Anatoly Zinchenko

DNA hydrogel as a template for synthesis of ultrasmall gold nanoparticles for catalytic applications.

DNA cross-linked hydrogel was used as a matrix for synthesis of gold nanoparticles. DNA possesses a strong affinity to transition metals such as gold, which allows for the concentration of Au precursor inside a hydrogel. Further reduction of HAuCl4 inside DNA hydrogel yields well dispersed, non-aggregated spherical Au nanoparticles of 2-3 nm size. The average size of these Au nanoparticles synthesized in DNA hydrogel is the smallest reported so far for in-gel metal nanoparticles synthesis. DNA hybrid hydrogel containing gold nanoparticles showed high catalytic activity in the hydrogenation reaction of nitrophenol to aminophenol. The proposed soft hybrid material is promising as environmentally friendly and sustainable material for catalytic applications.

DNA Compaction by Divalent Cations: Structural Specificity Revealed by the Potentiality of Designed Quaternary Diammonium Salts

DNA interaction with quaternary diammonium dications, R(CH3)2N+(CH2)nN+(CH3)2R, having various intercharge distances, lengths, and branching, and the chemical nature of the hydrophobic substituents were investigated by fluorescent microscopy and circular dichroism (CD) spectroscopy to reveal their structural specificity for binding to DNA. The conformational behavior of DNA was found to be highly sensitive to the structure of the dications with separated charges. The distance between two ammonium groups greatly influences the compaction activity of the dications. To explain this situation, we proposed a model that demonstrates that the charge density of the dication and the geometric fit between DNA phosphates and the ammonium groups in the dications play an important role in providing efficient DNA collapse. Elongation of the alkyl substituents (R) in the diammonium salts from ethyl to hexyl did not generate any significant alterations in the compaction activities, whereas the branching of substituents caused a drastic decrease in their compaction ability. Based on the results of CD spectroscopy, it was found that the ability of the dications to provoke a DNA transition from the B‐form to A‐form was also specific: it depended on their intercharge distances and was independent of the length of alkyl substituents.

Conformational Behavior of Giant DNA through Binding with Ag+ and Metallization

The conformational behavior of a long single-chain double-stranded DNA in solutions of free silver ions and silver nanoparticles generated via the reduction of AgNO3 by NaBH4 was monitored by fluorescence and electron microscopies and UV spectroscopy. The interaction of monovalent silver ions with DNA induces shrinking of a DNA-coiled polymer chain as a result of a decrease in the DNA persistence length through the complexation of Ag+ with DNA bases. In contrast, the reduction of silver ions by NaBH4 in DNA solutions triggers DNA compaction: a DNA transition from elongated coil state into a compact state. This transition is continuous, unlike the all-or-none discrete DNA compaction that is commonly seen with multications. It is suggested that the collapse of DNA is accompanied by growth aggregation of silver nanoparticles generated on the DNA template.

ATP-Induced Shrinkage of DNA with MukB Protein and the MukBEF Complex of Escherichia coli

Fluorescence microscopic observation of individual T4 DNA molecules revealed that the MukBEF complex (bacterial condensin) and its subunit, the MukB (a member of the SMC [structural maintenance of chromosomes] superfamily) homodimer, of Escherichia coli markedly shrunk large DNA molecules in the presence of hydrolyzable ATP. In contrast, in the presence of ADP or ATP-gammaS, the conformation of DNA was almost not changed. This suggests that the ATPase activity of subunit MukB is essential for shrinking large DNA molecules. Stretching experiments on the shrunken DNA molecules in the presence of ATP and MukBEF indicated a cross-bridging interaction between DNA molecules.

Crowding by Anionic Nanoparticles Causes DNA Double-Strand Instability and Compaction

Up to the present, DNA structural transitions caused by cationic polymers as well as in concentrated solutions of neutral polymers are well documented, while a little is known about DNA interaction with like-charge species. Herein, changes in the structure of DNA induced by anionic nanoparticles of different sizes (20-130 nm) were investigated by combining single-molecule DNA fluorescent microscopy, to monitor the conformational dynamics of long-chain DNA, with spectroscopic methods, to gain insight into changes in the secondary structure of DNA. The results showed that several percent of negatively charged silica nanoparticles induced DNA compaction from a coil to a globule, and this change was accompanied by a decrease in the melting temperature of the DNA double helix. DNA was compacted into toroidal condensates with reduced diameters of about 20-30 nm. Smaller 20 nm nanoparticles triggered a DNA coil-globule transition at lower concentrations, but the exclusion volume for each type of nanoparticle at the point of complete DNA collapse, as estimated by taking into account the depth of the ionic atmosphere, was found to be almost the same.

