Spectroscopic Study on the Effect of Imidazophenazine Tethered to 5′-End of Pentadecathymidilate on Stability of Poly(dA)·(dT)15 Duplex

The effect of imidazo[4,5-d]phenazine (Pzn) attached to the 5^′-end of (dT)₁₅ oligonucleotide via a flexible linker on the thermal stability of poly(dA)·(dT)₁₅ duplex was studied in aqueous buffered solution containing 0.1 М NaCl at the equimolar ratio of adenine and thymine bases (100?μM each) using spectroscopic techniques. Duplex formation was investigated by measuring UV absorption and fluorescence melting curves for the Pzn-modified system. Tethered phenazine derivative enhances the thermostability of poly(dA)·(dT)₁₅ duplex increasing the helix–to–coil transition temperature by 4.5?°С due to an intercalation of the dye chromophore between AT-base pairs. The thermodynamic parameters of the transition for non-modified and modified systems were estimated using “all–or–none” model. The modification of the (dT)₁₅ results in a decrease in the transition enthalpy, however, the observed gain in the Gibbs free energy of complex formation, ΔG, is provided with the corresponding decrease in entropy change. The increase of ΔG value at 37?°C in consequence of (dT)₁₅ modification was found to be equal to 1.3?kcal/mol per oligonucleotide strand.     

Spectroscopic study on binding of TMPyP4+ porphyrin to single-stranded poly(rA)

Abstract

Binding of tetracationic porphyrin (TMPyP⁴⁺) to poly(rA) has been studied in neutral buffered solution of low ionic strength in a wide range of molar phosphate-to-dye ratios (P/D) using absorption spectroscopy, polarized fluorescence and fluorimetric titration. Two competitive binding modes were identified: partial intercalation of porphyrin chromophores between adenine bases prevailing at P/D?>?20 and its outside binding to poly(rA) backbone dominating at P/D?<?6. Both of them were accompanied by enhancement of the porphyrin emission. Absence of the emission quenching near stoichiometric P/D ratios allowed us to assume that external binding occurs without the self-stacking of the chromophores.     

Isolation of bioactive preparations from alcoholic extracts ofChlorella vulgaris

Summary Three groups of bioactive substances (provitamins of the A group, vitamins of the F group, and sodium chlorophyllin) have been isolated from alcoholic extracts of the micro algaChlorella vulgaris. The conditions of separating these substances are given. The qualitative and quantitative compositions of the groups isolated have been investigated by paper chromatography, gas-liquid chromatography, and spectral analysis.Siberian Technological Institute, Krasnoyarsk. Translated from Khimiya Prirodnykh Soedinenii, No. 2, pp. 213–216, March–April, 1979.     

Boron atoms in the subsurface layers of diamond: Quantum chemical modeling

Results from quantum-chemical modeling of the configurations of boron impurities and BV complexes of “boron + monovacancy” on diamond surface C(100)–(2 × 1) are presented with their positions varied in subsurface layers. The geometric, electronic, and energy characteristics of these configurations are calculated. It is shown that the most stable BV complexes are complex defects consisting of an impurity defect in the fourth layer and an intrinsic defect in the third layer. The bonding energy of a hydrogen atom and a surface containing the most stable of the studied defects is estimated.     

Adsorption Properties of the C(100)-(2×1) Diamond Surface with Vacancy Defects and “Nitrogen + Vacancy” Complexes

Russian Journal of Physical Chemistry A - The results are presented from the quantum-chemical modeling of hydrogen chemisorption on a C(100)-(2×1) diamond surface that contains the most stable...     

Method of confidence domains in the analysis of noise-induced extinction for tritrophic population system

A problem of the analysis of the noise-induced extinction in multidimensional population systems is considered. For the investigation of conditions of the extinction caused by random disturbances, a new approach based on the stochastic sensitivity function technique and confidence domains is suggested, and applied to tritrophic population model of interacting prey, predator and top predator. This approach allows us to analyze constructively the probabilistic mechanisms of the transition to the noise-induced extinction from both equilibrium and oscillatory regimes of coexistence. In this analysis, a method of principal directions for the reducing of the dimension of confidence domains is suggested. In the dispersion of random states, the principal subspace is defined by the ratio of eigenvalues of the stochastic sensitivity matrix. A detailed analysis of two scenarios of the noise-induced extinction in dependence on parameters of considered tritrophic system is carried out.     

