Factors Affecting the Tailing of Blunt End DNA with Fluorescent Pyrimidine dNTPs

The transferase activity of non-proofreading DNA polymerases is a well-known phenomenon that has been utilized in cloning and sequencing applications. The non-templated addition of modified nucleotides at DNA blunt ends is a potentially useful feature of DNA polymerases that can be used for selective transformation of DNA 3′ ends. In this paper, we characterized the tailing reaction at perfectly matched and mismatched duplex ends with Cy3- and Cy5-modified pyrimidine nucleotides. It was shown that the best DNA tailing substrate does not have a perfect Watson–Crick base pair at the end. Mismatched duplexes with a 3′ dC were the most efficient in the Taq DNA polymerase-catalysed tailing reaction with a Cy5-modified dUTP. We further demonstrated that the arrangement of the dye residue relative to the nucleobase notably affects the outcome of the tailing reaction. A comparative study of labelled deoxycytidine and deoxyuridine nucleotides showed higher efficiency for dUTP derivatives. The non-templated addition of modified nucleotides by Taq polymerase at a duplex blunt end was generally complicated by the pyrophosphorolysis and 5′ exonuclease activity of the enzyme.     

Phylogenetic relationships of the genus <Emphasis Type="Italic">Armadolepis</Emphasis> Spassky, 1954 (Eucestoda,Hymenolepididae), with descriptions of two new species from Palaearctic dormice (Rodentia,Gliridae)

Two new species of hymenolepidid cestodes belonging to the genus Armadolepis Spassky, 1954 are described from dormice (Gliridae) from the southern East European Plain and the northwestern Caucasus, Russia. Armadolepis (Bremserilepis) longisoma n. sp., with a rudimentary, unarmed rostellar apparatus is described from the fat dormouse Glis glis (Linnaeus) from the Republic of Adygeya, Russia. Additionally, A. (Armadolepis) dryomi n. sp., characterised by a well-developed rostellar apparatus and armed rhynchus is described from the forest dormouse Dryomys nitedula Pallas from Rostov Oblast’, Russia. Armadolepis (Bremserilepis) longisoma n. sp. differs from A. (Bremserilepis) myoxi (Rudolphi, 1819) in having a substantially longer strobila and cirrus-sac, wider scolex and ovary and larger rostellar pouch and testes. Armadolepis (Armadolepis) dryomi n. sp. is distinguishable from A. (Armadolepis) spasskii Tenora & Baru?, 1958, A. (Armadolepis) jeanbaeri Makarikov, 2017 and A. (Armadolepis) tenorai Makarikov, 2017 in having a substantially longer and wider strobila, and larger rostellar pouch and cirrus-sac. Furthermore, A. dryomi n. sp. can be distinguished from its congeners by the number and size of rostellar hooks and the arrangement of the testes. Phylogenetic affinities of Armadolepis were studied for the first time using partial sequences of the nuclear ribosomal 28S DNA gene. Phylogenetic analysis strongly supported the status of Armadolepis as a separate genus belonging to the “Rodentolepis clade”.     

Modelling of the prebiotic synthesis of oligopeptides: silicate catalysts help to overcome the critical stage

On the basis of experimental studies of the initial stages of glycine oligomerization in aqueous suspension of zeolite and kaolinite catalysts, a model is suggested for the prebiotic synthesis of oligopeptides from -amino acids. The formation of linear dipeptides by hydrolysis of one amide bond in the cyclic piperazinedione intermediate (formed from glycine spontaneously) is found to be the critical stage of the reaction. This stage is base catalyzed and its rate increases when pH of the medium goes up. The linear glycyl-glycine yield rises under effect of hydroxyl anions generated from different sources including insoluble silicates and soluble sodium bicarbonate. During prebiotic evolution silicates capable of cation-exchange can serve as local sources of the hydroxyl anions which dramatically accelerate formation of linear dipeptides from cyclic ones. Oligopeptides of higher molecular weight are then easily formed from the linear dipeptides at neutral pH, even in the absence of catalysts or sources of energy (e.g. such as light). The described catalytic synthesis could occur in the proximity of submarine hydrothermal vents.     

