DNA Interaction with Coordination Compounds of Cd(II)containing 1,10-Phenanthroline.

The experimental study of the DNA interaction with three cadmium coordination compounds [Cd(phen)3](CH3CO2)2, [Cd(phen)2(H2O)2](CH3CO2)2, and [Cd2(phen)4(H2O)2](CH3CO2)4 was carried out using spectrophotometry, viscosity, and dynamic light scattering methods. The role of the solution ionic strength (concentration of NaCl) was analyzed. All compounds can penetrate (fully or partly) to the major or minor DNA grooves. It was shown that, in addition to the important role of electrostatic interactions in the formation of the complex, intercalation of the 1,10-phenanthroline ligand occurs for compounds [Cd(phen)2(H2O)2](CH3CO2)2 and [Cd2(phen)4(H2O)2](CH3CO2)4. Compound [Cd(phen)3](CH3CO2)2 binds to DNA externally. The coordination bond between cadmium and DNA was formed in DNA complexes with [Cd2(phen)4(H2O)2](CH3CO2)4. Preliminary computer modeling of the DNA interaction with the compounds used was performed.

Packaging of DNA Integrated with Metal Nanoparticles in Solution.

The transformation of high-molecular DNA from a random swollen coil in a solution to a discrete nanosized particle with the ordered packaging of a rigid and highly charged double-stranded molecule is one of the amazing phenomena of polymer physics. DNA condensation is a well-known phenomenon in biological systems, yet its molecular mechanism is not clear. Understanding the processes occurring in vivo is necessary for the usage of DNA in the fabrication of new biologically significant nanostructures. Entropy plays a very important role in DNA condensation. DNA conjugates with metal nanoparticles are useful in various fields of nanotechnology. In particular, they can serve as a basis for creating multicomponent nanoplatforms for theranostics. DNA must be in a compact state in such constructions. In this paper, we tested the methods of DNA integration with silver, gold and palladium nanoparticles and analyzed the properties of DNA conjugates with metal nanoparticles using the methods of atomic force microscopy, spectroscopy, viscometry and dynamic light scattering. DNA size, stability and rigidity (persistence length), as well as plasmon resonance peaks in the absorption spectra of systems were studied. The methods for DNA condensation with metal nanoparticles were analyzed.

Electrostatic Interactions in the Formation of DNA Complexes with Cis- and Trans-Isomers of Azobenzene-Containing Surfactants in Solutions with Di- and Trivalent Metal Ions.

The effect of the presence of divalent and trivalent metal ions in solutions upon DNA packaging induced by the photosensitive azobenzene-containing surfactant is considered. It has been shown that the addition of divalent and trivalent metal ions does not affect the DNA-surfactant interaction for both the cis- and the trans-isomers of the surfactant. At the same time, the ionic strength of the solution, which is provided by a certain concentration of the salt, has a huge impact. It affects the association of surfactant molecules with each other and their binding to DNA. It has been shown by computer simulation that cobalt hexamine is attracted to the N7 atom of guanine in the major groove of DNA and does not penetrate into grooves near the AT base pairs.

Hybridization-Driven Adsorption of Polyadenine DNA onto Gold Nanoparticles.

The attachment of functional DNA to gold nanoparticles via polyadenine adsorption is a well-established technology. This approach was mainly viewed through the lens of changing the DNA charge in order to reduce the electrostatic barrier created by a similarly charged gold surface. However, altering the DNA charge results in the loss of its functionality. This work considers the adsorption process of polyadenines by force that artificially brings them closer to the surface. As a force source, we used the hybridization of a DNA strand carrying polyadenines with a complementary strand already attached to the surface. It was shown that the hybridization forces facilitated the adsorption of polyadenines. We believe that this approach is applicable in various areas where it is essential to preserve the functionality of DNA during conjugation with nanoparticles.

Amyloid fibril length distribution from dynamic light scattering data.

The study of the aggregation of amyloid proteins is challenging. A new approach to processing dynamic light scattering data was developed and tested using aggregates of the well-known model Sup35NM amyloid. After filtering and calculating the moving averages of autocorrelation functions to reduce impacts of noise, each averaged autocorrelation function is converted to the fibril length distribution via numerical modeling. The processing results were verified using atomic force and scanning electron microscopy data. Analysis of fibril length distribution changes over time gives valuable information about the aggregation process.