Absorption and fluorescent spectral studies of imidazophenazine derivatives

Absorption and fluorescent spectra as well as fluorescence polarization degree of imidazo-[4,5-d]-phenazine (F1) and its two modified derivatives, 2-trifluoridemethylimidazo-[4,5-d]-phenazine (F2) and 1,2,3-triazole-[4,5-d]-phenazine (F3), were investigated in organic solvents of various polarities and hydrogen bonding abilities. Extinction coefficients of F2 and F3 are increased, their fluorescence Stokes shifts are reduced in comparison with those for unmodified imidazophenazine. For F3 a red shift of the longwave absorption band is observed by 15-20 nm. Modifications of imidazophenazine have led to a sufficient increase of fluorescence polarization degrees that enables to use F2 and F3 as promising fluorescent probes with polarization method application. The configuration, atomic charge distribution and dipole moments of the isolated dye molecules in the ground state were calculated by the DFT method. The computation has revealed that ground state dipole moments of F1, F2, and F3 differ slightly and are equal to 3.5, 3.2, and 3.7D, respectively. The changes in dipole moments upon the optical excitation for all derivatives estimated using Lippert equation were found to be Deltamu = 9 D. The energies of the electronic S1<--S0 transition in solvents of different proton donor abilities were determined, and energetic diagram illustrating the substituent effect was plotted. For nucleoside analogs of these compounds, covalently incorporated into a nucleotide chain, we have considered a possibility to use them as fluorescent reporters of hybridization of antisense oligonucleotides, as well as molecular anchors for its stabilization.     

Spectroscopic Detection of Tetracationic Porphyrin H-Aggregation on Polyanionic Matrix of Inorganic Polyphosphate

Self-assembly of tetracationic porphyrin TMPyP⁴⁺ onto polyanionic matrix of inorganic polyphosphate (PPS) in aqueous solutions has been studied in a wide range of molar phosphate-to-dye ratios using techniques of polarized fluorescence, absorption, resonance Raman spectroscopy and static light scattering. The binding of TMPyP⁴⁺ to PPS is characterized by the binding constant of 3 × 10⁵ M⁻¹ and the cooperativity parameter of about 150. The fluorescence quenching of the bound TMPyP⁴⁺ evidences the stacking of the porphyrine chromophores. Under the stoichiometric binding ratio TMPyP⁴⁺ forms extended continuous face-to-face aggregates (so-called H-aggregates) which manifest themselves by a blue shift (12 nm) and a large hypochromisity (51%) of the Soret absorption band. Each face-to-face TMPyP⁴⁺ stack is formed with participation of four PPS chains. Formation of such columnar aggregates is promoted by the ability of PPS chains to take a helix conformation where negative charges are arranged along two oppositely situated rows with intercharge distance of 0.36 nm which corresponds to the thickness of the porphyrin π-electronic system. The ability of each PPS strand to be template for formation of two porphyrin stacks results in the integration of the adjacent stacks into higher-order aggregates which dimension was estimated from the fluorescence polarization data.     

Pathogen-targeted hydroxyl radical generation during melanization in insect hemolymph: EPR study of a probable cytotoxicity mechanism

The main component of the insect immune system is melanotic encapsulation of pathogenic organisms. Molecular mechanisms of destruction of an encapsulated pathogen are poorly understood. Reactive oxygen species (ROS) are considered as probable cytotoxic agents responsible for destruction of pathogenic organisms in insect hemolymph. In the present work the formation of H₂O₂ during melanization in Galleria mellonella hemolymph in the presence of catalase inhibitor NaN₃ was detected. Enhanced rates of H₂O₂ generation were observed in the hemolymph of insects activated by injection of bacterial cells. Using spin trapping technique in combination with electron paramagnetic resonance spectroscopy we demonstrated that production of H₂O₂ in the hemolymph causes the formation of highly toxic reactive oxygen species, hydroxyl radical. However, neither H₂O₂ nor hydroxyl radical were detected in the absence of NaN₃ in agreement with the high catalase activity in the hemolymph. These observations allow us to propose a unique mechanism of pathogen-targeted cytotoxicity based on localized hydroxyl radical generation within a melanotic capsule.