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Programmable DNA cleavage by Ago nucleases from mesophilic bacteria Clostridium butyricum and Limnothrix rosea.

Kuzmenko A, Yudin D, Ryazansky S, Kulbachinskiy A, Aravin AA.

Nucleic Acids Res. 2019 May 22. pii: gkz379. doi: 10.1093/nar/gkz379. [Epub ahead of print]


Distinct effects of DNA lesions on RNA synthesis by Escherichia coli RNA polymerase.

Pupov D, Ignatov A, Agapov A, Kulbachinskiy A.

Biochem Biophys Res Commun. 2019 Feb 26;510(1):122-127. doi: 10.1016/j.bbrc.2019.01.062. Epub 2019 Jan 18.


Interactions in the active site of Deinococcus radiodurans RNA polymerase during RNA proofreading.

Esyunina D, Kulbachinskiy A.

Biochem Biophys Res Commun. 2019 Jan 29;509(1):161-166. doi: 10.1016/j.bbrc.2018.12.095. Epub 2018 Dec 19.


The Expanded Universe of Prokaryotic Argonaute Proteins.

Ryazansky S, Kulbachinskiy A, Aravin AA.

MBio. 2018 Dec 18;9(6). pii: e01935-18. doi: 10.1128/mBio.01935-18.


Dual role of the σ factor in primer RNA synthesis by bacterial RNA polymerase.

Esyunina D, Pupov D, Kulbachinskiy A.

FEBS Lett. 2019 Feb;593(3):361-368. doi: 10.1002/1873-3468.13312. Epub 2018 Dec 20.


DNA interference and beyond: structure and functions of prokaryotic Argonaute proteins.

Lisitskaya L, Aravin AA, Kulbachinskiy A.

Nat Commun. 2018 Dec 4;9(1):5165. doi: 10.1038/s41467-018-07449-7. Review.


Region 3.2 of the σ factor controls the stability of rRNA promoter complexes and potentiates their repression by DksA.

Pupov D, Petushkov I, Esyunina D, Murakami KS, Kulbachinskiy A.

Nucleic Acids Res. 2018 Nov 30;46(21):11477-11487. doi: 10.1093/nar/gky919.


Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA.

Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ.

Cell Rep. 2018 Jul 10;24(2):453-462. doi: 10.1016/j.celrep.2018.06.021.


The active site residues Gln55 and Arg73 play a key role in DNA damage bypass by S. cerevisiae Pol η.

Boldinova EO, Ignatov A, Kulbachinskiy A, Makarova AV.

Sci Rep. 2018 Jul 9;8(1):10314. doi: 10.1038/s41598-018-28664-8.


Argonaute Proteins and Mechanisms of RNA Interference in Eukaryotes and Prokaryotes.

Olina AV, Kulbachinskiy AV, Aravin AA, Esyunina DM.

Biochemistry (Mosc). 2018 May;83(5):483-497. doi: 10.1134/S0006297918050024. Review.


Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria.

Dulin D, Bauer DLV, Malinen AM, Bakermans JJW, Kaller M, Morichaud Z, Petushkov I, Depken M, Brodolin K, Kulbachinskiy A, Kapanidis AN.

Nat Commun. 2018 Apr 16;9(1):1478. doi: 10.1038/s41467-018-03902-9.


Interplay between σ region 3.2 and secondary channel factors during promoter escape by bacterial RNA polymerase.

Petushkov I, Esyunina D, Mekler V, Severinov K, Pupov D, Kulbachinskiy A.

Biochem J. 2017 Dec 1;474(24):4053-4064. doi: 10.1042/BCJ20170436.


Site-specific aptamer inhibitors of Thermus RNA polymerase.

Miropolskaya N, Feklistov A, Nikiforov V, Kulbachinskiy A.

Biochem Biophys Res Commun. 2018 Jan 1;495(1):110-115. doi: 10.1016/j.bbrc.2017.10.151. Epub 2017 Oct 31.


Identification of amino acid residues involved in the dRP-lyase activity of human Pol ι.

Miropolskaya N, Petushkov I, Kulbachinskiy A, Makarova AV.

Sci Rep. 2017 Aug 31;7(1):10194. doi: 10.1038/s41598-017-10668-5.


Possible roles of σ-dependent RNA polymerase pausing in transcription regulation.

Petushkov I, Esyunina D, Kulbachinskiy A.

RNA Biol. 2017 Dec 2;14(12):1678-1682. doi: 10.1080/15476286.2017.1356568. Epub 2017 Sep 13. Review.


Conserved functions of the trigger loop and Gre factors in RNA cleavage by bacterial RNA polymerases.

Miropolskaya N, Esyunina D, Kulbachinskiy A.

J Biol Chem. 2017 Apr 21;292(16):6744-6752. doi: 10.1074/jbc.M116.766592. Epub 2017 Feb 27.


Gfh factors and NusA cooperate to stimulate transcriptional pausing and termination.

Agapov A, Olina A, Esyunina D, Kulbachinskiy A.

FEBS Lett. 2017 Mar;591(6):946-953. doi: 10.1002/1873-3468.12609. Epub 2017 Mar 12.


