Sergey P. Radko

Institute of Biomedical Chemistry

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Svetlana A. Khmeleva

Institute of Biomedical Chemistry

Leonid K. Kurbatov

Institute of Biomedical Chemistry

K. G. Ptitsyn

Institute of Biomedical Chemistry

Elena V. Suprun

Institute of Biomedical Chemistry

Andrey Lisitsa

Institute of Biomedical Chemistry

Alexander I. Archakov

Institute of Biomedical Chemistry

Andreas Chrambach

National Institutes of Health

Y.Y. Kiseleva

Federal State Budgetary Institution Russian Scientific Center of Roentgenoradiology

Elena A. Ponomarenko

Institute of Biomedical Chemistry

Sergey A. Kozin

Engelhardt Institute of Molecular Biology

Cooperative Institutions

Russian Academy of Sciences

Institute of Biomedical Chemistry

Engelhardt Institute of Molecular Biology

Academy of Medical Sciences

Lomonosov Moscow State University

National Institutes of Health

Eunice Kennedy Shriver National Institute of Child Health and Human Development

Moscow State University

Pirogov Russian National Research Medical University

Bioinformatics Institute

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Deoxyuridine triphosphates modified with tyrosine or tryptophan aromatic groups for direct electrochemical detection of double-stranded DNA

Electrochimica Acta (2020)

Elena V. Suprun Svetlana A. Khmeleva Gulnaz R. Kutdusova Insaf F. Duskaev В. Е. Кузнецова

Deoxyuridine

10.1016/j.electacta.2020.137105

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Citations (16)

Comparative termodynamic analysis of thrombin interaction with anti-thrombin aptamers and their heterodimeric construct

Biomeditsinskaya Khimiya (2010)

S. Yu. Rakhmetova Sergey P. Radko O.V. Gnedenko Н. В. Бодоев Ivanov As

Aptamers interacting selectively with the anion-binding exosites 1 and 2 of thrombin were merged into dimeric oligonucleotide constructs with use of a poly-(dT)-linker of 35 nucleotides (nt) long. Complexes of thrombin with the aptamers and their hetero- and homodimeric constructs were measured using the optical biosensor Biacore-3000. KD values measured for the hetero- and homodimeric constructs were correspondingly 25-30- and 2-3-fold lower than those for the primary aptamers. Analysis of temperature dependencies of KD values within the temperature interval of 10°C-40°C has shown that the values of enthalpy change ΔH upon formation of complexes of thrombin with the aptamers and the hetrodimeric construct are close. The value of the entropy change ΔS upon complex formation of thrombin with the aptamer heterodimeric construct was 1.5-2-fold higher than ΔS values for the complexes with the aptamers. The complex formation and dissociation rates increased with the elevation of temperature from 10°С to 37°С. However, the dissociation rate for the complex of thrombin with the heterodimeric construct was evidently lower that that for the complexes with the aptamers.

Aptamer

Linker

Dissociation constant

10.18097/pbmc20105603404

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[Electrophoretic analysis of 53K protein presence in leukocytes of the newborn].

PubMed (1992)

V. D. Paponov Sergey P. Radko E. V. Shtein E. G. Shcheglova

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Влияние мутаций H6R и D7H на модулирование цинк-индуцированной агрегации амилоида-β гепарином

Молекулярная биология (2019)

Sergey P. Radko Svetlana A. Khmeleva Y.Y. Kiseleva Sergey A. Kozin Vladimir A. Mitkevich

Zinc ions and glycosaminoglycans (GAGs) are found in amyloid deposits and are known to modulate the β-amyloid peptide (Aβ) aggregation, which is thought to be a key event in the pathogenesis of Alzheimer's disease (AD). Correlation spectroscopy was used to study how the H6R and D7H mutations of the metal-binding domain (MBD) of Aβ42 affect the modulation of its zinc-induced aggregation by the model GAG heparin. The H6R mutation was shown to decrease and the D7H mutation to increase the Aβ42 propensity to aggregate in the presence of zinc ions. In addition, H6R diminished and D7H enhanced the modulating effect of heparin. The difference in the heparin-dependent modulation was associated with coordination of zinc ions within the MBDs of the mutant peptides. The findings indicate that anion-binding sites formed by complexes of zinc ions with the Aβ MBD play an essential role in the interaction of zinc-induced Aβ aggregates with heparin.

