Sergey Gontarev - Academia.edu (original) (raw)

Papers by Sergey Gontarev

Russian Journal of Bioorganic Chemistry, 2017

⎯The synthesis of phosphoramidite reagents and solid-phase supports based on hydroxyprolinol for ... more ⎯The synthesis of phosphoramidite reagents and solid-phase supports based on hydroxyprolinol for the introduction of the residues of biotin, lipoic acid, amino groups, and terminal acetylene groups at different positions of the oligonucleotide chain has been described. The efficiency of the reagents and supports has been confirmed by the synthesis of the corresponding modified oligonucleotides.

Molecular and Cellular Probes, 2016

Molecular beacons carrying JOE dye (4&amp... more 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 1α 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 probe's fluorescent properties and determine the usability of the probe at two different temperatures of fluorescence detection (55°С and 64°С).

The Analyst, 2014

Fluorescent properties of molecular beacons with two dyes or two quenchers in real-time PCR are r... more Fluorescent properties of molecular beacons with two dyes or two quenchers in real-time PCR are reported.

Bioconjugate chemistry

Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3',6'-O-dipivalate can be easily ... more Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3',6'-O-dipivalate can be easily separated in multigram quantities by column chromatography. The individual isomers were converted into stable phosphoramidites suitable for oligonucleotide synthesis. The use of the cyclohexylcarbonyl (Chc) protecting group instead of pivaloyl (Piv) facilitates the separation of isomers. The fluorescence spectra of 5- and 6-carboxyfluoresceins on oligonucleotides were compared.

Molecular and Cellular Probes, 2016

Molecular beacons carrying JOE dye (4&amp... more 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 1α 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 probe's fluorescent properties and determine the usability of the probe at two different temperatures of fluorescence detection (55°С and 64°С).

Molecular and Cellular Probes, 2016

Molecular beacons carrying JOE dye (4',5&... more 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 1α 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 probe's fluorescent properties and determine the usability of the probe at two different temperatures of fluorescence detection (55°С and 64°С).

Russian Chemical Bulletin, Nov 7, 2006

Simple Reagent for the Synthesis of Oligonucleotides Labeled with 3,3,3',3'-Tetramethyl-2,2'-indo... more Simple Reagent for the Synthesis of Oligonucleotides Labeled with 3,3,3',3'-Tetramethyl-2,2'-indodicarbocyanine. -Synthesis and application of the fluorescence dye (I), useful for the preparation of 5'-labeled oligodeoxyribonucleotides in an automated DNA synthesis, are described. -(KVACH, M. V.; GONTAREV, S. V.; PROKHORENKO, I. A.; STEPANOVA, I. A.; SHMANAI, V. V.; KORSHUN*, V. A.; Russ.

Nucleosides and Nucleotides, 1997

A series of pyrene-containing reagents have been synthesized and used for the fluorescent labelin... more A series of pyrene-containing reagents have been synthesized and used for the fluorescent labeling of oligonucleotides.

ChemInform, 1996

Oligodeoxynucleotides Using a Nucleoside-Like Synthon.

ChemInform, 1996

KORSHUN, V. A.; PESTOV, N. B.; NOZHEVNIKOVA, E. V.; PROKHORENKO, I. A.; GONTAREV, S. V.; BERLIN, ... more KORSHUN, V. A.; PESTOV, N. B.; NOZHEVNIKOVA, E. V.; PROKHORENKO, I. A.; GONTAREV, S. V.; BERLIN, YU. A.; Synth.

Russian Chemical Bulletin, 2006

Simple Reagent for the Synthesis of Oligonucleotides Labeled with 3,3,3',3'-Tetramethyl-2,2'-indo... more Simple Reagent for the Synthesis of Oligonucleotides Labeled with 3,3,3',3'-Tetramethyl-2,2'-indodicarbocyanine. -Synthesis and application of the fluorescence dye (I), useful for the preparation of 5'-labeled oligodeoxyribonucleotides in an automated DNA synthesis, are described. -(KVACH, M. V.; GONTAREV, S. V.; PROKHORENKO, I. A.; STEPANOVA, I. A.; SHMANAI, V. V.; KORSHUN*, V. A.; Russ.

Rapid Communications in Mass Spectrometry, 2007

The complexity of the human plasma proteome is greatly increased by post-translational modificati... more The complexity of the human plasma proteome is greatly increased by post-translational modifications. Besides physiological modifications, pathological conditions such as diabetes are responsible for adding to this complexity by producing advanced glycation endproducts (AGEs). When searching for specific biomarkers it is a prerequisite to reduce this complexity prior to analysis. To do this, agarose hydrogel was used to create a high-capacity affinity layer on the modified aluminum surface of MALDI (matrix-assisted laser desorption/ionization) targets. 3-Aminophenylboronic acid was immobilized via cyanogen bromide activation as a ligand for affinity sorption of glycated proteins, followed by their direct detection by MALDI. High protein capacity of prepared MALDI chips, efficient separation and low non-specific protein binding were demonstrated. The results show that phenylboronic acid modified hydrogels are very suitable for creating affinity surfaces for the high-throughput analysis of AGEs.

