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A T Karapetian

Publications and source records attributed to A T Karapetian.

14 recordsLinked to original sources
PubMed1996

Theoretical treatment of melting of complexes of DNA with ligands having several types of binding sites on helical and single-stranded DNA.

We treat theoretically conformational transitions in DNA-ligand complexes allowing for the existence of different binding parameters of the ligand to different DNA conformations. The parameters of binding are determined from the best fit of the theory to experimental data for the difference between transition point (Tm) and the width of transition curve (delta T) for the complexes and for naked DNA. The analysis shows that Ethidium Bromide (EB) and Actinomycin D (AMD) each may form at least five types of complexes: three types (one "strong" and two "weak") with helix DNA and two types ("strong" and "weak") with single-stranded DNA. The parameters of the complexes have been obtained. Some testable experimental predictions of the theory are also discussed.

Binding Sites↗
PubMed1990

Theory of helix-coil transition on DNA-ligand complexes: the effect to two types of interaction of ligand on the parameters of transition.

The effect of ligand interacting with native DNA by two types on the parameters of helix-coil transition in homopolymers is considered using the most probable distribution method (Yu.S. Lazurkin et al., Biopolymers 1970). It is shown that at a small relative concentration of ligand the melting enthalpy (delta H) of DNA may be obtained from the universal formula which contains only values directly known from the experiments. It is shown that the formula for the change of melting temperature and width of melting range depending on the total ligand concentration in solution is converted into the corresponding formulae which are defined for the case when only one type of interaction of ligand and DNA is considered.

Binding Sites↗
PubMed1990

Enthalpy of helix-coil transition of DNA: dependence on Na+ concentration and GC-content.

The enthalpy of helix-coil transition of DNA (delta H) is determined from the experiments on DNA melting with ligands by means of absolutely general formula, which contains only values directly known from the experiment (M.D. Frank-Kamenetskii, and A.T. Karapetian, Mol. Biol. USSR 6, 621 (1972)) with the combination of the "area" method (P.O. Vardevanian, et al., Biophysica 28, 130 (1983)). The experimentally obtained data show that delta H depends on both concentration of Na+ in solution and GC-content of DNA and is of high accuracy.

Base Composition↗
PubMed1977

[Discovery of a new type of restriction and modification in a group of intestinal bacteria].

The adsorption of 23 new lambdoid bacteriophages to 547 strains which isolated from natural population of Enterobacteriaceae was studied. The frequency of positive combinations of phage-bacterium with adsorption is not more than 2%. A study of possible causes of limited growth of lambdoid phages in the bacterial strains revealed that neither homoimmune prophage nor prophage P2 are single factors of the growth limitation. It is found that in natural populations a selection of bacterial strains with the least limitation of phage takes place. Three cases of killing bacteria after infection with high multiplicity are found. The reason of the killing effect is manifestation of some functions by infecting phages. A new restriction-modification system is found which differs from restriction-modification system A, B, K, 15, P1, EcoRI, EcoRII. The most of strains, which adsorb phages but do not support their growth, are supposed to possess several mechanisms of restriction. Thus, the search of new restriction system in Escherichia coli is worthwhile.

Adsorption↗
PubMed1976

[New lambdoid phages of Escherichia coli. II. Comparison of several genetic characteristics with lambda phages].

Functions of some newly isolated lambdoid phages and phage lambda genes were compared by their ability to interact with unrelated phages and the product of the bacterial gene gro P. 19 of 23 lambdoid phages studied interfere with prophage P2, that points out the presence of functionally active genes, essential for spi+ phenotype in their genomes. The development of 4 lambdoid phages with spi- phenotype is independent on the prophage P2 presence. Most of lambdoid phages show the reduced growth ability on the C600 groP- bacterial lawn. This indicates that they have a function similar to the gene P of phage lambda. The development of phage phi M417 in bacterial mutants groP- is not disturbed, which indicates that the gene P of phage phi M417 is different from that of the phage lambda. Newly isolated phages, that are homoimmune to phage lambda, restrict the development of T4 rII phage. The rest lambdoid phages have no rex function. The growth efficiency of lampodid phages on E. coli C cells, carrying Eco R1 plasmid, varies from 10(-6) to 10(-8) that presumbaly indicates on different amounts of restionci strites in DNA of these phages.

