Extending the applicability of the O-ring theory to protein–DNA complexes

Many biological processes depend on protein-based interactions, which are governed by central regions with higher binding affinities, the hot-spots. The O-ring theory or the “Water Exclusion” hypothesis states that the more deeply buried central regions are surrounded by areas, the null-spots, whose role would be to shelter the hot-spots from the bulk solvent. Although this theory is well-established for protein–protein interfaces, its applicability to other protein interfaces remains unclear. Our goal was to verify its applicability to protein–DNA interfaces. We performed Molecular Dynamics simulations in explicit solvent of several protein–DNA complexes and measured a variety of solvent accessible surface area (SASA) features, as well as, radial distribution functions of hot-spots and null-spots. Our aim was to test the influence of water in their coordination sphere. Our results show that hot-spots tend to have fewer water molecules in their neighborhood when compared to null-spots, and higher values of ΔSASA, which confirms their occlusion from solvent. This study provides evidence in support of the O-ring theory with its applicability to a new type of protein-based interface: protein–DNA.     

A supramolecular polymerisation model for the structurisation of DNA–lipid complexes

Complexes formed by DNA and lipid mixtures have great interest for the assessment of self-assembling mechanisms in open biological systems. X-ray diffraction has revealed that minor alterations of the cationic/neutral lipid composition produced major alterations to the liquid crystalline structure and the hydration of the complexes. We have extended to these systems by an approach based on the identification of a fundamental repeating unit that grows according to the general principles of supramolecular polymerisation and liquid crystallinity. Structural reorganisations that optimise the electrostatic and hydrophobic compensation are enhanced by competition between the rigidity of the polyelectrolyte and the cohesion of the lipid assembly. The non-hydrated hexagonal structure revealed by X-ray examination is represented by a dendritic-type supramolecular polymerisation of DNA units decorated by the aliphatic tails of dissociated liposomes. An increase in the cationic/neutral lipid component ratio enhances the stability of planar bilayers, favouring the formation of the partly hydrated lamellar structure revealed by X-ray diffraction.     

DNA modified with metal complexes: Applications in the construction of higher order metal–DNA nanostructures

DNA has recently emerged as a useful building block for higher order nanostructures, such as extended two-dimensional surfaces and discrete two- and three-dimensional structures. Transition metal complexes can introduce functionality to these otherwise passive nanostructures. This review examines the synthetic strategies used to introduce metals in a site-specific manner to DNA: either by attaching preformed metal complexes to DNA, or by metal coordination to unmodified or modified DNA. The applications of metal–DNA complexes in building higher order nanostructures and the utility of attaching luminescent or electrochemical labels are discussed.     

Application of the avidin–biotin interaction to immobilize DNA in the development of electrochemical impedance genosensors

Impedance spectroscopy is a rapidly developing technique for the transduction of biosensing events at the surface of an electrode. The immobilization of biomaterial as DNA strands on the electrode surface alters the capacitance and the interfacial electron transfer resistance of the conductive electrodes. The impedimetric technique is an effective method of probing modifications to these interfacial properties, thus allowing the differentiation of hybridization events. In this work, an avidin bulk-modified graphite–epoxy biocomposite (Av-GEB) was employed to immobilize biotinylated oligonucleotides as well as double-stranded DNA onto the electrode surface. Impedance spectra were recorded to detect the change in the interfacial electron transfer resistance (R _et) of the redox marker ferrocyanide/ferricyanide at a polarization potential of +0.17 V. The sensitivity of the technique and the good reproducibility of the results obtained with it confirm the validity of this method based on a universal affinity biocomposite platform coupled with the impedimetric technique.     

Study of titanocene–DNA and molybdenocene–DNA interactions by inductively coupled plasma–atomic emission spectroscopy

Titanocene and molybdenocene dichlorides belong to a new class of organometallic antitumor agent. Although these complexes are isostructural, they behave differently under physiological conditions and hence have different mechanisms of action. It was initially proposed that these species interact with DNA, inhibiting the cell cycle. Recent studies using nucleotides and oligonucleotides suggest that molybdenocene does not bind DNA constituents at physiological pH whereas titanocene apparently interacts weakly with nucleotides through the phosphoesters. The evidence for this was, however, obtained under non-physiological conditions. Herein we report an analytical method that enables determination of the amount of metal bound to DNA under physiological conditions (pH 7.4 and buffer solution) and with sample preparation (dialysis) that resembles the cell environment. It was found that more than 90% titanium was bound to DNA after 46 h whereas binding of molybdenum was no more than 5%.     

Metal–base pairing in DNA

The use of DNA as a molecular wire in nanoscale electronic architectures would greatly benefit from its capability of sequence-specific self-assembly. Although single electrons and positive charges have been shown to be transmitted by natural DNA over a distance of several base pairs, the high ohmic resistance of unmodified oligonucleotides imposes a serious obstacle. Exchanging some or all of the Watson–Crick base pairs in DNA by metal complexes may solve this problem and evolve DNA-like materials with superior conductivity for future nano-electronic applications. The so-called metal–base pairs are formed from suitable transition metal ions and ligand-like nucleosides which are introduced into both of the two pairing strands by automated DNA synthesis. This review illustrates the basic concepts of metal–base pairing and highlights recent developments in the field.     

