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A tRNA- and Anticodon-Centric View of the Evolution of Aminoacyl-tRNA Synthetases, tRNAomes, and the Genetic Code.

Kim Y, Opron K, Burton ZF.

Life (Basel). 2019 May 4;9(2). pii: E37. doi: 10.3390/life9020037. Review.


Ribosome Structure, Function, and Early Evolution.

Opron K, Burton ZF.

Int J Mol Sci. 2018 Dec 21;20(1). pii: E40. doi: 10.3390/ijms20010040. Review.


Type-II tRNAs and Evolution of Translation Systems and the Genetic Code.

Kim Y, Kowiatek B, Opron K, Burton ZF.

Int J Mol Sci. 2018 Oct 22;19(10). pii: E3275. doi: 10.3390/ijms19103275.


Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code.

Pak D, Kim Y, Burton ZF.

Transcription. 2018;9(4):205-224. doi: 10.1080/21541264.2018.1467718. Epub 2018 May 30.


Homology threading to generate RNA polymerase structures.

Kim Y, Benning N, Pham K, Baghdadi N, Caruso G, Colligan M, Grayson A, Hurley A, Ignatoski N, Mcclure S, Mckaig K, Neag E, Showers C, Tangalos A, Vanells J, Padmanabhan K, Burton ZF.

Protein Expr Purif. 2018 Jul;147:13-16. doi: 10.1016/j.pep.2018.02.002. Epub 2018 Feb 11. Review.


Rooted tRNAomes and evolution of the genetic code.

Pak D, Du N, Kim Y, Sun Y, Burton ZF.

Transcription. 2018;9(3):137-151. doi: 10.1080/21541264.2018.1429837. Epub 2018 Feb 6.


Hinge action versus grip in translocation by RNA polymerase.

Nedialkov YA, Opron K, Caudill HL, Assaf F, Anderson AJ, Cukier RI, Wei G, Burton ZF.

Transcription. 2018;9(1):1-16. doi: 10.1080/21541264.2017.1330179. Epub 2017 Aug 30.


tRNA structure and evolution and standardization to the three nucleotide genetic code.

Pak D, Root-Bernstein R, Burton ZF.

Transcription. 2017 Aug 8;8(4):205-219. doi: 10.1080/21541264.2017.1318811. Epub 2017 Jun 20.


tRNA evolution from the proto-tRNA minihelix world.

Root-Bernstein R, Kim Y, Sanjay A, Burton ZF.

Transcription. 2016 Oct 19;7(5):153-163.


A model for genesis of transcription systems.

Burton ZF, Opron K, Wei G, Geiger JH.

Transcription. 2016;7(1):1-13. doi: 10.1080/21541264.2015.1128518.


Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details.

Wang B, Opron K, Burton ZF, Cukier RI, Feig M.

Nucleic Acids Res. 2015 Jan;43(2):1133-46. doi: 10.1093/nar/gku1370. Epub 2014 Dec 30.


The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs.

Burton SP, Burton ZF.

Transcription. 2014;5(4):e967599. doi: 10.4161/21541264.2014.967599.


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.


Computational simulation strategies for analysis of multisubunit RNA polymerases.

Wang B, Feig M, Cukier RI, Burton ZF.

Chem Rev. 2013 Nov 13;113(11):8546-66. doi: 10.1021/cr400046x. Epub 2013 Aug 29. Review. No abstract available.


Energetic and structural details of the trigger-loop closing transition in RNA polymerase II.

Wang B, Predeus AV, Burton ZF, Feig M.

Biophys J. 2013 Aug 6;105(3):767-75. doi: 10.1016/j.bpj.2013.05.060.


Translocation and fidelity of Escherichia coli RNA polymerase.

Nedialkov YA, Burton ZF.

Transcription. 2013 May-Jun;4(3):136-43. Epub 2013 Jul 11.


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.


RNA polymerase stalls in a post-translocated register and can hyper-translocate.

Nedialkov YA, Nudler E, Burton ZF.

Transcription. 2012 Sep-Oct;3(5):260-9. doi: 10.4161/trns.22307. Epub 2012 Sep 1.


