Theoretical and experimental study of DNA helix-coil transition in acidic and alkaline medium.

The theoretical approach to the calculation of the influence of selective binding of small ligands on DNA helix-coil transition has been described in the previous paper (Lando D. Yu., J. Biomol. Struct. Dyn., (1994)). In the present paper that method is used for the study of DNA protonation and deprotonation in acidic and alkaline medium by theoretical analysis of pH effect on DNA heat denaturation. The mechanism of DNA protonation in acidic medium and pK values of nucleotides are well known. It gave us an opportunity to check the theory without any fitting of pK values. A good agreement between experimental and calculated functions Tm(pH) and delta T(pH) (melting temperature and melting range width) obtained for acidic medium proved the validity of the theory. However, for alkaline medium there was not even qualitative agreement when the agreed-upon mechanism of deprotonation was considered. Looking into the cause of the discrepancy, we have studied the DNA melting for different mechanisms of deprotonation by calculation of Tm(pH) and delta T(pH). As a result, it has been established that the discrepancy is due to deprotonation of bonded GC base pairs of helical DNA regions (pK = 11). It was shown that the early known protonation and newly found deprotonation of helical DNA essentially stabilised double helix in alkaline and acidic medium.

[DNA helix-coil transition in alkaline medium]. / Perekhod spiral'-klubok DNK v shchelochnoi srede.

Dna helix-coil transition in th alkaline medium was considered theoretically and experimentally. On the basis of the theory and experimental comparison the DNA double-stranded form deprotonation was revealed.

[Spectroscopic study of the effect of binding of bivalent manganese ions on the conformation of polyriboadenylic acid]. / Spektroskopicheskoe issledovanie vliianiia sviazyvaniia ionov dvukhalentnogo margantsa na konformatsiiu poliriboadenilovoi kisloty.

UV-differential spectra and CD spectra of poly(A) were studied in the presence of manganese ions at 10(-3) and 0.1 M Na+ in solution. It was shown that at at both low and high ionic strengths Mn2+ ions in low concentrations form bindings with phosphates of the polymer, increasing the degree of its helicity. At higher concentrations Mn2+ ions start to bind with poly(A) bases leading to a conformational helix-random coil transition. With manganese contents exceeding 10(-3) M, aggregates are formed, in which the mutual orientation of bases is characterized by a high degree of order. The calculation of concentration dependences of Mn2+ - poly(A) base binding constants shows that the process is cooperative. As the ionic strength increases from 10(-3) to 0.1 M Na+, the constant of the poly(A) - Mn2+ complex formation decreases by about an order of magnitude.

[Interaction of meso-tetra(N-hydroxyethylpyridyl)porphyrins with DNA. Effect of position of peripheral groups]. / Vzaimodeistvie mezo-tetra(N-oksiétilpiridil)porfirinov s DNK. Effekt polozheniia bokovykh grupp.

The interaction of meso-tetra(4-N-oxyethylpyridyl)porphyrin and its 3-N-substituted analogue with DNA was studied by UV spectrophotometry and circular dichroism methods. It was shown that the position of the side group on the pyridyl ring substantially affects the mechanism of interaction with DNA. 4-N-oxyethylpyridyl porphyrins more preferably intercalate into the DNA structure but worse realize the external binding than 3N-porphyrins.

[Selective effect of ligands on AT- and GC-pairs of DNA bases]. / Izbiratel'noe vliianie ligandov na AT- i GTs-pary osnovanii DNK.

A method is proposed for investigating the specific influence of ligands on DNA AT- and GC-pairs based on the comparison of the width of transition temperature interval of DNA with a strongly pronounced block-structure and dependence of the control DNA melting temperature on their GC-content. Such a comparison allows to define separately the contribution of nonspecific effects causing a change of the width of transition temperature interval. The method is used for studying the specific influence of beta-alanine and nu-aminobutyric acid on AT- and GC-pairs.

[Selective effect of ionization of nitrogen bases on the thermostability of AT- and GC-pairs of DNA]. / Izbiratel'noe vliianie ionizatsii azotistykh osnovanii na termostabil'nost' AT- i GTs-par DNK.

The ionization specific influence of nitrogen bases on thermostability of AT- and GC-pairs of DNA has been investigated by the method of DNAs melting temperature analysis. It has been shown that the change of temperature interval of DNA helix-coil transition when changing pH environment is due to specific ionization of AT- and GC-pairs of nitrogen bases.

[Modification of the DNA spatial structure when complexed with cisplatin]. / Modifikatsiia prostranstvennoi struktury DNK v komplekse s tsis-platinoi.

The experimental and theoretical analyses of the conformational transitions of DNA-cis-platinum complexes have been carried out. It is shown that at low concentrations of the ligand, the thermodynamic parameters of the helix-coil transition of the complexes are not the result of the local B-->A transition.

A method for determining the relative effect of ligands on A-T and G-C base pairs in DNA: applications to metal ions, protons and two amino acids.

A new method is described for the study of specific interactions of low-molecular ligands with the base pairs of DNA. This method is based on the comparative analysis of melting temperature changes in DNAs of different GC-content in the presence of low molecular weight ligands. In this paper, the method is applied to Mn2+, Ni2+, Co2+ ions, deprotonation, amino acids, beta-alanine and gamma-aminobutyric acid (gamma-ABA). Differences in Tm are affected not only by the changes of relative stability of AT- and GC-pairs, but also by other factors. A theoretical analysis of the sequence specificity of low-molecular ligands on the base pairs in DNA molecules characterized by a high degree of sequence heterogeneity is also presented.