[Effect of ligands with selective type of binding on the DNA helix-coil transition]. / Vliianie ligandov s izbiratel'nym kharakterom sviazyvaniia na perekhod spiral'-klubok DNK.

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.

[Influence of ligands characteristic of selective binding to a certain type of base pairs on DNA helix-coil transition I. Model. Theory]. / Vliianie ligandov s izbiratel'nym kharakterom vzaimodeistviia na perekhod spiral'-klubok DNK. I. Model'. Teoriia.

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.

[Effect of selectively reacting ligands on the helix-coil transition of DNA. III. Calculation of the melting curves of DNA-ligand complexes]. / Vliianie ligandov s izbiratel'nym kharakterom vzaimodeistviia na perekhod spiral'-klubok DNK. III. Raschet krivykh plavleniia komplekosov DNK s ligandami.

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.

[Calculation of DNA condensation, caused by adsorption of ligands]. / Raschet kondensatsii DNK, vyzvannoi adsorbtsiei ligandov.

A method for calculating the curves of DNA transition from linear to condensed state upon binding of condensing ligands has been developed. The character of the transition and ligand concentration necessary for condensation have been shown to be governed by the length of DNA molecule, energy and stoichiometry parameters of DNA-ligand complex (equilibrium constant between linear and condensed form in the absence of ligands, constants for ligand binding to linear and condensed forms, the number of base pairs covered by one ligand, etc.). The results of the calculations indicate that only slight difference in the free energies of these states in free DNA (less than 6 cal/mole(bp) for DNA of 500 bp long) is sufficient for the existence of stable linear state in the absence of ligands (in free DNA) and the formation of stable condensed state upon complexation.

[Effect of changes in the stoichiometry of DNA--ligand complexes during heat denaturation of DNA on helix-coil transition parameters]. / Vliianie izmeneniia stekhiometrii kompleksa DNK--ligand pri teplovoi denaturatsii DNK na parametry perekhoda spiral'--klubok.

The influence of a change in DNA-ligand complex stoichiometry in the process of denaturation on temperature and temperature range width of helix-coil transition (Tm, delta T) has been considered. The stoichiometry is characterized by two parameters: by the number of base pairs covered with one ligand (m) and by the number of base pairs per one binding centre (r). It is shown that the change of r and m during denaturation strongly influences the DNA melting process. If the product rm doesn't change during denaturation, the melting temperature shift caused by a ligand concentration growth has a finite limit. If r1m1 not equal to r2m2 (index 1 is related to the coil DNA from and index 2--to the helix DNA form), the melting temperature during concentration growth aspires to + infinity, when r1m1 > r2m2, and to absolute zero, when r1m1 < r2m2. The sign of the effect (stabilization or destabilization) is independent of a binding constant and a factor of cooperativity of DNA-ligand interaction. Dependences of Tm and delta T on ligand concentration for different r1, r2, m1, m2 are analysed.

[Fusion of complexes of DNA and extended ligands]. / Plavlenie kompleksov DNK s protiazhennymi ligandami

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.

[Nucleoprotein melting. I. Theory of helix-coil transition of DNA in the presence of proteins with cooperative character of interaction under conditions of reversible binding]. / Issledovanie plavleniia nukleoproteidov. I. teoriia perekhoda spiral'-klubok DNK v prisutstvii belkov pri obratinom sviazyvanii.

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.

[Effect of selectively reacting ligands on the helix-coil transition of DNA. IV. Heat denaturation of DNA in an acid medium]. / Vliianie ligandov s izbiratel'nym kharakterom vzaimodeistviia na perekhod spiral'-klubok DNK. IV. Teplovaia denaturatsiia DNK v kisloi srede.

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.

[Nucleoprotein fusion. III. Causes and conditions for development of the multiphase character of the DNA--protein fusion curve]. / Issledovanie plavleniia nukleoproteidov. III. Prichiny i usloviia vozniknoveniia mnogofaznosti krivoi plavleniia kompleksov DNK--belok.

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.

[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.

[Influence of ligands characteristic of selective binding on DNA helix-coil transition. II. Expansion of DNA melting curves into constitutents. Inverse problem of melting of the block heterogeneity DNA. Determination of the content ratio of binding centers to DNA degree of helicity]. / Vliianie ligandov s izbiratel'nym kharakterom vzaimodeistviia na perekhod spiral'-klubok DNK. II. Razloshenie krivoi plavleniia DNK na sostavliaiushchie. Obratnaia zadacha o plavlenii DNK s blochnym stroeniem. Opredelenie zavisimosti otnositel'nogo soderzhaniia tsentra sviazyvaniia ligandov ot stepeni spiral'nosti DNK.

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.

[The effect of long-range interactions between adsorbed ligands on the DNA helix-coil transition]. / Vliianie vzaimodeistviia dal'nego poriadka mezhdu adsorbirovannymi ligandami na perekhod spiral'-klubok DNK.

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.

[Nucleoprotein melting. II. Melting of irreversible DNA-protein complexes]. / Issledovanie plavleniia nukleoproteidov. II. Plavlenie kompleksov DNK--belok v usloviiakh neobratimogo sviazyvaniia.

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.

[The effect of ligands undergoing temperature conformational transitions on the stability of DNA double helix]. / Vliianie na stabil'nost' dvoinoi spirali DNK ligandov, preterpevaiushchikh temperaturnye konformatsionnye perekhody.

The influence of ligands, which undergo conformational transition, on DNA molecular melting is considered theoretically. Equations for computation of melting curves of DNA included in such complexes are obtained, which are used for studies of DNA double helix stability and of the binding to helical and coil regions influence on ligand conformational transitions. Calculated melting curves and experimental data for DNA-RNAase complex are compared.

[Effect of the size of the ligand molecule on the stability of the DNA double helix]. / O vliianii razmerov molekul ligandov na stabil'nost' dvoinoi spirali DNK.

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.

[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.