. I. Hydration effects

Luminescence excitation spectra reveal low-lying excited states in stacked adenine bases

Luminescence emission, polarization, and excitation spectra of polyadenylic acid (poly(A)) have been studied in room-temperature aqueous solution (pH 8). The temperature dependence of the luminescence of poly(A) at two different excitation wavelengths in the range 10-70 degrees C has also been studied and compared with that of adenosine 5'-monophosphate (AMP). It has been found that the luminescence excitation spectrum and the polarization curve of poly(A) solution reveal a low-intensity electronic transition at about 320 nm which is red-shifted by approximately 0.9 eV from the maximum of the absorption spectrum at 260 nm. A model of two luminescent stacked forms is suggested. The difference in the ground state levels of these two stacked forms obtained from the temperature dependencies of the emissions is insignificant ( approximately 1 kcal/mol). This means a lowering of the excited state of the stacked form with the 320 nm/420 nm absorption/emission bands by approximately 0.9 eV as compared to the main form with the 260 nm/400 nm absorption/emission bands. The low-lying excited states suggest the stronger electronic coupling of the bases in a certain stacked form. It is proposed that such clusters of the stacked bases could provide the wire-like conductivity in the short segments of DNA.

Interactions between esterified whey proteins (alpha-lactalbumin and beta-lactoglobulin) and DNA studied by differential spectroscopy

Spectroscopic study of interactions between esterified whey proteins and nucleic acids, at neutral pH, showed positive differential spectra over a range of wavelength between 210 and 340 nm. In contrast, native forms of whey proteins added to DNA did not produce any differential spectra. The positive difference in UV absorption was observed after addition of amounts of proteins as low as 138 molar ratio (MR) of protein/DNA, indicating high sensitivity of the applied method to detect interactions between basic proteins and DNA. UV-absorption differences increased with MR of added whey protein up to saturation. The saturation points were reached at relatively lower MR in the case of methylated forms of the esterified protein as compared to its ethylated form. Saturation of nucleic acid (2996 bp long) was achieved using 850 and 1100 MR of methylated beta-lactoglobulin and of methylated alpha-lactalbumin, respectively. Saturation with ethylated forms of the proteins was reached at MR of 3160 and 2750. Lysozyme, a native basic protein, showed a behavior similar to what was observed in the case of methylated forms of the dairy proteins studied. However, in the case of lysozyme, saturation was achieved at relatively lower MR (700). Methylated ,-casein failed to give positive spectra at pH 7 in the presence of DNA. It interacted with DNA only when the pH of the medium was lowered to 6.5, below its pI. Generally, amounts of proteins needed to saturate nucleic acid were much higher than those needed to neutralize it only electrostatically, demonstrating the presence on DNA of protein-binding sites other than the negative charges on the sugar-phosphate DNA backbones. Addition of 0.1% SDS to the medium suppressed totally all spectral differences between 210-340 nm. The presence of 5 M urea in the medium reduced only the spectral differences between 210-340 nm, pointing to the role played by hydrophobic interactions. Peptic hydrolysates of esterified and native proteins or their cationic fractions (pH > 7) produced negative differential spectra when mixed with DNA. The negative differences in UV absorption spectra were the most important in the case of peptic hydrolysates of methylated derivatives of whey proteins.

Synchrotron-excited time-resolved fluorescence spectroscopy of adenosine, protonated adenosine and 6N,6N-dimethyladenosine in aqueous solution at room temperature

The fluorescence behavior of adenosine in neutral solution has been studied by time-resolved spectroscopy using synchrotron excitation and time-correlated single photon counting, and by decay time measurements. Three emissions have been identified and correlated with three excitation spectra. The assignment of these transitions has been made by comparison with similar measurements on 6N,6N-dimethyladenosine (6DMA), and on adenosine in acid solution (ADO H+). It is proposed that two of the transitions of adenosine which correlate with 6DMA originate from coplanar and orthogonal rotational conformers of the amino group. The other transition, correlating with ADO H+ may originate either from the 3H-imino tautomer, or from a differently solvated rotational conformer.

Investigation of the nature of enzyme--coenzyme interactions in binary and ternary complexes of liver alcohol dehydrogenase with coenzymes, coenzyme analogues, and substrate analogues by ultraviolet absorption and phosphorescence spectroscopy

The difference spectra of binary and ternary complexes of horse liver alcohol dehydrogenase with oxidized and reduced nicotinamide adenine dinucleotides, nicotinamide 1,N6-ethenoadenine dinucleotide, and adenosine diphosphate ribose along with a number of substrate analogues have been measured. These spectra bear a very close resemblance to those obtained by perturbation of the coenzyme(s) and their analogues by acid, NaCl, dioxane, or tert-butyl alcohol. It is inferred that the coenzymes experience a combination of ionic and nonpolar environments at the adenine binding site of the enzyme. This is borne out by published X-ray crystallographic results. The phosphorescence spectra do not indicate the presence of ionized tyrosine in ternary complexes invovling enzyme, coenzyme, and substrate analogues. The ultraviolet spectra can be explained as arising from the perturbation of the coenzyme chromophores upon binding to the enzyme without having to invoke tyrosine ionization.

Thermal perturbation differential spectra of ribonucleic acids. III. Chain length effect

Thermal perturbation differential spectra of several adenylic acid oligomers, two single-strand polyribonucleotides, poly(A) and poly(C), and five trinucleoside diphosphates, U-A-A, U-A-G, U-G-A, C-U-C and C-U-A, were obtained and analysed. It is shown that these differential spectra cannot be entirely described by the nearest-neighbour approximation devised from the appropriate mononucleotides and dinucleoside monophosphates. In an attempt to determine the origin of this discrepancy, we have examined the possible optical changes arising from increased electronic interactions, changes in conformation, solvent accessibility or thermodynamic properties. This study indicates that dinucleoside monophosphates on one the hand and trinucleoside diphosphates on the other hand, are separate classes from the conformational point of view. The capacity to assume stacks, absent or negligible in higher oligomers or polymers, makes them poor models for the stacking interaction in longer nucleic acids. It is also shown that in trinucleoside diphosphates, interaction between the two terminal bases arising from bulging out of the middle base is very likely to occur. This type of interaction has to be taken into account in the description of the temperature perturbation differential spectra of trimers.