Recent Publications

Kim Y, Kowiatek B, Opron K, Burton ZF. “Type-II tRNAs and Evolution of Translation Systems and the Genetic Code” Int. J. Mol. Sci. (2018) Oct 18;19(10):3275. doi: 10.3390/ijms19103275

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. “Homology threading to generate RNA polymerase structures.” Protein Expr Purif. (2018) Jul;147:13-16. doi: 10.1016/j.pep.2018.02.002

Pak D, Kim Y, Burton ZF. “Aminoacyl-tRNA synthetase evolution and sectoring of the genetic code.” Transcription. (2018) May 4;1-36. doi: 10.1080/21541264.2018.1467718

Pak D, Du N, Kim Y, Sun Y, Burton ZF. “Rooted tRNAomes and evolution of the genetic code.” Transcription. (2018) Jan 26;1-31. doi: 10.1080/21541264.2018.1429837

Nedialkov YA, Opron K, Caudill HL, Assaf F, Anderson AJ, Cukier RI, Wei G, Burton ZF. “Hinge action versus grip in translocation by RNA polymerase.” Transcription. (2017) Aug 30;e1330179. doi: 10.1080/21541264.2017.1330179

Pak D, Root-Bernstein R, Burton ZF. “tRNA structure and evolution and standardization to the three nucleotide genetic code.” Transcription. (2017) Aug 8;8(4):205-219. doi: 10.1080/21541264.2017.1318811

Root-Bernstein R, Kim Y, Sanjay A, Burton ZF. “tRNA evolution from the proto-tRNA minihelix world.” Transcription. (2016) Oct 19;7(5):153-163. doi: 10.1080/21541264.2016.1235527

Opron K, Xia K, Burton Z, Wei GW. “Flexibility-rigidity index for protein-nucleic acid flexibility and fluctuation analysis.” J Comput Chem. (2016) May 30;37(14):1283-95. doi: 10.1002/jcc.24320

Burton, ZF. “Herpes Simplex Virus Serotype 2 Oral Infection.” JSM Biochem Mol Biol (2016) 3(1):1015.

Burton ZF, Opron K, Wei G, Geiger JH. “A model for genesis of transcription systems.” Transcription. (2016) Jan 6:0. doi:10.1080/21541264.2015.1128518

Burton ZF. “The Old and New Testaments of gene regulation. Evolution of multi-subunit RNA polymerases and co-evolution of eukaryote complexity with the RNAP II CTD.” Transcription. (2014);5(3):e28674. doi:10.4161/trns.28674

Wang B, Opron K, Burton ZF, Cukier RI, Feig M. “Five checkpoints maintaining the fidelity of transcription by RNA polymerases in structural and energetic details.” Nucleic Acids Res. (2015) Jan;43(2):1133-46. doi:10.1093/nar/gku1370

Burton SP, Burton ZF. “The σ enigma: bacterial σ factors, archaeal TFB and eukaryotic TFIIB are homologs.” Transcription. (2014);5(4):e967599. doi:10.4161/21541264.2014.967599

Burton ZF “Problematic polymerases.” International Innovation. (2014) vol. 161; pdf download

Kireeva ML, Kashlev M, Burton ZF. “RNA polymerase structure, function, regulation, dynamics, fidelity, and roles in gene expression.” Chem Rev. (2013) Nov 13;113(11):8325-30. doi:10.1021/cr400436m

Wang B, Feig M, Cukier RI, Burton ZF. “Computational simulation strategies for analysis of multisubunit RNA polymerases.” Chem Rev. (2013) Nov 13;113(11):8546-66. doi:10.1021/cr400046x

Wang B, Predeus AV, Burton ZF, Feig M. “Energetic and structural details of the trigger-loop closing transition in RNA polymerase II.” Biophys J. (2013) Aug 6;105(3):767-75. doi:10.1016/j.bpj.2013.05.060

Nedialkov YA, Burton ZF. “Translocation and fidelity of Escherichia coli RNA polymerase.” Transcription. (2013) May-Jun;4(3):136-43.

Nedialkov YA, Opron K, Assaf F, Artsimovitch I, Kireeva ML, Kashlev M, Cukier RI, Nudler E, Burton ZF. “The RNA polymerase bridge helix YFI motif in catalysis, fidelity and translocation.” Biochim Biophys Acta. (2013) Feb;1829(2):187-98. doi:10.1016/j.bbagrm.2012.11.005

Nedialkov YA, Nudler E, Burton ZF. “RNA polymerase stalls in a post-translocated register and can hyper-translocate.” Transcription. (2012) Sep-Oct;3(5):260-9. doi:10.4161/trns.22307

Kireeva ML, Opron K, Seibold SA, Domecq C, Cukier RI, Coulombe B, Kashlev M, Burton ZF. “Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase.” BMC Biophys. (2012) Jun 7;5:11. doi:10.1186/2046-1682-5-11

Kireeva ML, Domecq C, Coulombe B, Burton ZF, Kashlev M. “Interaction of RNA polymerase II fork loop 2 with downstream non-template DNA regulates transcription elongation.” J Biol Chem. (2011) Sep 2;286(35):30898-910. doi:10.1074/jbc.M111.260844

Feig M, Burton ZF. “RNA polymerase II with open and closed trigger loops: active site dynamics and nucleic acid translocation.” Biophys J. (2010) Oct 20;99(8):2577-86. doi:10.1016/j.bpj.2010.08.010

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. “Conformational coupling, bridge helix dynamics and active site dehydration in catalysis by RNA polymerase.” Biochim Biophys Acta. (2010) Aug;1799(8):575-87. doi:10.1016/j.bbagrm.2010.05.002