Yu. D. Nechipurenko

Magnetic Properties of Copper as a Constituent of Nanobridges Formed between Spatially Fixed Deoxyribonucleic Acid Molecules

The number of copper ions as constituents of a nanobridge that links two deoxyribonucleic acid (DNA) molecules that are fixed in a particle of a liquid-crystalline dispersion has been evaluated from the measurements of the magnetic susceptibility of particles in the liquid-crystalline dispersion of DNA. It has been shown that the experimental data are consistent with both theoretical assumptions on the possible structure of a nanobridge and a thermodynamic model that describes the formation of these bridges.

Ultrasonic Cleavage of DNA: Quantitative Analysis of Sequence Specificity

Looking for new means of assessing local conformational and dynamic heterogeneities in DNA structure, we have estimated the rates of phosphodiester bond cleavage in DNA fragments of known sequence caused by ultrasonic treatment. Among the 16 dinucleotide steps possible, those with 5′-ward cytosine [5′-d(CpN)-3′] are distinguished by significantly higher cleavage rates: CG > CA = CT > CC. The possible causes of this intriguing phenomenon are considered.

Ultrasonic cleavage of DNA in complexes with Ag(I), Cu(II), Hg(II)

We investigated a phenomenon of ultrasonic cleavage of DNA complexed with transition metal cations Ag(I), Cu(II) and Hg(II). We found the statistically significant dependence of relative intensity of cleavage on cation type and concentration. Each cation may cause two different types of distortion in the DNA double-helix depending on whether it binds to major or minor DNA groove. The intensity of ultrasonic cleavage decreases where the cation binds to the major DNA groove; the intensity of cleavage increases where the cation binds to the minor DNA groove and disturbs the hydrogen bonds of complementary base pairs or where it intercalates between bases. Both types of DNA distortion can affect the intensity of N↔S intercon-version of deoxyribose.

Analysis of binding of ligands to nucleic acids

The review demonstrates an application of methods of statistical thermodynamics for the analysis of binding of ligands to DNA and RNA. Reversible binding of ligands to nucleic acids is considered on the basis of the theory of adsorption. The binding of ligands to nucleic acids allows of describing quantitatively the process of binding and simulate the expression of genes in the simplest organisms. Description of the binding of ligands to nucleic acids is currently used in the broadest context for experimental systems of different types. Modern methods of biotechnology like molecular design or the use of microarrays are based on analysis of the binding of ligands to nucleic acids.

Properties of hybridization isotherms upon binding of ligands on microchips

A simple thermodynamic model describing microarray oligo-target hybridization has been constructed. The relationship between the hybridization signal intensity and Gibbs free energy for oligo-target duplex formation has been considered. The behavior of this function, which we called energy hybridization isotherm, in response to target concentration change was modeled at different ratios of oligo/target concentrations. The results of modeling were compared with the relevant and currently available data from microarray adsorption experiments.

Modeling of mechanochemical DNA cleavage by the action of ultrasound

In this study, we performed a simulation of stretching dynamics in double-stranded DNA fragments in a high-gradient liquid flow in the neighborhood of collapsing cavitation bubbles. We used calculated profiles of elastic tension along the polymer fragment model to determine the rates of mechanochemical cleavage at different positions in DNA restriction fragments. The obtained cleavage rate curves are qualitatively consistent with experimentally observed profiles of ultrasonic cleavage rates of DNA restriction fragments, which we showed earlier to be position-dependent. Based on the sum of our data, we propose a model that links the sequence specificity of ultrasonic DNA cleavage that has been proven experimentally to the sequence-specific conformational dynamics of β-D-deoxyribose in a B-form of the double helix. Furthermore, quantitative assessments of ultrasonic DNA cleavage rates for different conformational states of β-D-deoxyribose calculated based on the proposed model qualitatively agree with the experimental data.

Cleavage of DNA fragments induced by UV nanosecond laser excitation at 193 nm

The cleavage of dsDNA fragments in aqueous solution after irradiation with UV laser pulses at 193 nm has been studied. Samples were investigated using polyacrylamide gel electrophoresis. The intensity of damage of particular phosphodiester bond after hot alkali treatment was shown to depend on the base pair sequence. It was established that the probability of cleavage is twice higher for sites of DNA containing two or more successively running guanine residues. A possible mechanism of damage to the DNA molecule connected with the migration of holes along the helix is discussed.

Analysis of DNA-Ligand Binding in Solution and on Biochips

Ligand binding to DNA, as well as to microarrays, requires a system approach to description and analysis. This type of approach implies a fixed sequence of operations. Firstly, it is necessary to make a description of a binding scheme that realizes ligand and polymer in common spatial way. Secondly, a physical model of binding is required. Thirdly, a mathematical binding model should be constructed on the basis of the binding scheme and the physical model of binding. Every analysis of experimental data needs this preliminary work. A mathematical apparatus and classification of binding models have to follow on. Classification of different binding isotherms by different binding models is the direct problem. The inverse problem is a reconstruction of parameters of a binding model by experimental binding isotherm curves. The inverse problem can only be solved after solving the direct problem. An example of classification of binding models by oligonucleotides or proteins binding cooperativity and polymer properties like homo-or heteropolymer is presented.

Analysis of hybridization in DNA microarrays: Hybridization energy isotherms

The experimental data on hybridization in DNA microarrays can be presented in form of Hybridization Energy Isotherms (HEI)—relation between the level of saturation of microarray cells with target molecules and the free energy of formation of the target-probe duplex (ΔG). The study of HEI is important for optimization of the design of biological microarrays to expand its effective range of target concentrations. The effect of vertical shift of HEI with increase of concentration of the targets was found previously in experiment. We analyzed the behavior of HEI and introduced a model explaining the experimental data and the shift effect.

The damage of DNA induced by UV nanosecond laser excitation at 193 nm

Solutions containing dsDNA fragments were irradiated with UV laser pulses. The produced damage was investigated using polyacrylamid gel electrophoresis. The intensity of cleavage in particular phosphodiester bond after hot alkali treatment of irradiated samples was shown to depend on base pair sequence. The damage of DNA fragments has occurred predominantly in the sites containing guanine clusters.