Coliphages↗
PubMedDate not supplied

[Connection of ethidium bromide with single-stranded DNA].

The interaction of ethidium bromide with single-stranded synthetic and natural polynucleotides at high temperatures (t = 70 degrees C) and low pH values (pH 3.0) was studied. The isotherms of adsorption of ethidium bromide on single-stranded DNA were obtained. Two modes of binding of single-stranded DNA, strong and weak, were revealed. The values of the corresponding constants of interaction of this ligand and the number of bases per one binding site were determined.

DNA, Single-Stranded↗
PubMedDate not supplied

["Tie" calorimetry: theory and experiment].

The results of theoretical and experimental investigations of the interaction of ligands to DNA permit to suggest the method of "tie" calorimetry by means of which the thermodynamic parameters of the cooperative transitions of DNA such as helix-coil, B-A and B-Z transitions were obtained. The prominence of the method is that the experimental samples contain such concentration of DNA that intermolecular interaction may be neglected. Moreover the smaller is the magnitude of the measured parameter the greater is the accuracy of the experimentally obtained data.

Calorimetry↗
PubMedDate not supplied

[Splitting of the DNA of new lambdoid bacteriophages by the specific Eco RI endonuclease].

The number of EcoRI restriction sites in DNAs of several lombdoid phages varies from 2 to 7 and the size of fragments ranges from 0.6 . 10(6) to 25 . 10(6) daltons. Effectiveness of restriction determined in vivo weakly correlates with a number of restriction sites, suggesting different sensitivity of different sites to EcoRI action. No correlation between molecular weights of DNA of different phages and the rate of heat inactivation of the phage has been found. The variability of number of the restriction sites and of the molecular weights of the fragments permits to conclude that: 1) closely-related organisms can be possibly used as convenient sources of certain genes (if a construction of new vector lambdoid phages is essential); 2) there is an opportunity to find phages with different distribution of the restriction sites to other restrictases within a group of phages with non-identical EcoRI restriction sites.

Catalysis↗
PubMedDate not supplied

[Theory of cooperative transition of DNA complexes with multimodal ligands].

The theory of the cooperative transition of DNA.ligand complexes have been developed, in which a model was implied where the multimodal ligands simultaneously interacted with DNA. Obtained formula express the dependence of the experimentally estimated values of the changes of transition point and width of transition on the concentration of the ligands. These expressions make possible to obtain the thermodynamic parameters of the interaction of the multimodal ligands with DNA (binding constants, number of base pairs corresponding to one binding site of DNA etc.) by comparing the theoretical and the experimental data.

DNA↗
PubMedDate not supplied

[The Z-form of DNA. Nonmonotonous change in stability with increase in ionic strength].

To specify the stability area of the Z-DNA conformation as a function of ambient conditions (ionic strength, temperature, water activity) a 3-D phase diagram for the (B,Z) equilibrium as exemplified by poly(dG-5ethyldC) has been constructed in experiment. Its main peculiarity proves to be the nonmonotonic change in stability of the Z form with ionic strength, with a minimum at 0.1 M NaCl, i.e. the increase or decrease in salt concentration from the above value leads to stabilization of the Z form relatively to the B form. The shape of the phase diagram section (temperature, ionic strength) is indicative of the existence of two B-type conformations, equilibrium between them being unaffected by ionic strength though being sensitive to temperature. The B1 form is stable at t < 30 degrees C while the B2 one--at t > 30 degrees C. Using the general 3-D phase diagram together with a polyelectrolyte theory of the B-Z transition, thermodynamic parameters were calculated for the B1-Z, B2-Z, and B1-B2 conformational shifts as well as the B/Z junction energy. The totality of the obtained results with poly(dG-5ethyldC) and those earlier obtained by us with poly(dG-5methyldC) is in full qualitative and quantitative agreement with the polyelectrolyte model, and at the same time it makes unlikely the explanation suggested by others for the low-ionic Z to B transition as the one totally stipulated by a metal ion contamination.

Circular Dichroism↗