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.


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.


RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.

Feig M, Burton ZF.

Biophys J. 2010 Oct 20;99(8):2577-86. doi: 10.1016/j.bpj.2010.08.010.


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.


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.


RNA polymerase II flexibility during translocation from normal mode analysis.

Feig M, Burton ZF.

Proteins. 2010 Feb 1;78(2):434-46. doi: 10.1002/prot.22560.


Minimal promoter systems reveal the importance of conserved residues in the B-finger of human transcription factor IIB.

Thompson NE, Glaser BT, Foley KM, Burton ZF, Burgess RR.

J Biol Chem. 2009 Sep 11;284(37):24754-66. doi: 10.1074/jbc.M109.030486. Epub 2009 Jul 9.


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.


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.


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.


NTP-driven translocation and regulation of downstream template opening by multi-subunit RNA polymerases.

Burton ZF, Feig M, Gong XQ, Zhang C, Nedialkov YA, Xiong Y.

Biochem Cell Biol. 2005 Aug;83(4):486-96. Review.


Dynamic error correction and regulation of downstream bubble opening by human RNA polymerase II.

Gong XQ, Zhang C, Feig M, Burton ZF.

Mol Cell. 2005 May 13;18(4):461-70.


Spacing requirements for simultaneous recognition of the adenovirus major late promoter TATAAAAG box and initiator element.

Ren D, Nedialkov YA, Li F, Xu D, Reimers S, Finkelstein A, Burton ZF.

Arch Biochem Biophys. 2005 Mar 15;435(2):347-62.


Alpha-amanitin blocks translocation by human RNA polymerase II.

Gong XQ, Nedialkov YA, Burton ZF.

J Biol Chem. 2004 Jun 25;279(26):27422-7. Epub 2004 Apr 19.


Efficient production of recombinant human transcription factor IIE.

Moon WJ, Apostol JA, McBride AJ, Shukla LI, Dvir A, Burton ZF.

Protein Expr Purif. 2004 Apr;34(2):317-23.


Assay of transient state kinetics of RNA polymerase II elongation.

Nedialkov YA, Gong XQ, Yamaguchi Y, Handa H, Burton ZF.

Methods Enzymol. 2003;371:252-64. No abstract available.


Auto-acetylation of transcription factors as a control mechanism in gene expression.

Choi CH, Burton ZF, Usheva A.

Cell Cycle. 2004 Feb;3(2):114-5. Review.


NTP-driven translocation by human RNA polymerase II.

Nedialkov YA, Gong XQ, Hovde SL, Yamaguchi Y, Handa H, Geiger JH, Yan H, Burton ZF.

J Biol Chem. 2003 May 16;278(20):18303-12. Epub 2003 Mar 13.


A key role for the alpha 1 helix of human RAP74 in the initiation and elongation of RNA chains.

Funk JD, Nedialkov YA, Xu D, Burton ZF.

J Biol Chem. 2002 Dec 6;277(49):46998-7003. Epub 2002 Sep 26.


Structural and functional interactions of transcription factor (TF) IIA with TFIIE and TFIIF in transcription initiation by RNA polymerase II.

Langelier MF, Forget D, Rojas A, Porlier Y, Burton ZF, Coulombe B.

J Biol Chem. 2001 Oct 19;276(42):38652-7. Epub 2001 Aug 16.


Wrapping of promoter DNA around the RNA polymerase II initiation complex induced by TFIIF.

Robert F, Douziech M, Forget D, Egly JM, Greenblatt J, Burton ZF, Coulombe B.

Mol Cell. 1998 Sep;2(3):341-51.


RAP74 induces promoter contacts by RNA polymerase II upstream and downstream of a DNA bend centered on the TATA box.

Forget D, Robert F, Grondin G, Burton ZF, Greenblatt J, Coulombe B.

Proc Natl Acad Sci U S A. 1997 Jul 8;94(14):7150-5.


Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme.

Shi X, Chang M, Wolf AJ, Chang CH, Frazer-Abel AA, Wade PA, Burton ZF, Jaehning JA.

Mol Cell Biol. 1997 Mar;17(3):1160-9.

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