Biophysical and biochemical investigation on the binding of a manganese–cyanonitrosyl complex with DNA

The interaction of a cyanonitrosyl–manganate complex with DNA has been studied by u.v.–vis spectroscopy, circular dichroism, fluorescence and gel electrophoresis techniques. As the DNA 260 nm band remained insensitive to interaction, the interaction ratio was determined by monitoring the CN⁻→ Mn LMCT band observed at 222 nm, and the interaction ratio was found to be in the complex (D): DNA (P)=1:0.30 from the spectrophotometric titration. The above-mentioned physical measurements indicate that the binding mode is not intercalative and the cyanonitrosyl system is a groove binder.     

The influence of the temperature on the liquid–liquid equilibrium of the ternary system 1-pentanol–ethanol–water

Liquid–liquid equilibrium data for the ternary system 1-pentanol–ethanol–water have been determined experimentally at 25, 50, 85 and 95°C. These results have been correlated simultaneously by the uniquac method obtaining two sets of interaction parameters: one of them independent of the temperature and the other with a linear dependence. Both sets of parameters fit the experimental results well.     

Investigation on the toxic interaction of chrysoidine hydrochloride–CTMAB combined contamination with calf thymus DNA

The toxic interaction of the azo dye-chrysoidine hydrochloride combined with cetyltrimethyl ammonium bromide (CTMAB) in living tissue was studied in vitro. The absorption spectrum, resonance light scattering (RLS), circular dichroism (CD) and transmission electron microscopy (TEM) results showed that the toxicity of chrysoidine hydrochloride itself to calf thymus DNA (ct-DNA) is weak, while the chrysoidine hydrochloride–CTMAB combined pollution showed obvious toxic interaction with ct-DNA. The chrysoidine hydrochloride–CTMAB combined contamination can interact with ct-DNA to form an ion-associated complex through electrostatic and hydrophobic forces. The conformation of DNA was changed in the interaction process to show toxic. The experimental results showed that the combination of chrysoidine hydrochloride–CTMAB has higher toxicity to ct-DNA than either chrysoidine hydrochloride or CTMAB individually, and the combined pollution showed a strong toxic co-effect at a dose of 3.0 × 10^?4 mol L^?1 chrysoidine hydrochloride and 1.6 × 10^?5 mol L^?1 CTMAB.     

Phase equilibria in the palladium-rich part of the Pd–Au–Cu–Sn quaternary system

The solubility of tin in the phases of Pd–Au–Sn and Pd–Cu–Sn ternary systems and a Pd–Au–Cu–Sn quaternary system with a fixed Pd: Au: Cu ratio of 11.1: 1: 4.6 is studied via microstructural, X-ray diffraction, and energy dispersive analysis. It is found that a quaternary alloy in equilibrium with a solid solution based on Pd, Au, and Sn contains a τ₁ compound with structure which is derivative of the In type. It contains ~15 at % Sn and is a solid solution of the same compounds identified earlier in Pd–Au–Sn and Pd–Cu–Sn ternary systems. In addition, a quaternary alloy with a content of 20 at % Sn also contains a τ₂ compound with the Pd₂CuSn own type and can barely dissolve gold. The obtained data are used to construct a three-dimensional model of the Pd-rich part of the isothermal tetrahedron of the Pd–Au–Cu–Sn system and diagrams of the tin solubility isolines in palladium-rich alloys of the quaternary system at 500°С.     

Formation of the layering boundary in the water–benzene–perfluorobenzene system

The dynamics of the interface between liquid phases in the water–benzene–perfluorobenzene system was studied in a natural experiment. The interfacial tension was found to depend on the density of the organic layer. The range of interfacial tensions in which inversion of the organic and aqueous phases takes place was determined, and the working range of a separating flask as an element of the separation scheme for the mixture was revealed.     

Predicting the formation enthalpies of Cd–Ga–In–Sn–Zn liquid alloys by the limiting partial enthalpies

The formation enthalpies of Cd–Ga–Sn, In–Sn–Zn, Cd–Ga–In–Sn, Ga–In–Sn–Zn and Cd–Ga–In–Sn–Zn liquid alloys are calculated by molecular interaction volume model (MIVM), which only using the limiting partial enthalpies of binary systems and the coordination numbers of the constituent elements in liquid alloys. The predicted values are compared with the experimental data and the values calculated using Hoch–Arpshofen model, which indicate that the model is reliable and convenient.     

Kinetic analysis of the crystallization processes in the glasses of the Bi–As–S system

Kinetic analysis of the crystallization process in Bi₄(As₂S₃)₉₆ and Bi₆(As₂S₃)₉₄ glasses was performed based on DSC curves recorded under non-isothermal measurement conditions. Samples were thermally treated at different heating rates in the temperature range 300?C770?K. The activation energy of crystallization E and the pre-exponential factor K ₀ are determined by the Kissinger method and the characteristic crystallization parameters m and n of investigated glasses by the Matusita method. For both crystallization processes the glass with 4 at.% of Bi is characterized by the mechanism of volume nucleation, which is manifested in the form of two-dimensional growth at the first crystallization process, and as three-dimensional at the second one. On the other hand, in the sample with 6 at.% Bi, the average value of the parameter m is close to one, which indicates one-dimensional crystal growth. Compatibility of the values of the parameters m and n suggests that this sample has a large number of crystallization centers, which do not increase significantly during the thermal treatment.     

