Institute of Physical Organic Chemistry

Minsk, Belarus

Institute of Physical Organic Chemistry

Minsk, Belarus
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Korneenko T.V.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Pestov N.B.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Hurski A.L.,Institute of Physical Organic Chemistry | Fedarkevich A.M.,Institute of Physical Organic Chemistry | And 3 more authors.
Amino Acids | Year: 2017

Effects exerted by heavy isotope substitution in biopolymers on the functioning of whole organisms have not been investigated. We report on the decrease of permissive temperature of nematodes fed with bacteria containing 5,5-d2-lysine. We synthesized 5,5-dideuterolysine and, taking advantage of lysine being an essential amino acid, showed that C. elegans with modified lysine poorly develop from larvae into fertile adult hermaphrodites. This effect occurs only at high temperature within the permissible range for C. elegans (25 °C) and completely vanishes at 15 °C. The only known metabolic involvement of C5 in lysine is in post-translational modification through lysyl hydoxylases. Indeed, siRNA experiments showed that deficiency of let-268/plod lysyl-hydroxylase/glycosydase further amplifies the isotope effect making it apparent even at 20 °C, whereas control siRNAs as well as another lysyl-hydroxylase (psr-1/jmjdD) siRNA do not. We report for the first time that a site-specific deuteration may strongly affect the development of the whole animal organism especially under the conditions of deficiency of the corresponding enzyme. These findings provide the basis for our ongoing efforts to employ isotope effects for fine tuning of metabolic pathways to mitigate pathological processes. © 2017 Springer-Verlag Wien


Lebiadok Y.V.,SSPA optics | Bezyazychnaya T.V.,Institute of Physical Organic Chemistry | Zhuravlev K.S.,RAS Semiconductor Physics Institute
Proceedings of SPIE - The International Society for Optical Engineering | Year: 2016

The results of calculation of nitrogen vacancy geometry in GaN/AlN heterointerface and its comparison with experimental data are discussed in the paper. The methods of calculation of point defects geometry in the GaN/AlN interface within the frameworks of self-consistent field and density functional theory are compared. © 2016 SPIE.


Hildmann A.,Charité - Medical University of Berlin | Kairaliyeva T.,Max Planck Institute of Colloids and Interfaces | Kairaliyeva T.,Kazakh National Technical University | Danker K.,Charité - Medical University of Berlin | And 3 more authors.
Colloids and Surfaces A: Physicochemical and Engineering Aspects | Year: 2017

On the basis of surface tension and surface visco-elasticity measurements performed using profile analysis tensiometry with single pendent drops the surface properties of the alkyl phospholipid Inositol-C2-PAF were determined. Because of the very low bulk concentrations of Inositol-C2-PAF used in the studies, the obtained adsorption data had to be analysed including the depletion of the bulk concentration due to adsorption at the surface of the measured drops. The determined critical micellar concentration (CMC) of aqueous Inositol-C2-PAF solutions was found to be 1.1. μM, similar to other anti-tumour and anti-inflammatory substances. © 2017 Elsevier B.V.


Tsybulsky D.A.,Institute of Physical Organic Chemistry | Kvach M.V.,Institute of Physical Organic Chemistry | Stepanova I.A.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Korshun V.A.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Shmanai V.V.,Institute of Physical Organic Chemistry
Journal of Organic Chemistry | Year: 2012

A convenient procedure for the preparation of the fluorescent dye 4',5'-dichloro-2',7'-dimethoxy-5(6)-carboxyfluorescein (JOE) is reported; the overall yield achieved starting from isovanillin is 10 times higher (40% vs 4%) compared to the known procedure. Isomers (5- and 6-) are easily chromatographically separable as pentafluorophenyl esters of 3′,6′-O-bis(cyclohexylcarbonyl) derivatives. Four non-nucleoside JOE phosphoramidites based on 5- and 6-isomers and flexible 6-aminohexanol (AH) or rigid 4-trans-aminocyclohexanol (ACH) linkers have been prepared and used for oligonucleotide labeling. Spectral and photophysical properties of 5′-JOE-modified oligonucleotides have been studied. Fluorescence quantum yield of the dye correlates with the nature of the linker (rigid vs flexible) and with the presence of dG nucleosides in close proximity to a JOE residue. © 2011 American Chemical Society.


Ryazantsev D.Y.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Tsybulsky D.A.,Institute of Physical Organic Chemistry | Prokhorenko I.A.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Kvach M.V.,Institute of Physical Organic Chemistry | And 5 more authors.
Analytical and Bioanalytical Chemistry | Year: 2012

A typical TaqMan™ real-time PCR probe contains a 5'-fluorescent dye and a 3'-quencher. In the course of the amplification, the probe is degraded starting from the 5'- end, thus releasing fluorescent dye. Some fluorophores (including fluorescein) are known to be prone to self-quenching when located near each other. This work is aimed at studying dye-dye and dye-quencher interactions in multiply modified DNA probes. Twenty-one fluorogenic probes containing one and two fluoresceins (FAM), or a FAM-JOE pair, and one or two BHQ1 quenchers were synthesized using non-nucleoside reagents and "click chemistry" post-modification on solid phase and in solution. The probes were tested in real-time PCR using an ~300-bp-long natural DNA fragment as a template. The structural prerequisites for lowering the probe background fluorescence and increasing the end-plateau fluorescence intensity were evaluated and discussed. © Springer-Verlag 2012.