Dimensions of the ion channel in neuronal nicotinic acetylcholine receptor as estimated from analysis of conformation-activity relationships of open-channel blocking drugs

Summary Relationship between the size of the molecule in the series of organic ions Et₃N–(CH₂)₅–N⁺R¹R²R³ (R ⁱ -alkyl or cycloalkyl substituents) and their abilities to block nicotinic acetylcholine receptors (AChRs) due to their open-channel blockade in the neurons of autonomic ganglia and in frog end-plate was analyzed.All low-energy equilibrium conformations of the drugs were calculated by the molecular mechanics method. A unique rectangular channel profile 6.1×8.3 Å. for which the best correlation between blocking activity of the drugs and total population of their conformations being able to penetrate into the channel, was deduced from all those tested.     

Towards lead compounds as anti-cancer agents via new phaeosphaeride A derivatives

New derivatives of phaeosphaeride A (PPA) were synthesized and characterized. Anti-tumor studies were carried out on the U937, HCT-116, PC3, MCF-7, A549, К562, NCI-H929, Jurkat, THP-1, RPMI8228 tumor cell lines, and on the HEF cell line. All the compounds synthesized were found to have better efficacy than PPA towards the tumor cell lines mentioned. Compound 6 (IC₅₀?=?0.59?±?0.27?µM) was observed to be 11 times more active than PPA (IC₅₀?=?6.5?±?0.30?µM) towards the NCI-H929 cell line, with a therapeutic index of 18. Compound 6 was determined to be over half and 16 times more active than etoposide towards the NCI-H929 (IC₅₀?=?0.9?±?0.05?µM) and A549 (IC₅₀?=?100?±?7.0?µM) cell lines, respectively.     

Spectral properties of thioflavin T in solvents with different dielectric properties and in a fibril-incorporated form

The increase in the solvent polarity induces a significant shift of the long-wavelength absorption band of the thioflavin T (ThT) to the shorter wavelengths. This is due to the fact that the positive charge of the ThT molecule (Z = +1e) is unequally and very differently distributed between the benzthiazole and aminobenzene rings in the ground and excited states. Therefore, ThT ground state is stabilized by the orientational interactions of the polar solvent dipoles with the positively charged ThT fragments, whereas the configuration of the solvation shell of the ThT molecule in the excited Franck-Condon state is likely far from being equilibrium. ThT absorption spectrum has the shortest (412 nm) and the longest (450 nm) wavelengths in water and in water being incorporated to the amyloid fibrils, respectively. Intriguingly, the position of the ThT fluorescence spectrum depends on the polarity of solvent to a significantly lesser degree than its absorption spectrum: being excited at 440 nm, ThT has emission with maxima at 493 and 478 nm in water and fibrils, respectively. This can be due to the fact that, in the excited state, the rotational oscillations of the ThT fragments relative to each other prevent establishing equilibrium with the solvent and fluorescence occurs from the partially equilibrium excited stated to the partially equilibrium ground state. For the fibril-incorporated ThT, the maximum of the fluorescence excitation spectrum coincides with the maximum of the long wavelength absorption band (450 nm), whereas for ThT in aqueous and alcohol solutions, additional short-wavelength bands of fluorescence and fluorescence excitation spectra were described (Naiki et al. Anal. Biochem. 1989, 177, 244-249; Le Vine Methods Enzymol. 1999, 309, 274-284). These bands could result either from some fluorescent admixtures (including free benzthiazole and aminobenzene) or from the specific ThT conformers in which benzthiazole and aminobenzene rings, being oriented at phi angle close to 90 or 270 degrees, serve as independent chromophores. On the basis of the results of the quantum-chemical calculations, it is proposed that at phi = 90 degrees (270 degrees), the relatively low barrier (only 700 cm-1) of the internal rotation of the benzthiazole and aminobenzene rings relative to each other gives rise to a subpopulation of ThT molecules possessing a violated system of the pi-conjugated bonds of the benzthiazole and aminobenzene rings.     