Amyloid (mycology)

10.1134/s0026898419060144

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Biosensing platforms for DNA diagnostics based on CRISPR/Cas nucleases: towards the detection of nucleic acids at the level of single molecules in non-laboratory settings

Biomeditsinskaya Khimiya (2024)

Svetlana A. Khmeleva K. G. Ptitsyn Leonid K. Kurbatov О.С. Тимошенко Elena V. Suprun

The use of CRISPR/Cas nucleases for the development of DNA diagnostic systems in out-of-laboratory conditions (point-of-need testing, PONT) has demonstrated rapid growth in the last few years, starting with the appearance in 2017–2018 of the first diagnostic platforms known as DETECTR and SHERLOCK. The platforms are based on a combination of methods of nucleic acid isothermal amplification with selective CRISPR/Cas detection of target amplicons. This significantly improves the sensitivity and specificity of PONT, making them comparable with or even superior to the sensitivity and specificity of polymerase chain reaction, considered as the “gold standard” of DNA diagnostics. The review considers modern approaches to the coupling of CRISPR/Cas detection using Cas9, Cas12a, Cas12b, Cas13a, Cas14, and Cas3 nucleases to various methods of nucleic acid isothermal amplification, with an emphasis on works in which sensitivity at the level of single molecules (attomolar and subattomolar concentrations of the target) is achieved. The properties of CRISPR/Cas nucleases used for targeted DNA diagnostics and the features of methods of nucleic acid isothermal amplification are briefly considered in the context of the development of diagnostic biosensing platforms. Special attention is paid to the most promising directions for the development of DNA diagnostics using CRISPR/Cas nuclease.

Nuclease

Amplicon

Molecular diagnostics

10.18097/pbmc20247005287

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Polymerase incorporation of fluorescein or rhodamine modified 2′-deoxyuridine-5′-triphosphates into double-stranded DNA for direct electrochemical detection

Journal of Pharmaceutical and Biomedical Analysis (2023)

Elena V. Suprun Svetlana A. Khmeleva Konstantin V. Bibik K. G. Ptitsyn Leonid K. Kurbatov

Rhodamine

Rhodamine B

10.1016/j.jpba.2023.115737

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Detection of Potato Pathogen Clavibacter sepedonicus by CRISPR/Cas13a Analysis of NASBA Amplicons

International Journal of Molecular Sciences (2024)

Svetlana A. Khmeleva Leonid K. Kurbatov K. G. Ptitsyn О.С. Тимошенко Darya D. Morozova

The ring rot of potato caused by the bacterial pathogen Clavibacter sepedonicus is a quarantine disease posing a threat to the potato industry worldwide. The sensitive and selective detection of C. sepedonicus is of a high importance for its effective control. Here, the detection system is reported to determine viable bacteria of C. sepedonicus in potato tubers, based on the coupling of CRISPR/Cas13a nuclease with NASBA (Nucleic Acid Sequence Based Amplification)—the method of isothermal amplification of RNA. Detection can be conducted using both instrumental and non-instrumental (visual inspection of test tubes under blue light) modes. When NASBA and Cas13a analyses were carried out in separate test tubes, the limit of detection (LOD) for the system was 1000 copies of purified target 16S rRNA per NASBA reaction or about 24 colony-forming units (CFUs) of C. sepedonicus per 1 g of tuber tissue. The testing can also be conducted in the “one-pot” format (a single test tube), though with lower sensitivity: LOD was 10,000 copies of target RNA or about 100 CFU per 1 g of tuber tissue for both instrumental and visual detection modes. The overall time of NASBA/Cas13a analysis did not exceed 2 h. The developed NASBA/Cas13a detection system has the potential to be employed as a routine test of C. sepedonicus, especially for on-site testing.

NASBA

Amplicon

10.3390/ijms252212218

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Electrochemical detection of Zn(II)-induced amyloid-β aggregation: Insights into aggregation mechanisms

Journal of Electroanalytical Chemistry (2018)

Elena V. Suprun Sergey P. Radko Sergey A. Kozin Vladimir A. Mitkevich Alexander Makarov

Turbidimetry

10.1016/j.jelechem.2018.10.016

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Citations (10)

Reconstitution of Calcium-triggered Membrane Fusion Using “Reserve” Granules

Journal of Biological Chemistry (1998)

V. V. Chestkov Sergey P. Radko Myoung‐Soon Cho Andreas Chrambach Steven S. Vogel

Calcium-gated secretion of proteins involves the transfer of "reserve" granules, exocytotic vesicles that are cytoplasmic and, hence, plasma membrane-naive, from the cell interior to the surface membrane where they dock prior to fusion. Docking and subsequent priming steps are thought to require cytoplasmic factors. These steps are believed to induce fusion competence. We have tested this hypothesis by isolating reserve granules from sea urchin eggs and determining under which conditions these granules will fuse. We find that isolated reserve granules, lacking soluble cofactors, support calcium-dependent membrane fusion in vitro. Preincubation with adenosine 5′-3-O-(thio)triphosphate and guanosine 5′-3-O-(thio)triphosphate did not prevent fusion. Thus, isolated reserve granules have all the necessary components required for calcium-gated fusion prior to docking.

Adenosine triphosphate

10.1074/jbc.273.4.2445

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Citations (23)

Electrophoretic assay of protein 53K in neonatal blood leukocytes

Bulletin of Experimental Biology and Medicine (1992)

V. D. Paponov Sergey P. Radko E. V. Shtein E. G. Shcheglova

10.1007/bf00783768

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