DNA Conformational Changes Induced by Its Interaction with Binuclear Platinum Complexes in Solution Indicate the Molecular Mechanism of Platinum Binding.

Platinum anticancer drugs inhibit the division of cancer cells through a DNA binding mechanism. The bimetallic platinum compounds have a possibility for blocking DNA replication via the cross-linking of DNA functional groups at different distances. Many compounds with metals of the platinum group have been tested for possible antitumor activity. The main target of their biological action is a DNA molecule. A combined approach to the study of the interaction of DNA with biologically active compounds of this type is proposed. The capabilities of various methods (hydrodynamic, spectral, microscopy) in obtaining information on the type of binding of coordination compounds to DNA are compared. The analysis of DNA binding with platinum binuclear compounds containing pyrazine, tetrazole, 5- methyltetrazole, 3-propanediamine as bridging ligands in a solution was carried out with the methods of circular dichroism (CD), luminescent spectroscopy (LS), low gradient viscometry (LGV), flow birefringence (FB) and atomic force microscopy (AFM). The competitive binding of different platinum compounds to DNA and the analysis of platinum attachment to DNA after protonation of its nitrogen bases simply indicates the involvement of N7 guanine in binding. Fluorescent dye DAPI was also used to recognize the location of platinum compounds in DNA grooves. DNA conformational changes recorded by variations in persistent length, polyelectrolyte swelling, DNA secondary structure, and its stability clarify the molecular mechanism of the biological activity of platinum compounds.

Cis-Isomers of Photosensitive Cationic Azobenzene Surfactants in DNA Solutions at Different NaCl Concentrations: Experiment and Modeling.

The DNA interaction with cis-isomers of photosensitive azobenzene-containing surfactants was studied by both experimental methods and computer simulation. It was shown that before the organization of micelles, such surfactants in the cis-conformation form associates of only a single type with a disordered orientation of molecules. In contrast, for trans-isomers, there exist two types of associates with head-to-head or head-to-tail orientations of molecules in dependence on salt concentration in a solution. The comparison of cis- and trans-isomer binding to DNA and the influence of salt concentration on the formation of their complexes with DNA were studied. It was shown that cis-isomers interact with phosphate groups of DNA and that their molecules were also located along the minor groove of DNA.

Stabilization of DNA by sodium and magnesium ions during the synthesis of DNA-bridged gold nanoparticles.

Nanostructures synthesized using DNA-conjugated gold nanoparticles have a wide range of applications in the field of biosensorics. The stability of the DNA duplex plays a critical role as it determines the final geometry of these nanostructures. The main way to control DNA stability is to maintain a high ionic strength of the buffer solution; at the same time, high salt concentrations lead to an aggregation of nanoparticles. In this study, by means of the instrumentality of DNA-bridged seeds using tris(hydroxymethyl)aminomethane as a soft reducing agent the dumbbell-like gold nanoparticles up to 35 nm were synthesized with a high concentration of sodium ions of up to 100 mM and magnesium ions up to 1 mM. We also examined at the atomic level the details of the effect of the gold nanoparticle surface, as well as Na+ and Mg2+ ions, on the stability of nucleotide pairs located in close proximity to the grafting site.

Some Features of Surfactant Organization in DNA Solutions at Various NaCl Concentrations.

The photosensitive azobenzene-containing surfactant C4-Azo-OC6TMAB is a promising agent for reversible DNA packaging in a solution. The simulation of the trans-isomer surfactant organization into associates in a solution with and without salt as well as its binding to DNA at different NaCl concentrations was carried out by molecular dynamics. Experimental data obtained by spectral and hydrodynamic methods were used to verify the results of simulation. It was shown that head-to-tail aggregates with close to antiparallel orientation of surfactant molecules were formed at certain NaCl and surfactant concentrations (below critical micelle concentration). Such aggregates have two positively charged ends, and therefore, they can be attracted to negatively charged DNA phosphates far located along the chain, as well as those that belong to different molecules. This contributes to the formation of intermolecular DNA-DNA contacts, and this way, the experimentally observed precipitation of DNA can be explained.

