Лаборатория синтетической биологии

Довыденко Илья Сергеевич
с.н.с., к.х.н.,

телефон: (383) 363-51-35
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Базовые проекты

• «Разработка и создание искусственных систем для целей синтетической биологии» Нацпроект Наука. 0245-2019-0002 (Молодежные лаборатории) (ГЗ-0009) (2019 - 2020 гг.)
  

Гранты Российского научного фонда

• № 19-15-00217 «Многоуровневые транспортеры для эффективной доставки в клетки терапевтических нуклеиновых кислот с различным механизмом действия» (2019 - 2021 гг.)
  

Гранты Российского фонда фундаментальных исследований (РФФИ)

• № 19-44-543012 р_мол_а «Фундаментальные основы взаимодействия нуклеиновых кислот и наночастиц золота для создания диагностических систем». (2019 - 2020 гг.)

1. Thermodynamic parameters obtained for the formation of the Cas12a-RNA/DNA complex. Baranova S.V., Zhdanova P.V., Golyshev V.M., Lomzov A.A., Pestryakov P.E., Chernonosov A.A., Koval V.V. Biochem. and Biophys.Res. Com. 2025. V. 743. P. 151176. DOI: 10.1016/j.bbrc.2024.151176
2. Cold Atmospheric Plasma Jet and Conjugates of Gold Nanoparticles with Tyrp1 Antibodies Efficiently Suppress Growth of B16 Tumor. Biryukov M.M., Schweigert I., Polyakova A.A., Kryackova N.V., Varlamov M., Gorbunova E.A., Epanchintseva A.V., Pyshnaya I.A., Zakrevsky D., Milakhina E., Wang R., Koval O.A. Plasma Medicine. 2025. V. 15. N 1. P. 1-16. DOI: 10.1615/PlasmaMed.2025057895
3. Sequences in the Cytoplasmic Tail Contribute to the Intracellular Trafficking and the Cell Surface Localization of SARS-CoV-2 Spike Protein. Burkova E.E., Bakhno I.A. Biomolecules. 2025. V. 15. N 2. P. 280. DOI: 10.3390/biom15020280
4. Pulsed voltage cold atmospheric plasma jet and gold nanoparticles enhance cytotoxic anticancer effects. Schweigert I.V., Biryukov M.M., Polyakova A.A., Gorbunova E.A., Epanchintseva A.V., Pyshnaya I.A., Zakrevsky D., Milakhina E., Koval O.A. J. Phys. D: Appl. Phys. 2024. V. 57. N. 25. P. 255205. DOI: 10.1088/1361-6463/ad34df
5. The Role of Key Amino Acids of the Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3 in Structural Dynamics and Repair Activity toward Methylated DNA. Kanazhevskaya L.Y., Gorbunov A.A., Lukina M.V., Smyshliaev D.A., Zhdanova P.V., Lomzov A.A., Koval V.V. Int. J. Mol. Sci. 2024. V. 25. P. 1145. DOI: 10.3390/ ijms25021145
6. Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase. Lukina M.V., Zhdanova P.V., Koval V.V. Curr. Issues Mol. Biol. 2024. V. 46. P. 4119–4132. DOI: 10.3390/cimb46050253
7. Looking for miRNA from plasma microvesicles differentially expressed in prostate tumors and healthy men. Bryzgunova O.E., Yakovlev A.N., Ostaltsev I., Laktionov P.P., Konoshenko M.Y. exRNA. 2024. N 2. P. 0009. DOI: 10.55092/exrna20240009
8. Effect of the Phosphoryl Guanidine Modification in Chimeric DNA–RNA crRNAs on the Activity of the CRISPR-Cas9 System In Vitro. Prokhorova D.V., Kupryushkin M.S., Zhukov S., Zharkov T.D., Dovydenko I.S., Yakovleva K.I., Pereverzev I.M., Matveeva A.M., Pyshnyi D.V., Stepanov G.A. ACS Chem. Biol. 2024. V. 19. N 6. P. 1311-1319. DOI: 10.1021/acschembio.4c00147
9. MiRNA expression in plasma extracellular vesicles of prostate cancer patients after radical prostatectomy. Bryzgunova O.E., Yakovlev A.N., Ostaltsev I., Laktionov P.P., Konoshenko M.Y. exRNA. 2024. N 3. P. 0014. DOI: 10.55092/exrna20240014
10. Cleavage of DNA Substrate Containing Nucleotide Mismatch in the Complementary Region to sgRNA by Cas9 Endonuclease: Thermodynamic and Structural Features. Baranova S.V., Zhdanova P.V., Koveshnikova A.D., Pestryakov P.E., Vokhtantsev I.P., Chernonosov A.A., Koval V.V. Int. J. Mol. Sci. 2024. V. 25. P. 10862. DOI: 10.3390/ijms251910862
11. Study of Hard Protein Corona on Lipid Surface of Composite Nanoconstruction. Epanchintseva A.V., Baranova S.V., Poletaeva Y., Bakhno I.A., Ryabchikova E.I., Dovydenko I.S. Nanomaterials. 2024. V. 14. N 21. P. 1767. DOI: 10.3390/nano14211767