New Phase in the Bi–Sr–Ca–Cu–O System

Cooling a melt of a Bi–Sr–Ca–Cu–O system (Bi:Sr:Ca:Cu = 4:3:3:4 or 2:2:2:4) from 1000°C-1050°C yielded crystals of a new red-colored nonsuperconducting phase, accompanying the superconducting 2212 and 2201 phases. Based on the EPR spectra, it was concluded that copper is univalent in this compound. The new phase has a composition Bi_2.2Sr_1.6Ca_1.3Cu₂Ox. The X-ray diffraction pattern has been indexed, and the unit cell parameters of the phase have been determined: space group P2/m, a = 12.93, b = 4.55, c = 10.94 ; = 102.72°.     

On the kinetics of pozzolanic reaction in the system kaolin–lime–water

The kinetics of the pozzolanic reaction of enriched kaolin from the “Senovo” deposit (Bulgaria) with lime is the object of this article. The kaolin contains kaolinite as a major clay mineral as well as admixtures of quartz and illite. The experimental data of pozzolanic activity at temperatures of 100 and 23 °C are obtained for different reaction times. The reaction degrees of kaolinite and lime at 100 °C are determined from the pozzolanic activity data using a powder X-ray diffraction analysis. The kinetic analysis is performed by joint presentation of theoretical and experimental data in dimensionless coordinates having in mind the influence of particle size distribution on the reaction rate. It is found by the kinetic analysis that the rate of entire reaction is limited by the rate of chemical reaction on the reaction surface up to degree of reaction near to 0.4. The rate of penetration of the chemical reaction into the kaolinite particles for this area—from the beginning to degree of reaction 0.4, is determined to be equal to 2.10⁻¹¹ m/s.     

Polyaniline–DNA microsphere formation by simple electropolymerization

Polyaniline (PANI) microspheres were prepared by electrochemical polymerization. To obtain PANI having novel micro- and nanostructures, by the potential scan technique, aniline was electropolymerized in the presence of DNA using four polymerizing solutions containing different acids: H₂SO₄, C₆H₅SO₃H, HClO₄, and CF₃COOH. The growth rate of the PANI film on the electrode surface decreased by the presence of DNA, suggesting that DNA interacted with the growing PANI molecules during the electropolymerization. The growth rate also depended on the type of acid, i.e., the anion, in the polymerizing solution and was in the order of SO₄ ²⁻ > C₆H₅SO₃ ⁻ > ClO₄ ⁻ > CF₃COO⁻, which significantly coincided with the reverse order of the Hofmeister series representing the lyophilicity of the anion. When aniline was electropolymerized in the CF₃COOH polymerizing solution containing DNA, PANI microspheres were obtained without any templates. This PANI showed a sufficient redox activity in the less acidic solution in which the ordinary PANI has a slight redox activity. On the other hand, the electronic state of the PANI differed from the ordinary ones; a new absorption band was evident at 620 nm. The difference in the redox activity and electronic state suggested that the DNA molecules were incorporated in the PANI and electronically interacted with the PANI molecules.     

Disposable DNA biosensor with the carbon nanotubes–polyethyleneimine interface at a screen-printed carbon electrode for tests of DNA layer damage by quinazolines

A screen-printed carbon working electrode within a commercially available screen-printed three-electrode assembly was modified by using a composite of multiwalled carbon nanotubes (MWCNT) dispersed in polyethylenimine (PEI) followed by covering with the calf thymus dsDNA layer. Several electrochemical methods were used to characterize the biosensor and to evaluate damage to the surface-attached DNA: square wave voltammetry of the [Ru(bpy)₃]²⁺ redox indicator and mediator of the guanine moiety oxidation, cyclic voltammetry and electrochemical impedance spectroscopy in the presence of the [Fe(CN)₆]^3−/4− indicator in solution. Due to high electroconductivity and large surface area of MWCNT and positive charge of PEI, the MWCNT–PEI composite is an advantageous platform for the DNA immobilization by the polyelectrolyte complexation and its voltammetric and impedimetric detection. In this respect, the MWCNT–PEI interface exhibited better properties than the MWCNT–chitosan one reported from our laboratory previously. A deep DNA layer damage at incubation of the biosensor in quinazoline solution was found, which depends on the quinazoline concentration and incubation time. Figure Impedance spectra for the modified electrodes. Conditions: 1 mM [Fe(CN)₆]^3–/4– in 0.1 M PBS (pH = 7.0), potential amplitude 10 m V, frequency range 12–1×10₄ Hz. Dedicated to Professor Jan Garaj on the occasion of his 75th birthday     

Detecting Counterion Dynamics in DNA–Protein Association

Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so-called “ion atmosphere”. Although the release of counterions upon DNA–protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA–protein association. NMR-based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA–protein association.