Design of a New [PSI +]-No-More Mutation in SUP35 With Strong Inhibitory Effect on the [PSI +] Prion Propagation.

A number of [PSI +]-no-more (PNM) mutations, eliminating [PSI +] prion, were previously described in SUP35. In this study, we designed and analyzed a new PNM mutation based on the parallel in-register ß-structure of Sup35 prion fibrils suggested by the known experimental data. In such an arrangement, substitution of non-charged residues by charged ones may destabilize the fibril structure. We introduced Q33K/A34K amino acid substitutions into the Sup35 protein, corresponding allele was called sup35-M0. The mutagenized residues were chosen based on ArchCandy in silico prediction of high inhibitory effect on the amyloidogenic potential of Sup35. The experiments confirmed that Sup35-M0 leads to the elimination of [PSI +] with high efficiency. Our data suggested that the elimination of the [PSI +] prion is associated with the decreased aggregation properties of the protein. The new mutation can induce the prion with very low efficiency and is able to propagate only weak [PSI +] prion variants. We also showed that Sup35-M0 protein co-aggregates with the wild-type Sup35 in vivo. Moreover, our data confirmed the utility of the strategy of substitution of non-charged residues by charged ones to design new mutations to inhibit a prion formation.

DNA Integration with Silver and Gold Nanoparticles: Enhancement of DNA Optical Anisotropy.

DNA integration with silver and gold nanoparticles was carried out by the chemical reduction of silver and gold ions after the formation of their complexes with high molecular DNA in solution. It is shown that, for a good association of DNA with nanoparticles, the ions of silver and gold should be linked with DNA bases rather strongly. The proposed model of gold interaction with DNA is the coordination of gold to N7 guanine in a major groove followed by the transformation of the GC pair to Hoogsteen's type pairing, in which the gold atom is located between the bases and is bonded simultaneously to N7 guanine and N3 cytosine. For gold and silver nanoparticles associated with DNA, the peak of plasmon resonance shifts relative to that of free nanoparticles in solution. AFM (atomic force microscopy) images of both free and associated with DNA nanoparticles were obtained. Binding of high molecular DNA to gold and silver nanoparticles leads to a decrease in the size of its molecular coil in solution, but the bending rigidity of DNA helix (persistent length) does not change. The almost 3-fold increase in the optical anisotropy of DNA was observed when DNA was associated with gold nanoparticles. This result was obtained with the flow birefringence method using a light source with a wavelength of 550 nm, which is close to the peak of the plasmon resonance of gold nanoparticles. For DNA associated with silver nanoparticles, a similar result was obtained when using a light source with a wavelength of about 410 nm.

DNA Complexes with Cobalt(II) Phthalocyanine Disodium Disulfonate.

The interaction of cobalt phthalocyanine disodium disulfonate (CoPc) with calf thymus DNA in solutions was investigated by UV/vis spectrophotometry, circular dichroism (CD), and hydrodynamic methods (viscosity and flow birefringence). Two types of CoPc binding to DNA were observed. Fast CoPc interactions with DNA via external binding to phosphates were accompanied by the formation of stack-type phthalocyanine structures on the periphery of the DNA helix. The optical absorption spectra of such CoPc complexes with DNA were analyzed in order to obtain a binding constant K = (4.8 ± 0.4) × 104 M-1. CD spectra show the increasing optical activity of phthalocyanines bonded to DNA. DNA plays the role of a matrix, contributing to an increase in their stacking interactions. The CD spectrum of DNA varies slightly. The second type of cobalt-to-DNA binding manifests itself over a certain time. It can be associated with the reorganization of ligands in the cobalt coordination sphere by introducing DNA atoms. In our experiments, such binding was observed after storage of solutions for approximately 20 h at a temperature of 4 °C. It was shown that the minor groove of DNA remains free in CoPc-DNA complexes. CoPc does not bind with the most important group for metal coordinating to DNA in the major groove (N7 guanine). We completely excluded the intercalation binding model. The planes of phthalocyanines in CoPc-DNA complexes are oriented predominantly normal to the axis of the DNA helix. DNA rigidity (persistent length) does not change. This follows from the data on the measurement of the optical anisotropy and intrinsic viscosity of DNA in complexes.