Afadin controls p120-catenin-ZO-1 interactions leading to endothelial barrier enhancement by oxidized phospholipids

Afadin is a novel regulator of epithelial cell junctions assembly. However, its role in the formation of endothelial cell junctions and the regulation of vascular permeability remains obscure. We previously described protective effects of oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine (OxPAPC) in the in vitro and in vivo models of lung endothelial barrier dysfunction and acute lung injury, which were mediated by Rac GTPase. This study examined a role of afadin in the OxPAPC-induced enhancement of interactions between adherens junctions and tight junctions as a novel mechanism of endothelial cell (EC) barrier preservation. OxPAPC induced Rap1-dependent afadin accumulation at the cell periphery and Rap1-dependent afadin interaction with adherens junction and tight junction proteins p120-catenin and ZO-1, respectively. Afadin knockdown using siRNA or ectopic expression of afadin mutant lacking Rap1 GTPase binding domain suppressed OxPAPC-induced EC barrier enhancement and abolished barrier protective effects of OxPAPC against thrombin-induced EC permeability. Afadin knockdown also abolished protective effects of OxPAPC against ventilator-induced lung injury in vivo. These results demonstrate for the first time a critical role of afadin in the regulation of vascular barrier function in vitro and in vivo via coordination of adherens junction-tight junction interactions.     

Dissecting structural basis of the unique substrate selectivity of human enteropeptidase catalytic subunit

Enteropeptidase is a key enzyme in the digestion system of higher animals. It initiates enzymatic cascade cleaving trypsinogen activation peptide after a unique sequence DDDDK. Recently, we have found specific activity of human enteropeptidase catalytic subunit (L-HEP) being significantly higher than that of its bovine ortholog (L-BEP). Moreover, we have discovered that L-HEP hydrolyzed several nonspecific peptidic substrates. In this work, we aimed to further characterize species-specific enteropeptidase activities and to reveal their structural basis. First, we compared hydrolysis of peptides and proteins lacking DDDDK sequence by L-HEP and L-BEP. In each case human enzyme was more efficient, with the highest hydrolysis rate observed for substrates with a large hydrophobic residue in P2-position. Computer modeling suggested enzyme exosite residues 96 (Arg in L-HEP, Lys in L-BEP) and 219 (Lys in L-HEP, Gln in L-BEP) to be responsible for these differences in enteropeptidase catalytic activity. Indeed, human-to-bovine mutations Arg96Lys, Lys219Gln shifted catalytic properties of L-HEP toward those of L-BEP. This effect was amplified in case of the double mutation Arg96Lys/Lys219Gln, but still did not cover the full difference in catalytic activities of human and bovine enzymes. To find a missing link, we studied monopeptide benzyl-arginine-β-naphthylamide hydrolysis. L-HEP catalyzed it with an order lower K (m) than L-BEP, suggesting the monopeptide-binding S1 site input into catalytic distinction between two enteropeptidase species. Together, our findings suggest structural basis of the unique catalytic properties of human enteropeptidase and instigate further studies of its tentative physiological and pathological roles.     

Morphological and immunological characterization of immunostimulatory complexes based on glycoglycerolipids from Laminaria japonica

Some physicochemical properties of glycoglycerolipids (monogalactosyldiacylglycerol, digalactosyldiacylglycerol and sulfoquinovosyldiacylglycerol) from the sea algae Laminaria japonica, as well as their ability to become incorporate into immunostimulating complexes (ISCOMs), used as a delivery system of microbial and tumor antigens in vesicular form, were studied. These glycolipids were found to differ essentially in fatty acid composition, unsaturation index and thermotropic behavior. The possibility of ISCOM modification by embedding the glycolipids studied instead of a phospholipid component in vesicles was shown. A preliminary research of the immunogenicity of the pore-forming protein from Yersinia pseudotuberculosis in modified (by monogalactosyldiacylglycerol) and typical (egg phosphatidylcholine) ISCOMs did not reveal a significant enhancement of immune response in comparison with that of isolated protein.