σ38-dependent promoter-proximal pausing by bacterial RNA polymerase.

Petushkov I, Esyunina D, Kulbachinskiy A.

Nucleic Acids Res. 2017 Apr 7;45(6):3006-3016. doi: 10.1093/nar/gkw1213.


Regulation of transcription initiation by Gfh factors from Deinococcus radiodurans.

Agapov A, Esyunina D, Pupov D, Kulbachinskiy A.

Biochem J. 2016 Dec 1;473(23):4493-4505. Epub 2016 Oct 17.


Regulation of transcriptional pausing through the secondary channel of RNA polymerase.

Esyunina D, Agapov A, Kulbachinskiy A.

Proc Natl Acad Sci U S A. 2016 Aug 2;113(31):8699-704. doi: 10.1073/pnas.1603531113. Epub 2016 Jul 18.


Lineage-specific variations in the trigger loop modulate RNA proofreading by bacterial RNA polymerases.

Esyunina D, Turtola M, Pupov D, Bass I, Klimašauskas S, Belogurov G, Kulbachinskiy A.

Nucleic Acids Res. 2016 Feb 18;44(3):1298-308. doi: 10.1093/nar/gkv1521. Epub 2016 Jan 4.


Aptamers to the sigma factor mimic promoter recognition and inhibit transcription initiation by bacterial RNA polymerase.

Miropolskaya N, Kulbachinskiy A.

Biochem Biophys Res Commun. 2016 Jan 8;469(2):294-9. doi: 10.1016/j.bbrc.2015.11.100. Epub 2015 Dec 2.


Purification and Characterization of Recombinant Deinococcus radiodurans RNA Polymerase.

Esyunina DM, Kulbachinskiy AV.

Biochemistry (Mosc). 2015 Oct;80(10):1271-8. doi: 10.1134/S0006297915100077.


Mechanisms of Stress Resistance and Gene Regulation in the Radioresistant Bacterium Deinococcus radiodurans.

Agapov AA, Kulbachinskiy AV.

Biochemistry (Mosc). 2015 Oct;80(10):1201-16. doi: 10.1134/S0006297915100016. Review.


Mutations in the CRE pocket of bacterial RNA polymerase affect multiple steps of transcription.

Petushkov I, Pupov D, Bass I, Kulbachinskiy A.

Nucleic Acids Res. 2015 Jul 13;43(12):5798-809. doi: 10.1093/nar/gkv504. Epub 2015 May 18.


Single-stranded DNA aptamers for functional probing of bacterial RNA polymerase.

Pupov D, Kulbachinskiy A.

Methods Mol Biol. 2015;1276:165-83. doi: 10.1007/978-1-4939-2392-2_9.


Distinct pathways of RNA polymerase regulation by a phage-encoded factor.

Esyunina D, Klimuk E, Severinov K, Kulbachinskiy A.

Proc Natl Acad Sci U S A. 2015 Feb 17;112(7):2017-22. doi: 10.1073/pnas.1416330112. Epub 2015 Feb 2.


Roles of the active site residues and metal cofactors in noncanonical base-pairing during catalysis by human DNA polymerase iota.

Makarova AV, Ignatov A, Miropolskaya N, Kulbachinskiy A.

DNA Repair (Amst). 2014 Oct;22:67-76. doi: 10.1016/j.dnarep.2014.07.006. Epub 2014 Aug 9.


Structural basis of transcription initiation by bacterial RNA polymerase holoenzyme.

Basu RS, Warner BA, Molodtsov V, Pupov D, Esyunina D, Fernández-Tornero C, Kulbachinskiy A, Murakami KS.

J Biol Chem. 2014 Aug 29;289(35):24549-59. doi: 10.1074/jbc.M114.584037. Epub 2014 Jun 27.


Structural basis for promoter specificity switching of RNA polymerase by a phage factor.

Tagami S, Sekine S, Minakhin L, Esyunina D, Akasaka R, Shirouzu M, Kulbachinskiy A, Severinov K, Yokoyama S.

Genes Dev. 2014 Mar 1;28(5):521-31. doi: 10.1101/gad.233916.113.


Distinct functions of the RNA polymerase σ subunit region 3.2 in RNA priming and promoter escape.

Pupov D, Kuzin I, Bass I, Kulbachinskiy A.

Nucleic Acids Res. 2014 Apr;42(7):4494-504. doi: 10.1093/nar/gkt1384. Epub 2014 Jan 21.


Interplay between the trigger loop and the F loop during RNA polymerase catalysis.

Miropolskaya N, Esyunina D, Klimasauskas S, Nikiforov V, Artsimovitch I, Kulbachinskiy A.

Nucleic Acids Res. 2014 Jan;42(1):544-52. doi: 10.1093/nar/gkt877. Epub 2013 Oct 1.


Single-strand promoter traps for bacterial RNA polymerase.

Pupov D, Esyunina D, Feklistov A, Kulbachinskiy A.

Biochem J. 2013 Jun 1;452(2):241-8. doi: 10.1042/BJ20130069.