Role of Mono- and Divalent Ions in Peptide Glu-Asp-Arg-DNA Interaction.

The interaction of the regulatory biologically active peptide Glu-Asp-Arg (EDR) with DNA is considered by spectral, NMR, viscosimetry, and molecular dynamics methods. It was shown that EDR can partly penetrate into the major groove of DNA and affect the base atoms, mainly the N7 and O6 of guanine. It was observed that Mg2+ ions can promote DNA-EDR interaction due to their effective screening of the negatively charged phosphate groups of DNA. This action of Mg2+ remains in salted solution as well.

DNA Interaction with Head-to-Tail Associates of Cationic Surfactants Prevents Formation of Compact Particles.

Cationic azobenzene-containing surfactants are capable of condensing DNA in solution with formation of nanosized particles that can be employed in gene delivery. The ratio of surfactant/DNA concentration and solution ionic strength determines the result of DNA-surfactant interaction: Complexes with a micelle-like surfactant associates on DNA, which induces DNA shrinkage, DNA precipitation or DNA condensation with the emergence of nanosized particles. UV and fluorescence spectroscopy, low gradient viscometry and flow birefringence methods were employed to investigate DNA-surfactant and surfactant-surfactant interaction at different NaCl concentrations, [NaCl]. It was observed that [NaCl] (or the Debye screening radius) determines the surfactant-surfactant interaction in solutions without DNA. Monomers, micelles and non-micellar associates of azobenzene-containing surfactants with head-to-tail orientation of molecules were distinguished due to the features of their absorption spectra. The novel data enabled us to conclude that exactly the type of associates (together with the concentration of components) determines the result of DNA-surfactant interaction. Predomination of head-to-tail associates at 0.01 M < [NaCl] < 0.5 M induces DNA aggregation and in some cases DNA precipitation. High NaCl concentration (higher than 0.8 M) prevents electrostatic attraction of surfactants to DNA phosphates for complex formation. DAPI dye luminescence in solutions with DNA-surfactant complexes shows that surfactant tails overlap the DNA minor groove. The addition of di- and trivalent metal ions before and after the surfactant binding to DNA indicate that the bound surfactant molecules are located on DNA in islets.

DNA Binding with Acetate Bis(1,10-phenanthroline)silver(I) Monohydrate in a Solution and Metallization of Formed Structures.

The study of DNA interaction with the acetate bis(1,10-phenanthroline)silver(I) monohydrate in a solution is of interest both for understanding the mechanism of biological activity of silver compound and for forming ordered structures (DNA fibrils) that can be used to solve various problems in the field of nanotechnology. The analysis of changing the DNA conformation (secondary structure, persistent length and volume effects) during the interaction by the methods of UV spectroscopy with the analysis of DNA melting, circular dichroism, viscosity, flow birefringence, AFM (atomic force microscopy) and SEM (scanning electron microscopy) was performed. The formation of two types of complexes was observed. At lower concentration of compound in DNA solution, silver atoms form the coordination bonds with a macromolecule, while the released phenanthroline ligands intercalate between DNA bases. When the concentration of the compound increases, the phenanthroline ligands form an ordered "layer" around the helix. The excess of silver compounds in the DNA solution (with more than five silver atoms per base pair), DNA precipitation is observed with the formation of long fibrils. It was shown that the binding of silver to DNA during the formation of complexes provides further metallization of the resulting structures with the aid of reducing agents; phenanthroline ligands influence the result of such metallization.

Model system for multifunctional delivery nanoplatforms based on DNA-Polymer complexes containing silver nanoparticles and fluorescent dye.

Creation of multifunctional nanoplatforms is one of the new approaches to complex treatment and diagnosis with the monitoring of the curative process. Inclusion of various components into the drug delivery system may reduce toxicity and enhance or modify the therapeutic effects of medicines. In particular, some properties of metal nanoparticles and nanoclusters provide the ability to create new systems for treatment and diagnosis of diseases, biocatalysis and imaging of objects. For example, the ability of metal nanoparticles to enhance the quantum yield of luminescence can be used in bioimaging and therapy. The aim of the research was to construct and examine a multicomponent system based on DNA-polycation compact structure with the inclusion of silver nanoparticles and luminescent dye as a model system for delivery of genes and drugs with the possibility of modification and enhancement of their action.