Journal of Mass Spectrometry, 2007

Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI TOFMS) combin... more Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI TOFMS) combined with affinity chromatography on immobilized phenylboronic acid agarose gels was used for selective enrichment and detection of specifically modified proteins such as glycated proteins in complex biological samples. Physicochemical grafting of hydrophilic polymers on aluminum surface was developed to reduce nonspecific protein sorption and to create a proper support layer for a three-dimensional affinity hydrogel. Grafted agarose allowed the fixation of three-dimensional agarose hydrogel on the chip surface. Both pinched polymers and hydrogels were effectively derivatized. 3-Aminophenylboronic acid (mPBA) was covalently immobilized as an affinity ligand to achieve specific binding of glycated plasma proteins. Alternatively, the affinity sorbent was immersed into the hydrogel to increase binding capacity. MALDI TOFMS was used to evaluate binding efficiency and molecular mass changes of human serum albumin due to glycation. Glycated proteins were captured directly on the chip with high selectivity and efficacy, and low nonspecific binding. Thus they could easily be characterized by MALDI TOFMS.

Bioconjugate Chemistry, 2007

Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3&amp... more Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3',6'-O-dipivalate can be easily separated in multigram quantities by column chromatography. The individual isomers were converted into stable phosphoramidites suitable for oligonucleotide synthesis. The use of the cyclohexylcarbonyl (Chc) protecting group instead of pivaloyl (Piv) facilitates the separation of isomers. The fluorescence spectra of 5- and 6-carboxyfluoresceins on oligonucleotides were compared.

The Analyst, 2014

Convenient preparation of fluorogenic hairpin DNA probes (molecular beacons) carrying a pair of F... more Convenient preparation of fluorogenic hairpin DNA probes (molecular beacons) carrying a pair of FAM fluorophores (located close to 5 0 -terminus of the probe) or a pair of BHQ1 quenchers on 3 0 -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).

Russian Journal of Bioorganic Chemistry, 2017

⎯The synthesis of phosphoramidite reagents and solid-phase supports based on hydroxyprolinol for ... more ⎯The synthesis of phosphoramidite reagents and solid-phase supports based on hydroxyprolinol for the introduction of the residues of biotin, lipoic acid, amino groups, and terminal acetylene groups at different positions of the oligonucleotide chain has been described. The efficiency of the reagents and supports has been confirmed by the synthesis of the corresponding modified oligonucleotides.

Molecular and Cellular Probes, 2016

Molecular beacons carrying JOE dye (4&amp... more 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 1α 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 probe's fluorescent properties and determine the usability of the probe at two different temperatures of fluorescence detection (55°С and 64°С).

The Analyst, 2014

Fluorescent properties of molecular beacons with two dyes or two quenchers in real-time PCR are r... more Fluorescent properties of molecular beacons with two dyes or two quenchers in real-time PCR are reported.

Bioconjugate chemistry

Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3',6'-O-dipivalate can be easily ... more Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3',6'-O-dipivalate can be easily separated in multigram quantities by column chromatography. The individual isomers were converted into stable phosphoramidites suitable for oligonucleotide synthesis. The use of the cyclohexylcarbonyl (Chc) protecting group instead of pivaloyl (Piv) facilitates the separation of isomers. The fluorescence spectra of 5- and 6-carboxyfluoresceins on oligonucleotides were compared.

Molecular and Cellular Probes, 2016

Molecular beacons carrying JOE dye (4&amp... more 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 1α 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 probe's fluorescent properties and determine the usability of the probe at two different temperatures of fluorescence detection (55°С and 64°С).

Molecular and Cellular Probes, 2016

Molecular beacons carrying JOE dye (4',5&... more 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 1α 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 probe's fluorescent properties and determine the usability of the probe at two different temperatures of fluorescence detection (55°С and 64°С).

Russian Chemical Bulletin, Nov 7, 2006

Simple Reagent for the Synthesis of Oligonucleotides Labeled with 3,3,3',3'-Tetramethyl-2,2'-indo... more Simple Reagent for the Synthesis of Oligonucleotides Labeled with 3,3,3',3'-Tetramethyl-2,2'-indodicarbocyanine. -Synthesis and application of the fluorescence dye (I), useful for the preparation of 5'-labeled oligodeoxyribonucleotides in an automated DNA synthesis, are described. -(KVACH, M. V.; GONTAREV, S. V.; PROKHORENKO, I. A.; STEPANOVA, I. A.; SHMANAI, V. V.; KORSHUN*, V. A.; Russ.