12. The Photomodification Method Allows for Determining the Composition of the Full and Soft Protein Corona on the Lipid Surface of Composite Nanoparticles. Epanchintseva A.V., Baranova S.V., Poletaeva Y., Tupitsyna A.V., Ryabchikova E.I., Dovydenko I.S. Nanomaterials. 2024. V. 14. P. 1976. DOI: 10.3390/nano14231976
13. An Approach to Identifying Single-Nucleotide Mutations Using Noncovalent Associates of Gold Nanoparticles with Fluorescently Labeled Oligonucleotides. Epanchintseva A.V., Gorbunova E.A., Nekrasov M.D., Poletaeva Y., Pyshnaya I.A. Int. J. Mol. Sci. 2024. V. 25. P. 13230. DOI: 10.3390/ijms252413230
14. The Role of Key Amino Acids of the Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3 in Structural Dynamics and Repair Activity toward Methylated DNA. Kanazhevskaya L.Y., Gorbunov A.A., Lukina M.V., Smyshliaev D.A., Zhdanova P.V., Lomzov A.A., Koval V.V. Int. J. Mol. Sci. 2024. V. 25. N 2. P. 1145. DOI: 10.3390/ijms25021145
15. Attempts to preserve and visualize protein corona on the surface of biological nanoparticles in blood serum using photomodification. Poletaeva Y., Tupitsyna A.V., Grigoryeva A.E., Dovydenko I.S., Ryabchikova E.I. Beilstein Journal of Nanotechnology. 2024. V. 15. P. 1654–1666. DOI: 10.3762/bjnano.15.130
16. Enhancement of the Anticancer Effect during the Simultaneous Treatment of Cells by a Cold Atmospheric Plasma Jet and Gold Nanoparticles. Schweigert I.V., Zakrevsky D., Milakhina E., Gugin P., Biryukov M.M., Polyakova A.A., Kryachkova N., Gorbunova E.A., Epanchintseva A.V., Pyshnaya I.A., Koval O.A. Физика плазмы. 2024. V. 50. N 11. P. 1375–1387. DOI: 10.1134/S1063780X24601597. перевод
17. Dataset for Spectroscopic, Structural and Dynamic Analysis of Human Fe(II)/2OG-Dependent Dioxygenase ALKBH3. Kanazhevskaya L.Y., Gorbunov A.A., Zhdanova P.V., Koval V.V. Data. 2023. V. 8. P. 57. DOI: 10.3390/data8030057
18. Correlated target search by vaccinia virus uracil–DNA glycosylase, a DNA repair enzyme and a processivity factor of viral replication machinery. Diatlova E., Mechetin G.V., Yudkina A.V., Zharkov D.O., Torgasheva N.A., Endutkin A.V., Shulenina O.V., Konevega A.L., Gileva I.P., Shchelkunov S.N., Zharkov D.O. Int. J. Mol. Sci. 2023. V. 24. N 11. P. 9113. DOI: 10.3390/ijms24119113
19. Noncovalent Adsorption of Single-Stranded and Double-Stranded DNA on the Surface of Gold Nanoparticles. Gorbunova E.A., Epanchintseva A.V., Pyshnyi D.V., Pyshnaya I.A. Applied Sciences (Basel). 2023. V. 13. P. 7324. DOI: 10.3390/app13127324
20. Структура лед-связывающего белка из Myoxocephalus octodecemspinosus, полученная методом молекулярной динамики и на основе спектров кругового дихроизма. Закаблук Г.А., Жданова (�.П., Коваль В.В., Черноносов А.А., Баранова С.В. Биофизика. 2023. Т. 68. № 4. C. 640–645. DOI: 10.31857/S0006302923040026
21. Dynamic structural features of aqua complex formation for ice-binding protein from the fish Myoxocephalus octodecemspinosus based on the HDX-MS technique. Baranova S.V., Zhdanova P.V., Zakabkuk G.A., Chernonosov A.A., Koval V.V. Biophysical Reviews. 2023. V. 15. P. 1442-1443. 10.1007/s12551-023-01150-w. тезисы конференции
22. Structure of an ice-binding protein from the fish longhorn sculpin Myoxocephalus octodecemspinosus based on circular dichroism spectra. Zakabkuk G.A., Baranova S.V., Zhdanova P.V., Chernonosov A.A., Koval V.V. Biophysical Reviews. 2023. V. 15. P. 1477. 10.1007/s12551-023-01150-w тезисы конференции
23. Fixation and Visualization of Full Protein Corona on Lipid Surface of Composite Nanoconstruction. Epanchintseva A.V., Poletaeva Y., Bakhno I.A., Белов V.V., Grigoryeva A.E., Baranova S.V., Ryabchikova E.I., Dovydenko I.S. Nanomaterials. 2023. V. 13. P. 3094. DOI: 10.3390/nano13243094
24. Structure of an Ice-Binding Protein from Myoxocephalus octodecemspinosus Determined by Molecular Dynamics and Based on Circular Dichroism Spectra. Zakabkuk G.A., Zhdanova P.V., Koval V.V., Chernonosov A.A., Baranova S.V. Биофизика. 2023. V. 68. P. 513–518. DOI: 10.1134/s0006350923040152 перевод