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Contract number
Time span of the project
Head of the laboratory

As of 01.11.2022

Number of staff members
scientific publications
General information

Name of the project: Study of mechanisms of RNA interference and protection of genomes in bacteria and eukaryotes.

Goals and objectives

Research directions: Biogenesis of non-coding RNA in eukaryotes, RNA interference in bacteria, genome editing using non-coding RNA and Argonaute proteins

Project objective: Study of natural function of RNA interference systems in bacteria and eukaryotes, as well as development of new tools for gene and electronic engineering based on these systems

The practical value of the study

Scientific results:

  1. In the Laboratory created with support form the mega-grant, we have, for the first time in our country, started research of Argonaute proteins of bacteria. These proteins are programmable nucleases that use short single-chain guide nucleic acids for detecting and cutting a complementary target. The bioinformatics analysis of bacterial Argonautes conducted in the beginning of the project allowed to select several dozens of candidate proteins for further analysis. 
  2. We have researched the biochemical properties of more than 40 new Argonaute  proteins in vitro. For the first time in the world, we found and described Argonaute proteins with new properties that possess both a wide specificity and a narrow specificity towards the type of nucleic acids (DNA or RNA) used as the guide and the target. We found new groups of these proteins with unique specificity towards DNA or RNA targets. 
  3. For the first time, we have experimentally demonstrated the participation of bacterial Argonautes in protecting cells from bacteriophages and plasmids. We found a new phenomenon of DNA interference, conducted research of this process. In the domain of applied research, we demonstrated the possibility of using bacterial Argonautes for the specific cutting of plasmid DNA, similarly to restriction endonucleases, as well as for cutting RNA and for detecting its secondary structure. 
  4. We are currently working to use Argonaute proteins for genome editing, in particular, we have demonstrated such a possibility for modifying the genome of E. coli. The conducted research demonstrates that Argonaute proteins are a very promising molecular biological tool due to the capability of «directing» them onto specific targets using a short guide to the needed RNA or DNA sequence. 

Education and career development:

  • In 2021, we compiled a lecture course for master’s degree students of the Moscow Institute of Physics and Technology – Generium school,  «Gene engineering and methods of molecular biology». 
  • Relying of the results of the research, a Candidate of Sciences dissertation has been defended. One Doctor of Sciences dissertation and two Candidate of Sciences dissertations has been submitted for defense, two more Candidate of Sciences dissertations are currently being prepared. 


Previously, the Laboratory has collaborated with the laboratories of David Leach (The University of Edinburgh), Katsuhiko Murakami (Penn State University), Dinshaw Patel (Sloan Kettering Institute). Some of experiments were conducted in these laboratories, we discussed experiment plans, their results and published articles.

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kropocheva ev, lisitskaya la, agapov aa, musabirov aa, kulbachinskiy av, esyunina dm.
Prokaryotic Argonaute Proteins as a Tool for Biotechnology. Molecular Biology. 2022 Aug 30:1-20. doi: 10.1134/S0026893322060103. Импакт-фактор: 1.54, квартиль: Q4. 2022
lisitskaya l, shin y, agapov a, olina a, kropocheva e, ryazansky s, aravin aa, esyunina d, murakami ks, kulbachinskiy a.
Programmable RNA targeting by bacterial Argonaute nucleases with unconventional guide binding and cleavage specificity. Nature Communications. 2022 Aug 8;13(1):4624. doi: 10.1038/s41467-022-32079-5. Импакт-фактор: 17.694, квартиль: Q1. 2022
kropocheva e, kuzmenko a, aravin aa, esyunina d, kulbachinskiy a.
A programmable pAgo nuclease with universal guide and target specificity from the mesophilic bacterium Kurthia massiliensis. Nucleic Acids Research. 2021 Apr 19;49(7):4054-4065. doi: 10.1093/nar/gkab182. Импакт-фактор: 19.16, квартиль: Q1. 2022
lisitskaya l., petushkov i., esyunina d., aravin a., kulbachinskiy a.
Recognition of double-stranded DNA by the Rhodobacter sphaeroides Argonaute protein. Biochemical and Biophysical Research Communications. 533(4):1484-1489. doi: 10.1016/j.bbrc.2020.10.051. Импакт-фактор: 3.322, квартиль: Q3. 2020
kuzmenko a, oguienko a*, esyunina d*, yudin d*, petrova m, kudinova a, maslova o, ninova m, ryazansky s, leach d, aravin aa, kulbachinskiy a.
Adaptive dif modules in permafrost strains of Acinetobacter lwoffii and their distribution and abundance among present day Acinetobacter strains. Frontiers in Microbiology, 29 March 2019.
olina a., kuzmenko a., ninova m., aravin a.a., kulbachinskiy a., esyunina d.
DNA targeting and interference by a bacterial Argonaute nuclease. Nature. 587 (7835): 632-637 Jul 30. doi: 10.1038/s41586-020-2605-1. Импакт-фактор: 69.504, квартиль: Q1. 2020
liu y*, esyunina d*, olovnikov i, teplova m, kulbachinskiy a, aravin aa, patel dj.
Genome-wide DNA sampling by Ago nuclease from the cyanobacterium Synechococcus elongatus. RNA Biology. 17(5): 677-688. doi: 10.1080/15476286.2020.1724716. Импакт-фактор: 4.766, квартиль: Q2. 2020
олина а.в., кульбачинский а.в., аравин а.а., есюнина д.м.
Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. Cell Reports. 24(2): 453-462. Импакт-фактор: 9.995, квартиль: Q1. 2018
lisitskaya l, aravin aa, kulbachinskiy a.
Белки-аргонавты и механизмы РНК-интерференции у эукариот и прокариот. Биохимия 83: 645-661. Импакт-фактор: 2.824, квартиль: Q4. 2018
ryazansky s, kulbachinskiy a, aravin aa.
DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins. Nature Communication. 2018 Dec 4;9(1):5165. doi: 10.1038/s41467-018-07449-7. Импакт-фактор: 17.694, квартиль: Q1.
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