Nucleosides and Nucleotides, 1997

A series of pyrene-containing reagents have been synthesized and used for the fluorescent labelin... more A series of pyrene-containing reagents have been synthesized and used for the fluorescent labeling of oligonucleotides.

ChemInform, 1996

Oligodeoxynucleotides Using a Nucleoside-Like Synthon.

ChemInform, 1996

KORSHUN, V. A.; PESTOV, N. B.; NOZHEVNIKOVA, E. V.; PROKHORENKO, I. A.; GONTAREV, S. V.; BERLIN, ... more KORSHUN, V. A.; PESTOV, N. B.; NOZHEVNIKOVA, E. V.; PROKHORENKO, I. A.; GONTAREV, S. V.; BERLIN, YU. A.; Synth.

Russian Chemical Bulletin, 2006

Simple Reagent for the Synthesis of Oligonucleotides Labeled with 3,3,3',3'-Tetramethyl-2,2'-indo... more Simple Reagent for the Synthesis of Oligonucleotides Labeled with 3,3,3',3'-Tetramethyl-2,2'-indodicarbocyanine. -Synthesis and application of the fluorescence dye (I), useful for the preparation of 5'-labeled oligodeoxyribonucleotides in an automated DNA synthesis, are described. -(KVACH, M. V.; GONTAREV, S. V.; PROKHORENKO, I. A.; STEPANOVA, I. A.; SHMANAI, V. V.; KORSHUN*, V. A.; Russ.

Rapid Communications in Mass Spectrometry, 2007

The complexity of the human plasma proteome is greatly increased by post-translational modificati... more The complexity of the human plasma proteome is greatly increased by post-translational modifications. Besides physiological modifications, pathological conditions such as diabetes are responsible for adding to this complexity by producing advanced glycation endproducts (AGEs). When searching for specific biomarkers it is a prerequisite to reduce this complexity prior to analysis. To do this, agarose hydrogel was used to create a high-capacity affinity layer on the modified aluminum surface of MALDI (matrix-assisted laser desorption/ionization) targets. 3-Aminophenylboronic acid was immobilized via cyanogen bromide activation as a ligand for affinity sorption of glycated proteins, followed by their direct detection by MALDI. High protein capacity of prepared MALDI chips, efficient separation and low non-specific protein binding were demonstrated. The results show that phenylboronic acid modified hydrogels are very suitable for creating affinity surfaces for the high-throughput analysis of AGEs.

Journal of Mass Spectrometry, 2007

Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI TOFMS) combin... more Matrix-assisted laser desorption ionization time-of-flight mass spectroscopy (MALDI TOFMS) combined with affinity chromatography on immobilized phenylboronic acid agarose gels was used for selective enrichment and detection of specifically modified proteins such as glycated proteins in complex biological samples. Physicochemical grafting of hydrophilic polymers on aluminum surface was developed to reduce nonspecific protein sorption and to create a proper support layer for a three-dimensional affinity hydrogel. Grafted agarose allowed the fixation of three-dimensional agarose hydrogel on the chip surface. Both pinched polymers and hydrogels were effectively derivatized. 3-Aminophenylboronic acid (mPBA) was covalently immobilized as an affinity ligand to achieve specific binding of glycated plasma proteins. Alternatively, the affinity sorbent was immersed into the hydrogel to increase binding capacity. MALDI TOFMS was used to evaluate binding efficiency and molecular mass changes of human serum albumin due to glycation. Glycated proteins were captured directly on the chip with high selectivity and efficacy, and low nonspecific binding. Thus they could easily be characterized by MALDI TOFMS.

Bioconjugate Chemistry, 2007

Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3&amp... more Pentafluorophenyl esters of 5- and 6-carboxyfluorescein-3',6'-O-dipivalate can be easily separated in multigram quantities by column chromatography. The individual isomers were converted into stable phosphoramidites suitable for oligonucleotide synthesis. The use of the cyclohexylcarbonyl (Chc) protecting group instead of pivaloyl (Piv) facilitates the separation of isomers. The fluorescence spectra of 5- and 6-carboxyfluoresceins on oligonucleotides were compared.

The Analyst, 2014

Convenient preparation of fluorogenic hairpin DNA probes (molecular beacons) carrying a pair of F... more Convenient preparation of fluorogenic hairpin DNA probes (molecular beacons) carrying a pair of FAM fluorophores (located close to 5 0 -terminus of the probe) or a pair of BHQ1 quenchers on 3 0 -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).