Ryazantsev D.Y.,RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry | Kvach M.V.,Institute of Physical Organic Chemistry | Tsybulsky D.A.,Institute of Physical Organic Chemistry | Prokhorenko I.A.,RAS Gause Institute of New Antibiotics | And 6 more authors.
Analyst | Year: 2014

Convenient preparation of fluorogenic hairpin DNA probes (molecular beacons) carrying a pair of FAM fluorophores (located close to 5′-terminus of the probe) or a pair of BHQ1 quenchers on 3′-terminus (with (BHQ1)2 or BHQ1-BHQ1 composition) is reported. These probes were used for the first time in a real-time PCR assay and showed considerable improvements in fluorogenic properties (the total fluorescence increase or signal-to-background ratio) in assay conditions vs. conventional one-FAM-one-BHQ1 molecular beacon probes as well as vs. hydrolyzable one-FAM-one-BHQ1 TaqMan probes. At the same time, such multiple modifications of the probe do not influence its Cq (a fractional PCR cycle used for quantification). The probe MB14 containing a BHQ1-BHQ1 pair showed a PCR fluorescence/background value of 9.6 which is more than two times higher than that of a regular probe MB2 (4.6). This study demonstrates prospects for the design of highly fluorogenic molecular beacon probes suitable for quantitative real-time PCR and for other potential applications (e.g. intracellular RNA detection and SNP/mutation analysis). © the Partner Organisations 2014.


PubMed | Institute of Physical Organic Chemistry, Moscow State University, Primetech LLC, RAS Gause Institute of New Antibiotics and RAS Shemyakin Ovchinnikov Institute of Bioorganic Chemistry
Type: Journal Article | Journal: Molecular and cellular probes | Year: 2016

Molecular beacons carrying JOE dye (4,5-dichloro-2,7-dimethoxy-6-carboxyfluorescein) on a rigid or flexible linker and one or two BHQ1 quenchers have been prepared and tested in real-time PCR using Fusarium avenaceum elongation factor 1 DNA template. The probes were different in their structures (loop size and stem length), linkers for dye attachment (6-aminohexanol or trans-4-aminocyclohexanol), quencher composition (single and double BHQ1) to elucidate the influence of all these features. Fluorogenic properties of the probes were studied and compared to those of FAM (fluorescein)-based probes. All the factors - stem length, JOE vs FAM, rigid vs flexible linker, single vs double quencher - appeared to play a considerable role in the probes fluorescent properties and determine the usability of the probe at two different temperatures of fluorescence detection (55 and 64).


Pokutsa A.,Institute of Physical Organic Chemistry | Kubaj Y.,Institute of Physical Organic Chemistry | Zaborovskyi A.,Institute of Physical Organic Chemistry | Maksym D.,Institute of Physical Organic Chemistry | And 2 more authors.
Applied Catalysis A: General | Year: 2010

A new protocol for the effective oxidation of cyclohexane in acetonitrile at 40 °C and atmospheric pressure into cyclohexanol, cyclohexanone and cyclohexyl hydroperoxide using hydrogen peroxide as the oxidant, vanadyl(IV)-acetylacetonate as the catalyst, oxalic acid and glyoxal as additives is presented with some reaction mechanism proposals. © 2010 Elsevier B.V.


Lebiadok Y.V.,SSPA Optics | Bezyazychnaya T.V.,Institute of Physical Organic Chemistry | Kabanau D.M.,SSPA Optics | Ryabtsev G.I.,B. I. Stepanov Institute of Physics | Zhuravlev K.S.,RAS Semiconductor Physics Institute
Proceedings of SPIE - The International Society for Optical Engineering | Year: 2016

The results of the influence of point defects (vacancy with interstitial atom) on the GaN/AlN heterointerface is presented. It was ascertained that presence of Al atom vacancy in the heterointerface leads to the contacting layer atoms rearrangement. The presence of N atom vacancy does not influence on the contacting Ga and Al layers intermixing. © 2016 SPIE.


PubMed | RAS A.N. Bach Institute of Biochemistry, Institute of Physical Organic Chemistry and Academy Kuprevich Street
Type: | Journal: International journal of analytical chemistry | Year: 2015

A rapid immunochromatographic assay was developed for the control of tetracycline (TC). The assay is based on the competition between immobilized TC-protein conjugate and TC in a tested sample for binding with polyclonal anti-TC antibodies conjugated to colloidal gold during the flow of the sample along a membrane strip with immobilized reactants. Conjugation of colloidal gold and the total immunoglobulin (IgG) fraction of polyclonal antibodies was used to increase the assay sensitivity to ensure low content of specific antibodies in the conjugate. This allowed effective inhibition of free TC and conjugate binding in the strip test zone. Photometric marker registration allows control of the reduction of binding, thereby enhancing detection sensitivity. The proposed assay allows TC to be detected at concentrations up to 20ng/mL, exceeding the limit of detection of the known analogues, in a wide working range (more than two orders) of 60pg/mL to 10ng/mL, ensured through the use of polyclonal antibodies. The assay time is 10min. The efficiency of the designed assay is shown to identify TC in milk; the degree of recovery of TC ranges from 90 to 112%. The precision of the concentrations measurements was no more than 10%.

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