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Items: 1 to 50 of 95

1.

The Role of Pyrophosphorolysis in the Initiation-to-Elongation Transition by E. coli RNA Polymerase.

Imashimizu M, Kireeva ML, Lubkowska L, Kashlev M, Shimamoto N.

J Mol Biol. 2019 Jun 28;431(14):2528-2542. doi: 10.1016/j.jmb.2019.04.020. Epub 2019 Apr 26.

PMID:
31029704
2.

RNA-DNA and DNA-DNA base-pairing at the upstream edge of the transcription bubble regulate translocation of RNA polymerase and transcription rate.

KIreeva M, Trang C, Matevosyan G, Turek-Herman J, Chasov V, Lubkowska L, Kashlev M.

Nucleic Acids Res. 2018 Jun 20;46(11):5764-5775. doi: 10.1093/nar/gky393.

3.

Structural basis of transcriptional stalling and bypass of abasic DNA lesion by RNA polymerase II.

Wang W, Walmacq C, Chong J, Kashlev M, Wang D.

Proc Natl Acad Sci U S A. 2018 Mar 13;115(11):E2538-E2545. doi: 10.1073/pnas.1722050115. Epub 2018 Feb 27.

4.

Cotranscriptional Production of Chemically Modified RNA Nanoparticles.

Kireeva ML, Afonin KA, Shapiro BA, Kashlev M.

Methods Mol Biol. 2017;1632:91-105. doi: 10.1007/978-1-4939-7138-1_6.

PMID:
28730434
5.

A Cre Transcription Fidelity Reporter Identifies GreA as a Major RNA Proofreading Factor in Escherichia coli.

Bubunenko MG, Court CB, Rattray AJ, Gotte DR, Kireeva ML, Irizarry-Caro JA, Li X, Jin DJ, Court DL, Strathern JN, Kashlev M.

Genetics. 2017 May;206(1):179-187. doi: 10.1534/genetics.116.198960. Epub 2017 Mar 24.

6.

Production and characterization of a highly pure RNA polymerase holoenzyme from Mycobacterium tuberculosis.

Herrera-Asmat O, Lubkowska L, Kashlev M, Bustamante CJ, Guerra DG, Kireeva ML.

Protein Expr Purif. 2017 Jun;134:1-10. doi: 10.1016/j.pep.2017.03.013. Epub 2017 Mar 18.

7.

T7 replisome directly overcomes DNA damage.

Sun B, Pandey M, Inman JT, Yang Y, Kashlev M, Patel SS, Wang MD.

Nat Commun. 2015 Dec 17;6:10260. doi: 10.1038/ncomms10260.

8.

Erratum to: Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo.

Imashimizu M, Takahashi H, Oshima T, McIntosh C, Bubunenko M, Court DL, Kashlev M.

Genome Biol. 2015 Dec 2;16:270. doi: 10.1186/s13059-015-0845-4. No abstract available.

9.

Allosteric Activation of Bacterial Swi2/Snf2 (Switch/Sucrose Non-fermentable) Protein RapA by RNA Polymerase: BIOCHEMICAL AND STRUCTURAL STUDIES.

Kakar S, Fang X, Lubkowska L, Zhou YN, Shaw GX, Wang YX, Jin DJ, Kashlev M, Ji X.

J Biol Chem. 2015 Sep 25;290(39):23656-69. doi: 10.1074/jbc.M114.618801. Epub 2015 Aug 13.

10.

Visualizing translocation dynamics and nascent transcript errors in paused RNA polymerases in vivo.

Imashimizu M, Takahashi H, Oshima T, McIntosh C, Bubunenko M, Court DL, Kashlev M.

Genome Biol. 2015 May 15;16:98. doi: 10.1186/s13059-015-0666-5. Erratum in: Genome Biol. 2015;16:270.

11.

Productive mRNA stem loop-mediated transcriptional slippage: Crucial features in common with intrinsic terminators.

Penno C, Sharma V, Coakley A, O'Connell Motherway M, van Sinderen D, Lubkowska L, Kireeva ML, Kashlev M, Baranov PV, Atkins JF.

Proc Natl Acad Sci U S A. 2015 Apr 21;112(16):E1984-93. doi: 10.1073/pnas.1418384112. Epub 2015 Apr 6.

12.

Mechanism of RNA polymerase II bypass of oxidative cyclopurine DNA lesions.

