Mariam A. Shahinyan

The influence of GC/AT composition on intercalating and semi-intercalating binding of ethidium bromide to DNA

The binding parameters of ethidium bromide (EtBr) with DNA of various GC/AT ratios were determined using absorption and fluorescence spectroscopy. Our experimental data clearly demonstrate the co-existence of fluorescing and non-fluorescing types of “strong” binding at low concentration of EtBr. The fluorescent complex corresponds to the ordinary intercalative model. The non-fluorescent complex is referred to semi-intercalative binding of EtBr. The binding constant (K) and the number of base pairs corresponding to a binding site (n) of the fluorescent (K f and n f ) and non-fluorescent (K nf, nnf) types of interactions were determined. The average size of binding site (n) is equal to 1.5 bp (absorption spectroscopy), and nf ca. 2 bp (fluorescence spectroscopy). It was shown that nnf is dependent on GC-content and total n is independent of it.

Analysis of experimental binding curves of EtBr with single- and double-stranded DNA at small fillings

In this paper, a method that allows to analyze the binding curves of ligand (EtBr) with single-stranded (ss) and double-stranded (ds) DNA, when there are at least two modes of ligand binding to DNA at small fillings has been proposed. The obtained experimental binding curves for EtBr–ssDNA and EtBr–dsDNA have two clearly expressed linear regions. These curves were analyzed by two modes: Experimental points on linear regions were described by two different lines and all experimental points were described by single curve. It was revealed that the description by single curve permits obtaining more precise data of binding parameters (i.e. binding constant and number of base pairs that bind one ligand molecule). Moreover, the proposed method permits determining the value of proportion of binding sites of each binding mode.

Stabilities of Irradiated DNA Complexes from Sarcoma 45 Tumors with Mitoxantrone at Small Fillings

In the present work, the thermostabilities of mitoxantrone (MTX) complexes with DNA from sarcoma 45 and healthy rat liver were studied. DNAs from both sources were irradiated by resonant (64.5 GHz and 50.3 GHz) and nonresonant (48.3 GHz) frequencies of water. The obtained data showed that DNA solution irradiation by resonant frequencies of water induces a dehydration of nucleotides and Na+ ions in the solution. It is shown that at relatively low concentrations of MTX, when one MTX molecule binds to almost 100 pairs of bases of DNA, the thermostabilities of complexes decrease. Moreover, this change is more pronounced (∼0.8∘C) at the complex formation with DNA released from sarcoma 45 tumor.

Study of influence of millimeter range electromagnetic waves on water–saline solutions of albumin

In this work, the effect of electromagnetic waves of millimeter diapason (EMW MM) on both melting parameters of serum albumin from human blood and its solution density has been studied. It was shown that the irradiation of albumin solution results in protein denaturation at higher temperatures than in the case of nonirradiated samples, which indicates the increase of albumin packing degree. It was also shown that the enhancement of albumin solution density takes place which indicates the protein packing degree change as well. The obtained data show that the effect of EMW MM does not depend on frequency of these waves, because alterations are revealed at all studied frequencies — 41.8, 48 and 51.8GHz.

Behavior of Ethidium Bromide-Hoechst 33258-DNA and Ethidium Bromide-Methylene Blue-DNA Triple Systems by means of UV Melting

The study of EtBr and H33258 interaction as well as EtBr and MB interaction with DNA has been carried out. It was revealed that, at joint interaction, the effect of two ligands on the change of melting thermodynamic parameters of EtBr-DNA-H33258 or EtBr-DNA-MB complexes is not an addition of separate interaction influences. It was shown that, at joint, binding of EtBr and MB with DNA competition occurs, while in the case of EtBr and H33258, the mutual strengthening of stabilizing effect of each of them on DNA double-stranded structure mainly takes place.

