Amino Acid Sequence of Oligopeptide Causes Marked Difference in DNA Compaction and Transcription.

Compaction of T4 phage DNA (166 kbp) by short oligopeptide octamers composed of two types of amino acids, four cationic lysine (K), and four polar nonionic serine (S) having different sequence order was studied by single-molecule fluorescent microscopy. We found that efficient DNA compaction by oligopeptide octamers depends on the geometrical match between phosphate groups of DNA and cationic amines. The amino acid sequence order in octamers dramatically affects the mechanism of DNA compaction, which changes from a discrete all-or-nothing coil-globule transition induced by a less efficient (K4S4) octamer to a continuous compaction transition induced by a (KS)4 octamer with a stronger DNA-binding character. This difference in the DNA compaction mechanism dramatically changes the packaging density, and the morphology of T4 DNA condensates: DNA is folded into ordered toroidal or rod morphologies during all-or-nothing compaction, whereas disordered DNA condensates are formed as a result of the continuous DNA compaction. Furthermore, the difference in DNA compaction mechanism has a certain effect on the inhibition scenario of the DNA transcription activity, which is gradual for the continuous DNA compaction and abrupt for the all-or-nothing DNA collapse.

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.

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 dication's efficiency for DNA compaction; this is associated with a decrease in intercharge distance between ammonium groups and leads to a better match of the binder's 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.

Facile control of DNA-templated inorganic nanoshell size.

We elaborated a facile method to control the size of CdS nanoshells obtained by DNA assisted "double templating" approach. By changing the concentration of NaCl in solution to vary the extent of DNA electrostatic deposition on cationic silica beads, we succeeded to control the density of DNA adsorbed on the beads, and further the density of CdS material grown on DNA. Further dissolution of the silica core triggers shrinking of CdS shell to a different extent depending on the CdS shell density and results in formation of CdS nanoshells of different sizes from ca. 100 nm to ca. 400 nm. Therefore, the main advantage of the proposed method is that it can be used to synthesize hollow nanoshells of various sizes, from ca. 25% to ca. 75% size of the primary template (silica bead), by using only one single primary template.

DNA-assisted "double-templating" approach for the construction of hollow meshed inorganic nanoshells.

A "double-templating" approach was elaborated to produce meshed nanoshells made of semiconductor material in a two-step process. First, DNA adsorption is templated by spherical nanobeads, and second, DNA is mineralized by an inorganic material (CdS). Dissolution of the core beads leaves nanometer-size shells, the surface structure of which represents a mineralized network of DNAs. This method demonstrates the opportunity to metalize an arbitrary three-dimensional template by depositing a network of nanowires.

Conformational behavior of DNA-templated CdS inorganic nanowire.

We describe the conformational behavior and morphological control of DNA-mineralized CdS nanowires in a bulk solution. The conformational behavior of individual double-stranded DNA in the presence of cadmium ions and stoichiometric mixtures of cadmium ions and sulfide ions was directly visualized by fluorescence microscopy. It was found that in the presence of mixtures of cadmium ions and sulfide ions, DNA molecules exhibit a conformational transition from an elongated coil to a compacted state. Mineralized DNA nanowires possess a significant conformational freedom at a microscale, and flexibility in the micro- and nanodimensions. The density of the inorganic material on the nanowire can be controlled by varying the concentrations and the molar ratio of Na(2)S to Cd(ClO(4))(2).

Thermo-switching of the conformation of genomic DNA in solutions of poly(N-isopropylacrylamide).

We used poly(N-isopropylacrylamide) (PNIPAM) to control the conformation of genomic DNA by changing the temperature of a reaction solution and studied the DNA transition at the level of single DNA molecules. With this method, the conformation of long genomic DNA can be readily and reversibly switched between a very compact condensate and an unfolded macromolecule.

Methane in an open-cage [60]fullerene.

An endohedral methane complex of a fullerene derivative is first synthesized by insertion of a methane molecule through the opening of an open-cage C(60) derivative. The trapped methane is confirmed by NMR spectroscopy and mass spectrometry. Both methane carbon and protons show remarkable upfield shifts in NMR, characteristic of a chemical species in a fullerene cage. CH(4) protons appear as one equivalent signal in the (1)H NMR spectrum, suggesting that even methane can rotate in a C(60) cage.

Encapsulation of Long Genomic DNA into a Confinement of a Polyelectrolyte Microcapsule: A Single-Molecule Insight.

Encapsulation of nucleic acids is an important technology in gene delivery, construction of "artificial cells", genome protection, and other fields. However, although there have been a number of protocols reported for encapsulation of short or oligomeric DNAs, encapsulation of genome-sized DNA containing hundreds of kilobase pairs is challenging because the length of such DNA is much longer compared to the size of a typical microcapsule. Here, we report a protocol for encapsulation of a ca. 60 µm contour length DNA into several micrometer-sized polyelectrolyte capsules. The encapsulation was carried out by (1) compaction of T4 DNA with multivalent cations, (2) entrapment of DNA condensates into micrometer-sized CaCO3 beads, (3) assembly of polyelectrolyte multilayers on a bead surface, and (4) dissolution of beads resulting in DNA unfolding and release. Fluorescence microscopy was used to monitor the process of long DNA encapsulation at the level of single-DNA molecules. The differences between long and short DNA encapsulation processes and morphologies of products are discussed.

Putting ammonia into a chemically opened fullerene.

