[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: 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.
[Show abstract][Hide abstract] ABSTRACT: The influence of the extended interacted under adsorption ligands with a selective binding on the DNA helix-coil transition has been theoretically studied. It was found that contact interaction between ligands or/and their extent give rise to a marked non-linearity of the GC-content dependence of the melting temperature. This non-linearity causes a few features of the dependence of the melting range width on ligand concentration [delta T(C0)]. Such as a non-monotony of the delta T (C0) increase in the presence of ligands increasing the difference between the thermostabilities of poly(d(A-T)] and poly[d(G-C)] polymers. The degree of a non-linearity defines the character of changes of the form of the differential melting curves in the presence of ligands.
[Show abstract][Hide abstract] ABSTRACT: The influence of ligand length on helix-coil transition parameters in the presence of different ligand concentrations has been considered theoretically. A decrease of this influence with an increase of ligand length when the binding constant has a constant value was shown. When binding free energy is proportional to the ligand length, i. e. when K = K0m (K-binding constant, m-ligand length) the length effect is unambigous. In the presence of low-ligand concentration the stability of DNA double helix increases with their length, whereas in the presence of high concentrations it decreases.
[Show abstract][Hide abstract] ABSTRACT: The calculation of variations in the helix-coil transition parameters, melting curves and differential melting curves of DNA characteristic of different degree of heterogeneity in the presence of ligands interacting selectively with a certain type or types of base pairs has been carried out. It has been shown that ligands with a selective and non-selective manner of binding influence identically the denaturation process in the case of low DNA heterogeneity (synthetic periodic polynucleotides and satellite DNA fractions). In the case of high heterogeneity (the main fraction of DNA of higher organisms) this influence is quite different. The phenomenon of AT- and GC-base pairs thermostability inversion is considered.
[Show abstract][Hide abstract] ABSTRACT: The DNA thermal denaturation in acidic medium has been investigated experimentally and theoretically. The formulae describing a dependence of the helix--coil transition parameters (melting temperature (Tm) and melting range width (delta T) on ionisation constants values of all kinds of DNA bases in the helix and coil regions and medium acidity have been obtained. Dependences Tm (pH) and delta T (pH) have been determined experimentally and calculated for different models of protonation. Based on the comparison of theoretical and experimental dependences Tm (pH) and delta T (pH) a strict examination of the theory is conducted. The mechanism of DNA protonation is discussed.
[Show abstract][Hide abstract] ABSTRACT: The method for determination of distribution density function of base pairs at blocks with different GC-content in DNA (p(kappa)) was developed. For this purpose a differential melting curve is expanded into constituents possessing Gaussian form. Dependences of the content ratio of DNA ligand binding centres of different kinds at helical and coil regions were expressed through p(kappa). These dependences are used for calculation of the ligand influence on a helix--coil transition. It is shown that in spite of incorrectness of p(kappa) determination, the problem of determining content ratio of different kind binding centres expressed through p(kappa) is a correct problem.
[Show abstract][Hide abstract] ABSTRACT: The DNA helix-coil transition in the presence of ligands interacting selectively with a certain type or types of base pairs has been considered. A calculation method for estimation the influence of lignads on the melting process for which the knowledge of DNA primary structure is not required was proposed. It has been shown that the reverse temperature shift caused by ligands bound to a given type of base pairs at given kind of regions (helix or coli) is in direct proportion to the fist derivative with respect to the degree of helicity from ratio beta ji/n, where beta ji--number of nitrogen bases of i-type at the regions of j-kind; N--total number of DNA base pairs. It was assumed earlier that this shift was in direct proportion to beta ji/Nj, where Nj--number of base pairs in DNA regions of j-kind. The specificity of lignads interaction with given kinds of bases alters the manner of the melting process of the heteropolynucleotide in comparison with homopolynucleotide only in the case when the DNA primary structure has a strong influence on the position of helix and coli regions along the DNA chain. Only when this conditions is fulfilled the inversion of thermostability of AT- and GC-pairs may affect the shape of the melting curve.
[Show abstract][Hide abstract] ABSTRACT: The influence of proteins reversibly and irreversibly bound to DNA on the shape of melting curve has been considered. It is shown that the melting curve becomes biphasic in two cases: (i) cooperative binding of proteins with DNA (II) STRONG DIFFERENCE IN THE BINDING CONSTANTS WITH HELICAL AND COILED REGIONS. Simple formulae permitting to determine which of two causes stipulate for biphasic profile of a given experimental melting curve are obtained. Melting curves of DNA-basic oligopeptides complexes have been investigated. It is shown that the oligopeptides, when their chain length does not exceed 10, are able to migrate along DNA and biphasic shape of the melting curve is stipulated by the cooperative manner of their binding with DNA.
[Show abstract][Hide abstract] ABSTRACT: The theory of melting of DNA complexes with extended ligands (ties) is considered. Influence of ties interacting electorally with certain DNA regions and influence of extender ties, interacting unelectorally on the helix coil transition parameters is compared. It has been shown that both types of ties cause, coincided qualitatively, but differed quantatively, shifts of melting temperature and change of the melting range width of DNA. Comparison of theory with experiment in the case of DNA complexes with ribonuclease is given.
[Show abstract][Hide abstract] ABSTRACT: Helix-coil transition of DNA with attached extended ligands able to interact with one another during adsorption on DNA (cooperative or uncooperative binding) has been considered. The general formulae describing dependence of polymer melting curve on concentration of attached ligands have been obtained. It has been shown that cooperativity of interaction with DNA stipulates for two phase profile of the melting curve. The results obtained show that proteins which interact with DNA cooperatively may cause two phase helix-coil transition under conditions of reversible binding.
[Show abstract][Hide abstract] ABSTRACT: Three with different complexity models: single-stranded, periodic theeropolymer, two-stranded periodic heteropolymer and complex of DNA with irreversible bound proteins have been considered. It is shown that the individual bands on the differential melting curve appear if the length of protein bound regions exceed 25 base pairs. In this case the melting temperature of free and protein bound regions depends on their reciprocal length in almost linear manner. Moreover, the temperature of the peak corresponding to the protein bound regions is independent on the length of the adjacent free DNA regions if their length exceeds 15 base pairs. If the length of free and protein bound regions exceed 300 base pairs, their melting temperatures becomes almost equal to that of infinitely long polymer with the analogous structure. A simple method for determination of length of the free and the protein bound regions length has been proposed.
[Show abstract][Hide abstract] ABSTRACT: The influence of different types of long-range interaction of ligands adsorbed on DNA on the helix-coil transition was theoretically considered. The contact interaction was shown to differ significantly from the long-rang one. It was shown also that even weak dependence of a long-range potential on a degree of helicity resulted in the strong changes of a DNA melting curve. This result allowed to understand the different experimental data on DNA melting in the presence of different substances which reduced AT-and GC-base pairs thermostability difference.