93 Spectroscopic investigation of methylene blue binding to DNA

The interaction of methylene blue (MB) with DNA has been investigated by UV absorption spectra, Fluorescence spectra and UV-melting method. Analysis of the results of the melting experiments shows that melting temperature (T m) of the complexes increases with the [total ligand]: DNA ratio (r) at two concentrations of Na+ (2 mM Na+ and 20 mM Na+) providing support for conclusion that MB is a stabilizer of DNA helix structure. By contrast, the shapes of dependences of width of transition (ΔT) on r at low and high [Na+] are different which points to the existence of different types of binding modes of MB with DNA. UV-spectroscopy experiments and fluorescence spectra indicated that the binding modes of MB with DNA depended on r. At high r (r > 0.25), remarkable hypochromic effect with no shift of λ max in the absorption spectra of MB was observed. The fluorescence of MB was quenched which indicated that MB was bound to phosphate groups of DNA by electrostatic interaction. At low r ratios (r < 0.2), the absorption spectra of MB upon increasing the concentration of DNA showed gradually decrease in the peak intensities with a red shift. This phenomenon is usually associated with molecular intercalation into the base stack of the ds-DNA. Using the Scatchard’s model, the complex formation constants for MB with DNA were determined: the binding constant K ≈ 6.5 × 105 and binding site size n ≈ 4. Obtained data are not typical for intercalation model of ligands to DNA. Moreover, comparison between these data and our early experimental results of interaction of ethidium bromide with DNA made it possible to suggest that this binding type of MB is, more probably, semi-intercalation mode (Vardevanyan et al., 2003). This conclusion is in accordance with the analysis of the model structures of MB–DNA complexes which clearly shows the importance of solvent contributions in suggested structural form (Tong et al., 2010).

Peculiarities of interaction of synthetic polyribonucleotide poly(rA)-poly(rU) with some intercalators

The structural organization of RNA plays a key role in different processes of the cell cycle, which is why different forms of this molecule are appropriate targets for investigating of metabolic processes. From this perspective, RNAs have different roles in medical and chemicalbiological areas which is caused by the active participation of this biomacromolecule both in gene expression and in enzymatic processes (Corey, 2007; N’soukpoe’Kossi et al., 2008). Further, the interest in this macromolecule is influenced by the fact that RNA may be applied in diagnostic measurements of viral diseases (Fulle & Gohlke, 2010). There are several ways to regulate cell apoptosis by using RNA because it is known that the genome of various retroviruses, including oncoviruses contains RNA (Khaitan et al., 2011). As with DNA, RNA has a large structural variety due to its ability to form secondary and tertiary structures (Tyagi, Agarwal, & Mehrotra, 2015). Special attention has been paid to the preparation and screening of anti-bacterial and anti-viral drugs that show high specificity to certain types of RNA bases or sites in vivo modifying the substituents that presumably bind to specific domains of the RNA. One of the approaches for the screening of compounds is to study the interaction of such drugs with RNA, the properties of which are revealed by its interaction with DNA (Tyagi et al., 2015). For this aim, we examined the interaction of various intercalators such as phenothiazinium dye methylene blue (MB), the phenantridinium dye ethidium bromide (EtBr) and the acridinium dye acridine orange (AO) with double-stranded (ds-) poly(rA)-poly(rU), used as a model for RNA. The binding of biologically active compounds with ds-RNA has been studied less frequently than it has with ds-DNA. The goal of this work is to study the interaction of MB, EtBr and AO with double-stranded synthetic polyribonucleotide poly(rA)-poly(rU), identify the binding properties and determine the binding constant K and number of base pairs (n) per binding site.

Interaction of Antitumor Agent Mitoxantrone with Double Helical Synthetic Polyribonucleotides Poly(G)⋅Poly(C) and Poly(I)⋅Poly(C)

The interaction of antitumor drug mitoxantrone (MTX) with double-stranded synthetic RNA homopolymers has been studied by means of spectroscopic (UV-Visible absorption, circular dichroism) technique...

Time-Dependent Changes of Albumin Water Solutions After Irradiation by Electromagnetic Waves with Extremely High Radio Frequencies

The effect of electromagnetic irradiation with extremely high radio frequencies on several parameters of albumin water-saline solutions has been studied and the changes invoked by this irradiation after long time of its effect were observed. It was shown that the electromagnetic irradiation with 51.8GHz frequency, which is resonant for water, is preserved up to 48h after which the system returns to the initial state. It was shown as well that albumin thermostability also enhances and it is preserved during 48h, after that the system tends to return to the initial state.

145 Spectral characteristics of DNA-EtBr and DNA-MB complexes

References Kalantaryan, V., Martirosyan, R., Babayan, Y., Nersesyan, L., & Stepanyan, H. (2014). Preliminary results of influence of nonionizing electromagnetic radiation on tumor and healthy DNA and role of water. American Journal of Medical and Biological Research, 2, 18–25. Moodi, A., Khorasani-Motlagh, M., Noroozifar, M., & Niroomand, S. (2013). Binding analysis of ytterbium (III) complex containing 1,10-phenanthroline with DNA and its antimicrobial activity. Journal of Biomolecular Structure and Dynamics, 31, 937–950.