Monitoring of single nicks in duplex DNA by gel electrophoretic mobility-shift assay

We demonstrate that the gel electrophoretic mobility-shift assay (EMSA) can be used for site-selective and quantitative monitoring of nicks in linear double-stranded DNA (dsDNA) thus allowing to expediently follow the nicking activity of enzymes or other agents targeted to a designated dsDNA site. At elevated temperature and/or in the presence of urea, DNA fragments carrying a single nick produced by the nicking enzyme N.BstNBI exhibit a well-detectable gel retardation effect. On the basis of permutation analysis, the decreased electrophoretic mobility of nicked dsDNA fragments is attributed to a bend (or hinge) in the DNA double helix sequence-specifically generated by a nick. Since nick-induced DNA bending depends on interaction between base pairs adjacent to a nick, the change in mobility is different for nicked DNA sites with different sequences. Therefore, EMSA monitoring of differential mobility change caused by nicks within various DNA sequences could be useful for studying the differential base stacking and nearest-neighbor energetics.     

Oligodeoxynucleotides Containing 2′‐Deoxy‐1‐methyladenosine and Dimroth Rearrangement

2′‐Deoxy‐1‐methyladenosine was incorporated into synthetic oligonucleotides by phosphoramidite chemistry. Chloroacetyl protecting group and controlled anhydrous deprotection conditions were used to avoid Dimroth rearrangement. Hybridization studies of intramolecular duplexes showed that introduction of a modified residue into the loop region of the oligonucleotide hairpin increases the melting temperature. It was shown that modified oligonucleotides may be easily transformed into oligonucleotides containing 2′‐deoxy‐N⁶‐methyladenosine.     

Study of a New Version of Classical Thin-Layer Chromatography with a Closed Adsorbent Layer

JPC – Journal of Planar Chromatography – Modern TLC -     

Three-component reactions of polynitromethanes with alkynes. The first synthesis of gem-dinitroaziridines

Three-component one-pot reactions of tetranitro- and bromotrinitromethanes with alkoxyacetylenes, mediated by diazomethane or bicyclobutylidene, yielding gem-dinitroaziridines via sequential electrophile transfer followed by [3+2]-cycloaddition, have been studied. A series of novel N-alkoxy-2,2-dinitroaziridines have been prepared by these reactions.     

Role of donor-acceptor strengths and separation on the two-photon absorption response of cytotoxic dyes: a TD-DFT study

Time-dependent density functional theory (TD-DFT) is applied to model one-photon (OPA) and two-photon (TPA) absorption spectra in a series of conjugated cytotoxic dyes. Good agreement with available experimental data is found for calculated excitation energies and cross sections. Calculations show that both OPA and TPA spectra in the molecules studied are typically dominated by two strong peaks corresponding to different electronic states. We find that donor-acceptor strengths and conjugated bridge length have a strong impact on the cross-section magnitudes of low- and high-frequency TPA maxima, respectively. These trends are analyzed in terms of the natural transition orbitals of the corresponding electronic states. Observed structure-property relationships may have useful implications on design of organic conjugated chromophores with tunable two-photon absorption properties for photodynamic therapy applications.     

State-resolved collisional quenching of vibrationally excited pyrazine (E(vib) = 37,900 cm(-1)) by D35Cl(v = 0)

Supercollision relaxation of highly vibrationally excited pyrazine (E(vib) = 37,900 cm(-1)) with D35Cl is investigated using high-resolution transient IR diode laser absorption spectroscopy at 4.4 microm. Highly excited pyrazine is prepared by pulsed UV excitation at 266 nm, followed by rapid radiationless decay to the ground electronic state. The rotational energy distribution of the scattered DCl (v = 0,J) molecules with J = 15-21 is characterized by T(rot) = 755+/-90 K. The relative translational energy increases as a function of rotational quantum number for DCl with T(rel) = 710+/-190 K for J = 15 and T(rel) = 1270+/-240 K for J = 21. The average change in recoil velocity correlates with the change in rotational angular momentum quantum number and highlights the role of angular momentum in energy gain partitioning. The integrated energy-transfer rate for appearance of DCl (v = 0,J = 15-21) is k(2)(int) = 7.1x10(-11) cm3 molecule(-1) s(-1), approximately one-eighth the Lennard-Jones collision rate. The results are compared to earlier energy gain measurements of CO2 and H2O.     

Ti2Nb6Cl14O4: A Unique 2D–1D Network Combination in Niobium Cluster Chemistry

Layers of niobium clusters that are linked to each other through zigzag chains of edge-sharing [TiCl₄O₂] ocatahedra are the central structural features of the title compound. Bridging of the chains by [(Nb₆Cl₈ⁱO₄ⁱ)Cl₆^a]⁶⁻ clusters results in the formation of empty tunnels (a section of the structure is shown on the right).     

Computer simulation studies of aggregates of associating polymers: Influence of low-molecular-weight additives solubilizing the aggregates

The structure of aggregates in solutions of chain molecules with associating groups at one of the ends is studied by Monte Carlo computer simulations using the bond fluctuation model. The main attention is paid to the influence of additives of low-molecular-weight solvent solubilizing the aggregates. It is shown that upon the addition of solvent the aggregates adopt a three-layer structure with the ‘lake’ of the solvent molecules in the central region surrounded by the layer of associating end-groups of polymer chains, which in turn is surrounded by the outer corona formed by the chain tails. The equilibrium form of the aggregates becomes close to that of a droplet of low-molecular-weight liquids. The regimes are found when the addition of the low-molecular-weight solvent stabilizes the multiplets and even induces the aggregate formation.     

The First Selenoanhydride in the Series of Chlorophyll a Derivatives,Its Stability and Photoinduced Cytotoxicity

In this work, we obtained the first selenium-containing chlorin with a chalcogen atom in exlocycle E. It was shown that the spectral properties were preserved in the target compound and the stability increased at two different pH values, in comparison with the starting purpurin-18. The derivatives have sufficiently high fluorescence and singlet oxygen quantum yields. The photoinduced cytotoxicity of sulfur- and selenium-anhydrides of chlorin p₆ studied for the first time in vitro on the S37 cell line was found to be two times higher that of purpurin-18 and purpurinimide studied previously. Moreover, the dark cytotoxicity increased four-fold in comparison with the latter compounds. Apparently, the increase in the dark cytotoxicity is due to the interaction of the pigments studied with sulfur- and selenium-containing endogenous intracellular compounds. Intracellular distributions of thioanhydride and selenoanhydride chlorin p₆ in S37 cells were shown in cytoplasm by diffusion distribution. The intracellular concentration of the sulfur derivative turned out to be higher and, as a consequence, its photoinduced cytotoxicity was higher as well.     

The Synthesis of Blood Group Antigenic A Trisaccharide and Its Biotinylated Derivative

Blood group antigenic A trisaccharide represents the terminal residue of all A blood group antigens and plays a key role in blood cell recognition and blood group compatibility. Herein, we describe the synthesis of the spacered A trisaccharide by means of an assembly scheme that employs in its most complex step the recently proposed glycosyl donor of the 2-azido-2-deoxy-selenogalactoside type, bearing stereocontrolling 3-O-benzoyl and 4,6-O-(di-tert-butylsilylene)-protecting groups. Its application provided efficient and stereoselective formation of the required α-glycosylation product, which was then deprotected and subjected to spacer biotinylation to give both target products, which are in demand for biochemical studies.