Walmacq C, Wang L, Chong J, Scibelli K, Lubkowska L, Gnatt A, Brooks PJ, Wang D, Kashlev M.

Proc Natl Acad Sci U S A. 2015 Feb 3;112(5):E410-9. doi: 10.1073/pnas.1415186112. Epub 2015 Jan 20.

13.

A genetic assay for transcription errors reveals multilayer control of RNA polymerase II fidelity.

Irvin JD, Kireeva ML, Gotte DR, Shafer BK, Huang I, Kashlev M, Strathern JN.

PLoS Genet. 2014 Sep 18;10(9):e1004532. doi: 10.1371/journal.pgen.1004532. eCollection 2014 Sep.

14.

Coliphage HK022 Nun protein inhibits RNA polymerase translocation.

Vitiello CL, Kireeva ML, Lubkowska L, Kashlev M, Gottesman M.

Proc Natl Acad Sci U S A. 2014 Jun 10;111(23):E2368-75. doi: 10.1073/pnas.1319740111. Epub 2014 May 22.

15.

Unveiling translocation intermediates of RNA polymerase.

Imashimizu M, Kashlev M.

Proc Natl Acad Sci U S A. 2014 May 27;111(21):7507-8. doi: 10.1073/pnas.1406413111. Epub 2014 May 14. No abstract available.

16.

In silico design and enzymatic synthesis of functional RNA nanoparticles.

Afonin KA, Kasprzak WK, Bindewald E, Kireeva M, Viard M, Kashlev M, Shapiro BA.

Acc Chem Res. 2014 Jun 17;47(6):1731-41. doi: 10.1021/ar400329z. Epub 2014 Apr 23.

17.

Bacteriophage λ N protein inhibits transcription slippage by Escherichia coli RNA polymerase.

Parks AR, Court C, Lubkowska L, Jin DJ, Kashlev M, Court DL.

Nucleic Acids Res. 2014 May;42(9):5823-9. doi: 10.1093/nar/gku203. Epub 2014 Apr 7.

18.

Transcription factors IIS and IIF enhance transcription efficiency by differentially modifying RNA polymerase pausing dynamics.

Ishibashi T, Dangkulwanich M, Coello Y, Lionberger TA, Lubkowska L, Ponticelli AS, Kashlev M, Bustamante C.

Proc Natl Acad Sci U S A. 2014 Mar 4;111(9):3419-24. doi: 10.1073/pnas.1401611111. Epub 2014 Feb 18.

19.

Transcription elongation. Heterogeneous tracking of RNA polymerase and its biological implications.

Imashimizu M, Shimamoto N, Oshima T, Kashlev M.

Transcription. 2014;5(1):e28285. doi: 10.4161/trns.28285. Review.

20.

RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression.

Kireeva ML, Kashlev M, Burton ZF.

Chem Rev. 2013 Nov 13;113(11):8325-30. doi: 10.1021/cr400436m. No abstract available.

21.

Co-transcriptional production of RNA-DNA hybrids for simultaneous release of multiple split functionalities.

Afonin KA, Desai R, Viard M, Kireeva ML, Bindewald E, Case CL, Maciag AE, Kasprzak WK, Kim T, Sappe A, Stepler M, Kewalramani VN, Kashlev M, Blumenthal R, Shapiro BA.

Nucleic Acids Res. 2014 Feb;42(3):2085-97. doi: 10.1093/nar/gkt1001. Epub 2013 Nov 4.

22.

Complete dissection of transcription elongation reveals slow translocation of RNA polymerase II in a linear ratchet mechanism.

Dangkulwanich M, Ishibashi T, Liu S, Kireeva ML, Lubkowska L, Kashlev M, Bustamante CJ.

Elife. 2013 Sep 24;2:e00971. doi: 10.7554/eLife.00971.

23.

Direct assessment of transcription fidelity by high-resolution RNA sequencing.

Imashimizu M, Oshima T, Lubkowska L, Kashlev M.

Nucleic Acids Res. 2013 Oct;41(19):9090-104. doi: 10.1093/nar/gkt698. Epub 2013 Aug 7.

24.

Intrinsic translocation barrier as an initial step in pausing by RNA polymerase II.

Imashimizu M, Kireeva ML, Lubkowska L, Gotte D, Parks AR, Strathern JN, Kashlev M.

J Mol Biol. 2013 Feb 22;425(4):697-712. doi: 10.1016/j.jmb.2012.12.002. Epub 2012 Dec 10.