We put ammonia into an open-cage fullerene with a 20-membered ring ( 1) as the orifice and examined the properties of the complex using NMR and MALDI-TOF mass spectroscopy. The proton NMR shows a broad resonance corresponding to endohedral NH 3 at delta H = -12.3 ppm relative to TMS. This resonance was seen to narrow when a (14)N decoupling frequency was applied. MALDI spectroscopy confirmed the presence of both 1 ( m/ z = 1172) and 1 + NH 3 ( m/ z = 1189), and integrated intensities of MALDI peak trains and NMR resonances indicate an incorporation fraction of 35-50% under our experimental conditions. NMR observations showed a diminished incorporation fraction after 6 months of storage at -10 degrees C, which indicates that ammonia slowly escapes from the open-cage fullerene.

Efficient prevention of nanomaterials transport in the porous media by treatment with polyelectrolytes.

Contamination of soil by engineered nanomaterials (ENM) is an emergent environmental problem that urges the development of robust treatment protocols to prevent ENM transport through soil. We developed a method for efficient entrapment and retention of ENM in solid porous media of quartz sand with grain size of 300-500 µm used as a simple model of soil and studied the transport properties of multi-walled carbon nanotubes, fullerenes, silica and gold nanoparticles through the sand-packed column by UV-vis and fluorescent spectroscopy. The treatment of ENM-contaminated porous media with a mixture of oppositely charged polyelectrolytes, cationic poly(diallyldimethylammonium chloride) and anionic poly(acrylic acid) sodium salt, dissolved in NaCl solution followed by dilution in the column results in strong electrostatic interaction between the polyelectrolytes and a formation of inter-polyelectrolyte complexes (IPEC) that induce flocculation of ENM and adsorption to the surface of sand. The method demonstrates excellent ENM entrapment efficiency (>90%) and high capacity of several grams of ENM per 1 g of polyelectrolytes. The IPEC network formed after the treatment also serves as an efficient protection barrier for newly added ENM contaminants. The method is universal for various types of ENM (carbon ENM, metal and oxide nanoparticles) and equally efficient for distilled water, tap water, or lake water eluents.

Molecular mechanism for pterin-mediated inactivation of tyrosine hydroxylase: formation of insoluble aggregates of tyrosine hydroxylase.

Tyrosine hydroxylase (TH), an iron-containing enzyme, catalyzes the first and rate-limiting step of catecholamine biosynthesis, and requires tetrahydrobiopterin (BH4) as a cofactor. We found that preincubation of recombinant human TH with BH4 results in the irreversible inactivation of the enzyme at a concentration far less than the Km value toward BH4 in spite of its cofactor role, whereas oxidized biopterin, which has no cofactor activity, does not affect the enzyme activity. We show that TH is inactivated by BH4 in competition with the binding of dopamine. The sequential addition of BH4 to TH results in a gradual decrease in the intensity of the fluorescence and CD spectra without changing their overall profiles. Sedimentation velocity analysis demonstrated an association of TH molecules with each other in the presence of BH4, and studies using gel-permeation chromatography, turbidity measurements, and transmission electron microscopy demonstrated the formation of amorphous aggregates with large molecular weights following the association of the TH proteins. These results suggest that BH4 not only acts as a cofactor, but also accelerates the aggregation of TH. We propose a novel mechanism for regulating the amount of TH protein, and discuss its physiological significance.

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.

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.

Uptake of aromatic compounds by DNA: Toward the environmental application of DNA for cleaning water.

HYPOTHESIS: Although the interaction of DNA with various types of intercalating chemicals, such as planar polycyclic aromatic compounds, has been extensively investigated over the past several decades, little is known about the relationship between the structure of a DNA binder and its affinity for DNA. The use of DNA as an adsorbent for environmental cleaning purposes requires information on its affinity for organic chemicals with different structures. EXPERIMENT: In the present study we investigated the binding of DNA to aromatic chemicals with various structures and charges by three methods: binding of organic chemicals to DNA followed by removal by precipitation with cationic nanoparticles (1) or a cationic surfactant (2), and absorption of organic chemicals by a DNA hydrogel (3). FINDINGS: The results showed that, for most neutral organic chemicals, the hydrophobicity of the organic molecule is the main driving force for efficient binding to DNA. The double-helicity of DNA contributed to stronger binding to most of the compounds. The efficiency of the uptake of organic chemicals increased substantially when a hydrophobic cationic surfactant was used for DNA-complex condensation and removal. The potential environmental application of DNA as an adsorbent for the removal of aromatic organic pollutants from water is discussed.

A novel photorearrangement of a cyclohexadiene derivative of C60.

[reaction: see text] Photorearrangement of tetraalkoxycarbonyl-substituted cyclohexadiene derivatives of C(60) yields not only well-known bis(fulleroid) but also bis(methano)fullerene. Existence of a labile and structurally new intermediate is observed in the reaction mixture. The discovery of the compound suggests the existence of another possible pathway giving those two products other than the widely accepted [4 + 4]/[2 + 2 + 2] mechanism.

A novel migrative addition reaction of hydrazines to the diketone derivative of C60.

A novel addition reaction of an aromatic hydrazine to the diketone derivative of C60 occurs highly regioselectively with an unusual migration of two hydrogen atoms from the hydrazine to the fullerene and affords a fluorescent product having a methylene carbon along the orifice.

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.

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.

Extraction of Noble and Rare-Earth Metals from Aqueous Solutions by DNA Cross-Linked Hydrogels.

Invited for this month's cover is the group of Prof. Shizuaki Murata and Dr. Anatoly Zinchenko from Nagoya University and the group of Prof. Vladimir Sergeyev from Moscow State University. The cover picture shows the accumulation of noble and rare-earth metals by DNA cross-linked hydrogel. Read the full text of the article on page 619 ff..