Control of a catalytic activity of gold nanoparticles embedded in DNA hydrogel by swelling/shrinking the hydrogel’s matrix

HYPOTHESIS By incorporating catalytically active nanoparticles into polymeric hydrogel one can tune the catalytic activity of such a hybrid material by affecting the state of polymer matrix. EXPERIMENT Herein, hybrid hydrogel was prepared by metallization of DNA cross-liked hydrogel via absorption of gold precursor and reduction by NaBH4, and its catalytic activity under various swelling ratio was studied spectroscopically. FINDINGS Catalytic activity of Au nanoparticles in hydrogel was shown to depend drastically on a swelling degree of hydrogel easily controlled by a change in an ionic strength of solution. Increase of the catalytic reaction rate was proportional to the volume of hybrid hydrogel indicating that diffusion of reactants toward catalytic centers inside hydrogel is crucial for the efficient catalysis by soft-matter-based hybrid material.

Compaction of DNA on nanoscale three-dimensional templates.

There exist several important in vivo examples, where a DNA chain is compacted on interacting with nanoscale objects such as proteins, thereby forming complexes with a well defined molecular architecture. One of the well known manifestations of such a natural organization of a semi-flexible DNA chain on nanoscale objects is hierarchical DNA molecule assembly into a chromosome, which is mediated by cationic histone proteins at the first stages of compaction. The biological importance of this and other natural nanostructural organizations of the DNA molecule has inspired many theoretical and numerical studies to gain physical insight into this problem. On the other hand, the experimental model systems containing DNA and nanoobjects, which are important to extend our knowledge beyond natural systems, were almost unavailable until the last decade. Accelerating progress in nanoscale chemistry and materials science has brought about various nanoscale three-dimensional structures such as dendrimers, nanoparticles, and nanotubes, and thus has provided a basis for the next important step in creating novel DNA-containing nanostructures, modelling of natural DNA compaction, and verification of accumulated theoretical predictions on the interaction between DNA and nanoscale templates. This review is written to highlight this early stage of nano-inspired progress and it is focused on physico-chemical and biophysical experimental investigations as well as theoretical and numerical studies dedicated to the compaction of DNA on nanoscale three-dimensional templates.

Entrapping of Fullerenes, Nanotubes, and Inorganic Nanoparticles by a DNA−Chitosan Complex: A Method for Nanomaterials Removal

We report a protocol for entrapping of various water-dispersed nanomaterials: fullerenes, multiwall carbon nanotubes, quantum dots (semiconductor nanoparticles), and gold nanorods, into a DNA-chitosan complex. In contrast to small-size nanomaterial particles, the bulky DNA-chitosan interpolyelectrolyte complex incorporating the dispersed nanomaterials can be easily separated from aqueous media by centrifugation, filtration, or decantation. While the removal of nanoparticles by centrifugation is equally efficient for every type of nanoparticles and reaches 100%, the higher efficiency of the nanomaterials removal by other two methods is favored by larger size of nanoparticles. The application of this entrapping protocol for removal of nanomaterials from water is discussed.

DNA-Assisted Solubilization of Carbon Nanotubes and Construction of DNA-MWCNT Cross-Linked Hybrid Hydrogels

A simple method for preparation of DNA-carbon nanotubes hybrid hydrogel based on a two-step procedure including: (i) solubilization of multi-walled carbon nanotubes (MWCNT) in aqueous solution of DNA, and (ii) chemical cross-linking between solubilized MWCNT via adsorbed DNA and free DNA by ethylene glycol diglycidyl ether is reported. We show that there exists a critical concentration of MWCNT below which a homogeneous dispersion of MWCNT in hybrid hydrogel can be achieved, while at higher concentrations of MWCNT the aggregation of MWCNT inside hydrogel occurs. The strengthening effect of carbon nanotube in the process of hydrogel shrinking in solutions with high salt concentration was demonstrated and significant passivation of MWCNT adsorption properties towards low-molecular-weight aromatic binders due to DNA adsorption on MWCNT surface was revealed.

Photochemical Modulation of DNA Conformation by Organic Dications

A group of azobenzene derivatives containing two quaternary ammonium groups with various intercharge distances between them was synthesised and used to control photochemically the conformation of genomic DNA by switching the distance between cationic ammonium groups in the dications. It was found that isomerisation of either dication from the trans form to cis resulted in an increase in the dications efficiency for DNA compaction; this is associated with a decrease in intercharge distance between ammonium groups and leads to a better match of the binders cationic groups to adjacent phosphate groups of DNA. Ammonium dications have several important advantages over the photosensitive surfactant type of diazobenzene reported earlier: they can be used at significantly lower (>100‐fold) concentrations than photosensitive surfactants, and DNA conformation control can be performed over a broader concentration range of dications. The influence of intercharge distance in photosensitive dications on photo‐induced DNA binding discrimination is discussed, and the molecular mechanism is proposed.