PMID:
23238253
25.

Isolation and characterization of RNA polymerase rpoB mutations that alter transcription slippage during elongation in Escherichia coli.

Zhou YN, Lubkowska L, Hui M, Court C, Chen S, Court DL, Strathern J, Jin DJ, Kashlev M.

J Biol Chem. 2013 Jan 25;288(4):2700-10. doi: 10.1074/jbc.M112.429464. Epub 2012 Dec 5.

26.

The fidelity of transcription: RPB1 (RPO21) mutations that increase transcriptional slippage in S. cerevisiae.

Strathern J, Malagon F, Irvin J, Gotte D, Shafer B, Kireeva M, Lubkowska L, Jin DJ, Kashlev M.

J Biol Chem. 2013 Jan 25;288(4):2689-99. doi: 10.1074/jbc.M112.429506. Epub 2012 Dec 5.

27.

The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.

Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, Cukier RI, Nudler E, Burton ZF.

Biochim Biophys Acta. 2013 Feb;1829(2):187-98. doi: 10.1016/j.bbagrm.2012.11.005. Epub 2012 Nov 30.

28.

Sensitivity of mitochondrial transcription and resistance of RNA polymerase II dependent nuclear transcription to antiviral ribonucleosides.

Arnold JJ, Sharma SD, Feng JY, Ray AS, Smidansky ED, Kireeva ML, Cho A, Perry J, Vela JE, Park Y, Xu Y, Tian Y, Babusis D, Barauskus O, Peterson BR, Gnatt A, Kashlev M, Zhong W, Cameron CE.

PLoS Pathog. 2012;8(11):e1003030. doi: 10.1371/journal.ppat.1003030. Epub 2012 Nov 15.

29.

Nucleosomal elements that control the topography of the barrier to transcription.

Bintu L, Ishibashi T, Dangkulwanich M, Wu YY, Lubkowska L, Kashlev M, Bustamante C.

Cell. 2012 Nov 9;151(4):738-749. doi: 10.1016/j.cell.2012.10.009.

30.

Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs.

Afonin KA, Kireeva M, Grabow WW, Kashlev M, Jaeger L, Shapiro BA.

Nano Lett. 2012 Oct 10;12(10):5192-5. doi: 10.1021/nl302302e. Epub 2012 Sep 27.

31.

Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.

Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, Kashlev M, Burton ZF.

BMC Biophys. 2012 Jun 7;5:11. doi: 10.1186/2046-1682-5-11.

32.

Mechanism of translesion transcription by RNA polymerase II and its role in cellular resistance to DNA damage.

Walmacq C, Cheung AC, Kireeva ML, Lubkowska L, Ye C, Gotte D, Strathern JN, Carell T, Cramer P, Kashlev M.

Mol Cell. 2012 Apr 13;46(1):18-29. doi: 10.1016/j.molcel.2012.02.006. Epub 2012 Mar 8.

33.

Isolation and characterization of transcription fidelity mutants.

Strathern JN, Jin DJ, Court DL, Kashlev M.

Biochim Biophys Acta. 2012 Jul;1819(7):694-9. doi: 10.1016/j.bbagrm.2012.02.005. Epub 2012 Feb 16. Review.

PMID:
22366339
34.

The elongation rate of RNA polymerase determines the fate of transcribed nucleosomes.

Bintu L, Kopaczynska M, Hodges C, Lubkowska L, Kashlev M, Bustamante C.

Nat Struct Mol Biol. 2011 Nov 13;18(12):1394-9. doi: 10.1038/nsmb.2164.

35.

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing.

Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, Oberdoerffer P, Sandberg R, Oberdoerffer S.

Nature. 2011 Nov 3;479(7371):74-9. doi: 10.1038/nature10442.

PMID:
21964334
36.

Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.

Kireeva ML, Domecq C, Coulombe B, Burton ZF, Kashlev M.

J Biol Chem. 2011 Sep 2;286(35):30898-910. doi: 10.1074/jbc.M111.260844. Epub 2011 Jul 5.

37.

Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.

Seibold SA, Singh BN, Zhang C, Kireeva M, Domecq C, Bouchard A, Nazione AM, Feig M, Cukier RI, Coulombe B, Kashlev M, Hampsey M, Burton ZF.

Biochim Biophys Acta. 2010 Aug;1799(8):575-87. doi: 10.1016/j.bbagrm.2010.05.002. Epub 2010 May 15.