Structure of human DNA polymerase iota and the mechanism of DNA synthesis.

Makarova AV, Kulbachinskiy AV.

Biochemistry (Mosc). 2012 Jun;77(6):547-61. doi: 10.1134/S0006297912060016. Review.


Distinct functions of regions 1.1 and 1.2 of RNA polymerase σ subunits from Escherichia coli and Thermus aquaticus in transcription initiation.

Miropolskaya N, Ignatov A, Bass I, Zhilina E, Pupov D, Kulbachinskiy A.

J Biol Chem. 2012 Jul 6;287(28):23779-89. doi: 10.1074/jbc.M112.363242. Epub 2012 May 17.


A novel phage-encoded transcription antiterminator acts by suppressing bacterial RNA polymerase pausing.

Berdygulova Z, Esyunina D, Miropolskaya N, Mukhamedyarov D, Kuznedelov K, Nickels BE, Severinov K, Kulbachinskiy A, Minakhin L.

Nucleic Acids Res. 2012 May;40(9):4052-63. doi: 10.1093/nar/gkr1285. Epub 2012 Jan 11.


Structural transitions in the transcription elongation complexes of bacterial RNA polymerase during σ-dependent pausing.

Zhilina E, Esyunina D, Brodolin K, Kulbachinskiy A.

Nucleic Acids Res. 2012 Apr;40(7):3078-91. doi: 10.1093/nar/gkr1158. Epub 2011 Dec 2.


Characteristics of σ-dependent pausing by RNA polymerases from Escherichia coli and Thermus aquaticus.

Zhilina EV, Miropolskaya NA, Bass IA, Brodolin KL, Kulbachinskiy AV.

Biochemistry (Mosc). 2011 Oct;76(10):1098-106. doi: 10.1134/S0006297911100038.


Modulation of RNA polymerase activity through the trigger loop folding.

Miropolskaya N, Nikiforov V, Klimasauskas S, Artsimovitch I, Kulbachinskiy A.

Transcription. 2010 Sep-Oct;1(2):89-94. doi: 10.4161/trns.1.2.12544.


Multiple roles of the RNA polymerase {beta}' SW2 region in transcription initiation, promoter escape, and RNA elongation.

Pupov D, Miropolskaya N, Sevostyanova A, Bass I, Artsimovitch I, Kulbachinskiy A.

Nucleic Acids Res. 2010 Sep;38(17):5784-96. doi: 10.1093/nar/gkq355. Epub 2010 May 10.


Allosteric control of catalysis by the F loop of RNA polymerase.

Miropolskaya N, Artsimovitch I, Klimasauskas S, Nikiforov V, Kulbachinskiy A.

Proc Natl Acad Sci U S A. 2009 Nov 10;106(45):18942-7. doi: 10.1073/pnas.0905402106. Epub 2009 Oct 23.


Analysis of RNA cleavage by RNA polymerases from Escherichia coli and Deinococcus radiodurans.

Pupov DV, Barinova NA, Kulbachinskiy AV.

Biochemistry (Mosc). 2008 Jun;73(6):725-9.


Structural modules of RNA polymerase required for transcription from promoters containing downstream basal promoter element GGGA.

Barinova N, Kuznedelov K, Severinov K, Kulbachinskiy A.

J Biol Chem. 2008 Aug 15;283(33):22482-9. doi: 10.1074/jbc.M802445200. Epub 2008 Jun 23.


Methods for selection of aptamers to protein targets.

Kulbachinskiy AV.

Biochemistry (Mosc). 2007 Dec;72(13):1505-18. Review.


Lineage-specific amino acid substitutions in region 2 of the RNA polymerase sigma subunit affect the temperature of promoter opening.

Barinova N, Zhilina E, Bass I, Nikiforov V, Kulbachinskiy A.

J Bacteriol. 2008 Apr;190(8):3088-92. doi: 10.1128/JB.00008-08. Epub 2008 Feb 15.


Specific recognition of the -10 promoter element by the free RNA polymerase sigma subunit.

Sevostyanova A, Feklistov A, Barinova N, Heyduk E, Bass I, Klimasauskas S, Heyduk T, Kulbachinskiy A.

J Biol Chem. 2007 Jul 27;282(30):22033-9. Epub 2007 May 29.


Region 1.2 of the RNA polymerase sigma subunit controls recognition of the -10 promoter element.

Zenkin N, Kulbachinskiy A, Yuzenkova Y, Mustaev A, Bass I, Severinov K, Brodolin K.

EMBO J. 2007 Feb 21;26(4):955-64. Epub 2007 Feb 1.


A basal promoter element recognized by free RNA polymerase sigma subunit determines promoter recognition by RNA polymerase holoenzyme.

Feklistov A, Barinova N, Sevostyanova A, Heyduk E, Bass I, Vvedenskaya I, Kuznedelov K, Merkiene E, Stavrovskaya E, Klimasauskas S, Nikiforov V, Heyduk T, Severinov K, Kulbachinskiy A.

Mol Cell. 2006 Jul 7;23(1):97-107. Epub 2006 Jun 22.


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