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Anatoly A Zinchenko

Publications and source records attributed to Anatoly A Zinchenko.

10 recordsLinked to original sources
PubMed2006

Transcription of giant DNA complexed with cationic nanoparticles as a simple model of chromatin.

We prepared complexes of giant double-stranded DNA with cationic nanoparticles of 10-40 nm in diameter as an artificial model of chromatin and characterized the properties of changes in their higher-order conformation. We measured the changes in transcriptional activity that accompanied the DNA conformational transitions. Complete inhibition was found at excess concentrations of nanoparticles. In contrast, at intermediate stages of DNA binding with nanoparticles, the transcription activity of DNA survived, and this strongly depended on the size of the nanoparticles. For large nanoparticles of 40 nm, a decrease in transcriptional activity can be caused by the addition of only a small amount of nanoparticles. On the other hand, there was almost no inhibition of DNA transcriptional activity with the addition of small nanoparticles (10 nm) until very high concentrations, even under conditions that induced DNA compaction as revealed by single-DNA observation. At higher concentrations of 10-nm nanoparticles, DNA transcription activity decreased abruptly until it was completely inhibited. These results are discussed in relation to the actual size of the histone core, together with the mechanism of switching of transcriptional activity in eukaryotic cells.

Bacteriophage T4↗
PubMed2005

Compaction of single-chain DNA by histone-inspired nanoparticles.

We elaborated a versatile experimental model of chromatin which consists of a single chain of long duplex DNA that interacts with well-defined cationic nanoparticles of various sizes. We found that the DNA compaction by nanoparticles is stepwise and progressive at the single-chain level. It is controlled by the ability of DNA to wrap nanoparticles, which is more efficient for larger particles and, similar to DNA-histone interaction, is optimal at a physiological salt concentration.

Chromatin↗
PubMed2005

Specific formation of beads-on-a-chain structures on giant DNA using a designed polyamine derivative.

Fluorescence microscopy was used to study the folding transition of giant DNAs, T4 DNA (ca. 166 kbp), and lambda DNA (ca. 48 kbp), which proceeds through intermediates with intramolecular segregation induced by pteridine-polyamine conjugates, i.e., 2-amino-6,7-dimethyl-4-(4,9,13-triazatridecylamino)pteridine and -4-(3-(aminopropyl)amino)pteridine. According to the results of DNA denaturation, UV and fluorescent spectroscopy, and transmission electron microscopic observations, it became clear that DNA folding induced by the polyamine derivative is not a continuous shrinking process but a combination of discontinuous processes.

Bacteriophage T4↗
PubMed2005

Na+ shows a markedly higher potential than K+ in DNA compaction in a crowded environment.

Whereas many physicochemical investigations have shown that among monovalent cations Na(+) ion possesses minimal potential for DNA binding, biological assays have shown that Na(+) ion (in contrast to K(+) ion) plays a primary role in chromatin compaction and related processes. It is difficult to explain this inverse relationship between the compaction potentials of Na(+) and K(+) and their binding abilities. In this study we sought to resolve this contradiction and emphasize the phenomenological distinction between DNA compaction and DNA binding processes in the case of DNA compaction by monocations. Using polyethylene glycol solutions as a model of a crowded cell environment, we studied DNA compaction by alkali metal salts LiCl, NaCl, KCl, RbCl, and CsCl, and found that all of these monocations promote DNA compaction. Among these monovalent cations Na(+) produces the greatest compaction and the ratio of K(+) cand Na(+) oncentrations for DNA compaction is approximately 1.5-2. A comparative analysis of recent experimental results indicates that a higher binding activity of monocation generally corresponds to a low compaction potential of the corresponding monovalent ion. This inverse relation is explained as a result of partial dehydration of monocations in the compact state.

Bacteriophage T4↗
PubMed2005

How does DNA compaction favor chiral selectivity with cationic species? Higher selectivity with lower cationic charge.

A single-molecule study on giant DNA compaction by enantiomeric dications and tetracations demonstrates that strong chiral discrimination in DNA compaction is manifested only if the positive charge on enantiomeric multications is relatively low. The increase in cationicity of the chiral compaction agent inevitably leads to an increase in nonspecific electrostatic interactions and quenching of chiral discrimination in the DNA-folding phase transition.

Bacteriophage T4↗
PubMed2004

DNA compaction by divalent cations: structural specificity revealed by the potentiality of designed quaternary diammonium salts.

DNA interaction with quaternary diammonium dications, R(CH(3))(2)N(+)(CH(2))(n)N(+)(CH(3))(2)R, 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.

Cations, Divalent↗
PubMed2003

Controlling the intrachain segregation on a single DNA molecule.

Intrachain segregation in single DNA molecules induced by quaternary ammonium dications was studied. By means of fluorescent and electron microscopy, it was found that variations in the chemical structure of condensing agents provide one with the opportunity to control the average amount of intrachain segregation centers on the DNA single chain. The manner of interaction between the diammonium molecules was considered to be the key factor for controlling the morphology of the partially collapsed DNA molecules.

Bacteriophage T4↗
PubMed2003

Ascorbic acid induces a marked conformational change in long duplex DNA.

Ascorbic acid is often regarded as an antioxidant in vivo, where it protects against cancer by scavenging DNA-damaging reactive oxygen species. However, the detailed mechanism of the action of ascorbic acid on genetic DNA is still unclear. We examined the effect of ascorbic acid on the higher-order structure of DNA through real-time observation by fluorescence microscopy. We found that ascorbic acid generates a pearling structure in single giant DNA molecules, with elongated and compact regions coexisting along a molecular chain. Results from electron microscopy and atomic force microscopy indicate that the compact regions assume a loosely packed conformation. A possible mechanism for the induction of this conformational change is discussed in relation to the interplay between the higher-order and second-order structures of DNA.

Ascorbic Acid↗
PubMed2002

Secondary structure of DNA is recognized by slightly cross-linked cationic hydrogel.

Interaction of salmon sperm DNA (300-500 bp) and ultrahigh molecular mass DNA (166 kbp) from bacteriophage T4dC with linear poly(N-diallyl-N-dimethylammonium chloride) (PDADMAC) and slightly cross-linked (#) PDADMAC (#PDADMAC) hydrogel in water has been studied by means of UV-spectroscopy, ultracentrifugation, atomic force, and fluorescence microscopy (FM). It is found that the linear polycation induced compaction of either native (double-stranded) or denatured (single-stranded) DNA by forming PDADMAC-DNA interpolyelectrolyte complexes (IPEC)s. At the same time, #PDADMAC hydrogel is able to distinguish between native and denatured DNA. Native DNA is adsorbed and captured in the hydrogel surface layer, while denatured DNA diffuses to the hydrogel interior until the whole hydrogel sample is transformed into the cross-linked IPEC. Both native and denatured DNA can be completely released from the hydrogel in appropriate conditions with no degradation by adding a low molecular salt. The data observed using conventional physicochemical methods with respect to DNA of a moderate molecular mass remarkably correlate with the pictures directly observed for ultrahigh molecular mass DNA in dynamics by using FM.

Animals↗