38.

Synergistic action of RNA polymerases in overcoming the nucleosomal barrier.

Jin J, Bai L, Johnson DS, Fulbright RM, Kireeva ML, Kashlev M, Wang MD.

Nat Struct Mol Biol. 2010 Jun;17(6):745-52. doi: 10.1038/nsmb.1798. Epub 2010 May 9.

39.

Translocation by multi-subunit RNA polymerases.

Kireeva M, Kashlev M, Burton ZF.

Biochim Biophys Acta. 2010 May-Jun;1799(5-6):389-401. doi: 10.1016/j.bbagrm.2010.01.007. Epub 2010 Jan 25. Review.

PMID:
20097318
40.

Nucleosomal fluctuations govern the transcription dynamics of RNA polymerase II.

Hodges C, Bintu L, Lubkowska L, Kashlev M, Bustamante C.

Science. 2009 Jul 31;325(5940):626-8. doi: 10.1126/science.1172926.

41.

Site-directed mutagenesis, purification and assay of Saccharomyces cerevisiae RNA polymerase II.

Domecq C, Kireeva M, Archambault J, Kashlev M, Coulombe B, Burton ZF.

Protein Expr Purif. 2010 Jan;69(1):83-90. doi: 10.1016/j.pep.2009.06.016. Epub 2009 Jun 28.

42.

Rpb9 subunit controls transcription fidelity by delaying NTP sequestration in RNA polymerase II.

Walmacq C, Kireeva ML, Irvin J, Nedialkov Y, Lubkowska L, Malagon F, Strathern JN, Kashlev M.

J Biol Chem. 2009 Jul 17;284(29):19601-12. doi: 10.1074/jbc.M109.006908. Epub 2009 May 13.

43.

Mechanism of sequence-specific pausing of bacterial RNA polymerase.

Kireeva ML, Kashlev M.

Proc Natl Acad Sci U S A. 2009 Jun 2;106(22):8900-5. doi: 10.1073/pnas.0900407106. Epub 2009 Apr 24.

44.

Millisecond phase kinetic analysis of elongation catalyzed by human, yeast, and Escherichia coli RNA polymerase.

Kireeva M, Nedialkov YA, Gong XQ, Zhang C, Xiong Y, Moon W, Burton ZF, Kashlev M.

Methods. 2009 Aug;48(4):333-45. doi: 10.1016/j.ymeth.2009.04.008. Epub 2009 May 4.

45.

DNA sequences in gal operon override transcription elongation blocks.

Lewis DE, Komissarova N, Le P, Kashlev M, Adhya S.

J Mol Biol. 2008 Oct 17;382(4):843-58. doi: 10.1016/j.jmb.2008.07.060. Epub 2008 Jul 27.

46.

Transient reversal of RNA polymerase II active site closing controls fidelity of transcription elongation.

Kireeva ML, Nedialkov YA, Cremona GH, Purtov YA, Lubkowska L, Malagon F, Burton ZF, Strathern JN, Kashlev M.

Mol Cell. 2008 Jun 6;30(5):557-66. doi: 10.1016/j.molcel.2008.04.017.

47.

DNA bubble formation in transcription initiation.

Tchernaenko V, Halvorson HR, Kashlev M, Lutter LC.

Biochemistry. 2008 Feb 19;47(7):1871-84. doi: 10.1021/bi701289g. Epub 2008 Jan 19.

PMID:
18205393
48.

DNA bending in transcription initiation.

Tchernaenko V, Radlinska M, Lubkowska L, Halvorson HR, Kashlev M, Lutter LC.

Biochemistry. 2008 Feb 19;47(7):1885-95. doi: 10.1021/bi7012883. Epub 2008 Jan 19.

PMID:
18205392
49.

Backtracking determines the force sensitivity of RNAP II in a factor-dependent manner.

Galburt EA, Grill SW, Wiedmann A, Lubkowska L, Choy J, Nogales E, Kashlev M, Bustamante C.

Nature. 2007 Apr 12;446(7137):820-3. Epub 2007 Mar 14.

PMID:
17361130
50.

Effects of Friedreich's ataxia (GAA)n*(TTC)n repeats on RNA synthesis and stability.

Krasilnikova MM, Kireeva ML, Petrovic V, Knijnikova N, Kashlev M, Mirkin SM.

Nucleic Acids Res. 2007;35(4):1075-84. Epub 2007 Jan 30.

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