Characterization of oligonucleotides with LNA-monomers for PCR detection of point mutations in <Emphasis Type="Italic">Mycobacterium tuberculosis</Emphasis> genome

Point mutations associated with isoniazid resistance in Mycobacterium tuberculosis (MTB) have been analyzed in codon 315 of the katG gene by conventional polymerase chain reaction (PCR) using primers containing locked nucleic acid (LNA) modified nucleotides. Purity and structure of primers containing 5 LNA monomers of 17 nucleotides in length were characterized by matrix assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF MS) and a 17-mer duplex formed by two complementary oligonucleotides was characterized by the method of thermal denaturation. The duplex containing five LNA monomers per each strand was characterized by a higher melting temperature than it was expected using extrapolation of theoretical calculation for nucleotide modification of one strand of the duplex. Detection of any of six possible mutations in katG codon 315 (i.e. discrimination between sensitive and resistant MTB) requires just one PCR employing a set of two primers with one LNA-modified primer; this is an important advantage of oligonucleotides containing LNA over unmodified nucleotides: employment of multiplex PCR would require up to 12 primers. Problems of control of oligonucleotide modification by LNA monomers are discussed.     

The Novel Approach to the Protein Design: Active Truncated Forms of Human 1-CYS Peroxiredoxin

Abstract

The object of the present study is the verification of a new approach to the design of the active truncated forms of enzymes. The method is based on a new way of investigating the protein sequences—the ANalysis of Informational Structure (ANIS). The analysis of informational structure allows to determine the hierarchically organized structures (IDIC-trees) formed by the sites with the Increased Degree of Informational Coordination between residues. The proposed approach involves the consequent removal of the fragments corresponding to the individual IDIC-trees from the wild-type enzyme sequences. The described procedure was applied to the design of the active truncated form of human 1-CYS peroxiredoxin (PrxVI). Two variants of the PrxVI truncated sequences were proposed according to ANIS method. These truncated forms of the enzyme were expressed in E. coli and purified. The respective antioxidant activities were measured. It was shown that one of the truncated recombinant proteins retains more than 90% of the wild-type PrxVI enzymatic activity. According to the results of our study we can assume that ANIS method can be an effective tool for the design of the active truncated forms of the enzymes or the chimeric proteins which combine the enzymatic activities of their wild-type prototypes.     

Polymorphism of microsatellite loci in cultivars and species of pear (Pyrus L.)

Using five SSR markers, polymorphism ofmicrosatellite loci was examined in 46 cultivars and five species of pear (Pyrus ussuriensis, P. bretscgneideri, P. pyraster, and P. elaegnifolia). Most of the accessions examined demonstrated the presence of unique allele sets. The degree of relationship between Russian and Western European pear cultivar was established. It was demonstrated that P. ussuriensis and its first generation progeny were genetically distant from typical cultivars of P. communis, as well as from the P. communis x P. ussuriensis hybrids of later generations. SSR estimates of the cultivar relatedness were shown to correlate with the corresponding pedigree-based estimates. A number of SSR alleles specific to P. ussuriensis were identified. Based on the analysis of microsatellite loci, the allelic composition was determined for each cultivar examined. These data can serve as a molecular certificate of the cultivar.     

Preparing of a ssDNA target in a single-round PCR with low-melt excess primer for hybridization with microarrays

Method of ssDNA preparing in single-round PCR for microarray application is described. The approach is exemplified on genotyping of DARC gene. It is opposed to two-round PCR that consists of separate symmethric and asymmethric stages. Implementation of reaction in single round is achieved by means of low-melt excess internal primer application. The primer do not anneal during symmethric stage but after decreasing of annealing temperature on asymmethric stage. The results indicate effective oligonucleotide microarray genotyping. The approach reduces time requirements and risk of contamination.     

Polymorphism of microsatellite loci in cultivars and species of pear (<Emphasis Type="Italic">Pyrus</Emphasis> L.)

Using five SSR markers, polymorphism of microsatellite loci was examined in 46 cultivars and five species of pear (Pyrus ussuriensis, P. bretscgneideri, P. pyraster, and P. elaegnifolia). Most of the accessions examined showed the presence of unique allele sets. The degree of relationship between Russian and Western European pear cultivar was established. It was demonstrated that P. ussuriensis and its first generation progeny were genetically distant from typical cultivars of P. communis, as well as from the P. communis × P. ussuriensis hybrids of later generations. SSR estimates of the cultivar relatedness were shown to correlate with the corresponding pedigree-based estimates. A number of SSR alleles specific to P. ussuriensis were identified. Based on the analysis of microsatellite loci, the allelic composition was determined for each cultivar examined. These data can serve as a molecular certificate of the cultivar.     

Critical periods of the mitotic cycle: influence of aminopterin and thymidine on production of chromosomal aberrations by radiation in Crepis capillaris.

The influence of aminopterin (AP), tritiated thymidine ([3H] TdR) and "cold" thymidine (TdR) on production of chromosomal aberrations in meristematic cells of Crepis capillaris irradiated in different stages of the mitotic cycle with 300 rad of 63Co gamma-rays was studied. All the chemical treatments increased most of all the frequency of aberrations induced during two "critical periods" localized before the stage of DNA synthesis (fixation 9 h after irradiation) and before that of mitosis (4 h). Treatments with TdR and [3H]TdR increased most of all the frequency of chromatid aberrations when irradiation was performed in G1, and the frequency of gaps when irradiated in G2. Treatment with AP increased the yield of different types of aberration more uniformly. The modifying effect of the chemicals tested appeared to be independent of replicative synthesis. The "critical periods" are suggested to be the stages when regular "proof reading" and correction of spontaneous errors takes place [9,13]. In addition to this regular mechanism, radiation induces an "emergency" mechanism of repair. AP inhibits the mechanism of regular repair; in addition TdR and [3H] TdR suppress the lateral spread of primary injuries across the chromosome.     

Comparative effectiveness of antioxidants in protecting the bacterial plasmatic membrane from the active froms of oxygen

The effect of hydroxyl radicals OH. generated by the decomposition of H2O2 by Fe2+ ions (Fenton reaction) on the barrier properties of plasma membranes of Escherichia coli cells K-12 was studied by electroorientation spectroscopy. It was found that the administration of hydrogen peroxide led to the disturbance of the barrier properties of plasma membranes only when the cells were preincubated with Fe2+ ions and their constant concentration in the system was maintained by ascorbate or dithiotreitol (150-500 microM). The extent of the toxic action on plasma membranes depended on the concentration of reacting elements and the substance used as a reducer Fe2+. The efficiency of protection of antioxidants of different classes (enzymic, SH-containing, and phenolic compounds) against the toxic action of hydroxyl radicals on plasmatic membranes was shown.