Pupov Danil Vladimirovich | Institute of Molecular Genetics

Pupov Danil Vladimirovich

Academic degree:
Doctor of Philosophy (Biology)

Academic title:
without academic rank

Division of IMG:
Laboratory of molecular genetics of microorganisms

Senior Researcher


Resume (CV):

Main research interests

My current research is focused on studies of molecular mechanisms of transcription in bacteria, including analysis of transcription regulation by DNA and RNA-encoded signals, protein transcription factors and small molecules. I also develop novel types of promoter substrates and RNA polymerase inhibitors based on highly specific aptamer ligands to bacterial RNA polymerase.
My recent projects include:
1) investigation of the mechanisms of action of different transcription inhibitors, including rifampicin;
2) selection of aptamers to different epitopes of bacterial RNAP;
3) analysis of the mechanisms of nucleotide selection by RNAP;
4) analysis of general principles of transcription on single-stranded templates;
5) investigation of the roles of different regions of the sigma subunit in transcription initiation;
6) analysis of the roles of conserved DNA-interacting regions of RNAP at various stages of transcription.

Teaching activities

Supervisor of 7 diploma students, 7 defended diploma theses.

Awards, achievements, memberships

  1. Medal of Russian Academy of Science for young scientists (2016)
  2. Stipend of the “Future of Molecular Genetics” Foundation (2010, 2012, 2014)
  3. Member of the Russian Biochemical Society (2010)
  4. Member of the Biochemical Society (United Kingdom) (2010)


  1. Shikalov AB, Esyunina DM, Pupov DV, Kulbachinskiy AV, Petushkov IV. 2019. The σ24 Subunit of Escherichia coli RNA Polymerase Can Induce Transcriptional Pausing in vitro. Biochemistry (Mosc). 84(4):426-434
  2. Pupov D., Ignatov A., Agapov A., Kulbachinskiy A. 2019. Distinct effects of DNA lesions on RNA synthesis by Escherichia coli RNA polymerase. Biochem Biophys Res Commun. 510:122-127.
  3. Esyunina D., Pupov D., Kulbachinskiy A. 2019. Dual role of the σ factor in primer RNA synthesis by bacterial RNA polymerase. FEBS Lett. 593:361-368.
  4. Pupov D., Petushkov I., Esyunina D., Murakami K.S., Kulbachinskiy A. 2018. Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA. Nucl. Acids Res. 46:11477-11487.
  5. Petushkov I., Esyunina D., Mekler V., Severinov K., Pupov D., Kulbachinskiy A. 2017. Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase. Biochem J. 474: 4053–4064.
  6. Agapov A., Esyunina D., Pupov D., Kulbachinskiy A. 2016. Regulation of transcription initiation by Gfh factors from Deinococcus radiodurans. Biochem J. 473(23):4493-4505.
  7. Esyunina D., Turtola M., Pupov D., Bass I., Klimašauskas S., Belogurov G., Kulbachinskiy A. 2016. Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases. Nucl. Acids Res. 44:1298-1308.
  8. Petushkov I., Pupov D., Bass I., Kulbachinsky A. 2015. Mutations in the CRE pocket of bacterial RNA polymerase affect multiple steps of transcription. Nucl. Acids Res. 43:5798-5809.
  9. Pupov D., Kulbachinskiy A. 2015. Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase. Methods in Molecular Biology. 1276:165-83.
  10. Basu R.S., Warner B.S., Molodtsov V., Pupov D., Esyunina D., Fernandez-Tornero C., Kulbachinskiy A., Murakami K.S. 2014. Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme. J. Biol. Chem. 289, 24549-24559.
  11. Pupov D., Kuzin I.A., Bass I., Kulbachinskiy A. 2014. Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape. Nucl. Acids Res. 42:4494-4504.
  12. Pupov D., Esyunina D., Feklistov A. and Kulbachinskiy A. 2013. Single-strand promoter traps for bacterial RNA polymerase. Biochem. J. 452(2): 241-248
  13. Miropolskaya N., Ignatov A., Bass I., Zhilina E., Pupov D., Kulbachinskiy A. 2012. Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation. J. Biol. Chem. 287: 23779-23789.
  14. Pupov D., Miropolskaya N., Sevostyanova A., Bass I., Artsimovitch I., Kulbachinskiy A. 2010. Multiple roles of the RNA polymerase β′-SW2 region in transcription initiation, promoter escape, and RNA elongation. Nucl. Acids Res. 38: 5784-5796.
  15. Pupov D.V., Kulbachinskiy A.V. 2010. Structural dynamics of the active center of multisubunit RNA polymerases during RNA synthesis and proofreading. Review. Mol. Biol. (Mosk). 44: 573-590.
  16. Pupov D.V., Barinova N.A., Kulbachinskiy A.V. 2008. Analysis of RNA Cleavage by RNA Polymerases from Escherichia coli and Deinococcus radiodurans. Biochemistry (Moscow), 73: 725-729.
  17. Mozhina N.V., Burmistrova O.A., Pupov D.V., Rudenskaya G.N., Dunaevsky Ya.E., Demiduk I.V., and Kostrov S.V. 2008. Isolation and properties of Serratia proteamaculans 94 Cysteine Protease. Russian Journal of Bioorganic Chemistry, Vol. 34, No. 3, p.274.
  18. Rudenskaya G.N., Pupov D.V. 2008. Cysteine proteinases of microorganisms and viruses. Review. Biochemistry (Moscow), Jan 73(1), p.1-13.