Similarities and differences in the influence of polycations and oligomers on DNA conformation and packaging.

A comparison of DNA conformational changes in a solution containing the poly-l-lysine with the number of monomers z=3, 5, 17, 20, 270, 325 and polyamines (spermine and spermidine) was carried out in 1M and 5mM NaCl solutions. It was shown that despite the identical results of DNA condensation induced by compounds, their influence on the DNA conformation prior to packaging depends on whether they belong to a long polycations or short oligomers. DNA secondary and tertiary structures were examined using Circular Dichroism, UV-vis Spectrophotometry, Dynamic Light Scattering, Low Gradient Viscometry, Flow Birefringence, and AFM. The phase diagrams for systems of DNA-polycations, DNA-oligomers, DNA-polyamines were drawn.

Fluorescent silver nanoclusters in condensed DNA.

We study the formation and fluorescent properties of silver nanoclusters encapsulated in condensed DNA nanoparticles. Fluorescent globular DNA nanoparticles are formed using a dsDNA-cluster complex and polyallylamine as condensing agents. The fluorescence emission spectrum of single DNA nanoparticles is obtained using tip-enhanced fluorescence microscopy. Fluorescent clusters in condensed DNA nanoparticles appear to be more protected against destructive damage in solution compared to clusters synthesized on a linear polymer chain. The fluorescent clusters on both dsDNA and ssDNA exhibit the same emission bands (at 590 and 680 nm) and the same formation efficiency, which suggests the same binding sites. By using density functional theory, we show that the clusters may bind to the Watson-Crick guanine-cytosine base pairs and to single DNA bases with about the same affinity.

DNA compaction by azobenzene-containing surfactant.

We report on the interaction of cationic azobenzene-containing surfactant with DNA investigated by absorption and fluorescence spectroscopy, dynamic light scattering, and atomic force microscopy. The properties of the surfactant can be controlled with light by reversible switching of the azobenzene unit, incorporated into the surfactant tail, between a hydrophobic trans (visible irradiation) and a hydrophilic cis (UV irradiation) configuration. The influence of the trans-cis isomerization of the azobenzene on the compaction process of DNA molecules and the role of both isomers in the formation and colloidal stability of DNA-surfactant complexes is discussed. It is shown that the trans isomer plays a major role in the DNA compaction process. The influence of the cis isomer on the DNA coil configuration is rather small. The construction of a phase diagram of the DNA concentration versus surfactant/DNA charge ratio allows distancing between three major phases: colloidally stable and unstable compacted globules, and extended coil conformation. There is a critical concentration of DNA above which the compacted globules can be hindered from aggregation and precipitation by adding an appropriate amount of the surfactant in the trans configuration. This is because of the compensation of hydrophobicity of the globules with an increasing amount of the surfactant. Below the critical DNA concentration, the compacted globules are colloidally stable and can be reversibly transferred with light to an extended coil state.

First ruthenium organometallic complex of antibacterial agent ofloxacin. Crystal structure and interactions with DNA.

An organometallic ruthenium complex of quinolone antibacterial agent ofloxacin, [(η(6)-p-cymene)RuCl(O,O-oflo)]·2.8H(2)O (1·2.8H(2)O), was isolated, and its crystal structure was determined. In this "piano-stool" complex, quinolone is bidentately coordinated to the metal through the ring carbonyl and one of the carboxylic oxygen atoms. Interactions of the title complex with DNA were studied by spectroscopic methods [electronic, fluorescence, and circular dichroism (CD)] and atomic force microscopy (AFM). It was established that the electrostatic attraction between the ruthenium complex and DNA in a solution is important for binding because interactions were observed only in a solution with low ionic strengths. An induced-CD (ICD) signal was observed in a solution of DNA and the title complex, which proves interaction between ruthenium and macromolecules. Competitive binding between cisplatin and 1 to DNA revealed that cisplatin prevents binding of 1. Our experiments revealed that binding of the title complex to DNA occurs also if guanine N7 is protonated. AFM has shown that the title complex provokes DNA shrinkage. Preliminary biological tests have also been performed.