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Items: 41

1.

Direct removal of RNA polymerase barriers to replication by accessory replicative helicases.

Hawkins M, Dimude JU, Howard JAL, Smith AJ, Dillingham MS, Savery NJ, Rudolph CJ, McGlynn P.

Nucleic Acids Res. 2019 Mar 14. pii: gkz170. doi: 10.1093/nar/gkz170. [Epub ahead of print]

PMID:
30869136
2.

An Orthogonal Multi-input Integration System to Control Gene Expression in Escherichia coli.

Annunziata F, Matyjaszkiewicz A, Fiore G, Grierson CS, Marucci L, di Bernardo M, Savery NJ.

ACS Synth Biol. 2017 Oct 20;6(10):1816-1824. doi: 10.1021/acssynbio.7b00109. Epub 2017 Jul 25.

PMID:
28723080
3.

BSim 2.0: An Advanced Agent-Based Cell Simulator.

Matyjaszkiewicz A, Fiore G, Annunziata F, Grierson CS, Savery NJ, Marucci L, di Bernardo M.

ACS Synth Biol. 2017 Oct 20;6(10):1969-1972. doi: 10.1021/acssynbio.7b00121. Epub 2017 Jun 23.

PMID:
28585809
4.

Understanding bias in DNA repair.

Strick TR, Savery NJ.

Proc Natl Acad Sci U S A. 2017 Mar 14;114(11):2791-2793. doi: 10.1073/pnas.1701549114. Epub 2017 Mar 6. No abstract available. Erratum in: Proc Natl Acad Sci U S A. 2017 May 9;114(19):E3869.

5.

The structure and function of an RNA polymerase interaction domain in the PcrA/UvrD helicase.

Sanders K, Lin CL, Smith AJ, Cronin N, Fisher G, Eftychidis V, McGlynn P, Savery NJ, Wigley DB, Dillingham MS.

Nucleic Acids Res. 2017 Apr 20;45(7):3875-3887. doi: 10.1093/nar/gkx074.

6.

In-Silico Analysis and Implementation of a Multicellular Feedback Control Strategy in a Synthetic Bacterial Consortium.

Fiore G, Matyjaszkiewicz A, Annunziata F, Grierson C, Savery NJ, Marucci L, di Bernardo M.

ACS Synth Biol. 2017 Mar 17;6(3):507-517. doi: 10.1021/acssynbio.6b00220. Epub 2016 Dec 20.

PMID:
27997140
7.

Inhibiting translation elongation can aid genome duplication in Escherichia coli.

Myka KK, Hawkins M, Syeda AH, Gupta MK, Meharg C, Dillingham MS, Savery NJ, Lloyd RG, McGlynn P.

Nucleic Acids Res. 2017 Mar 17;45(5):2571-2584. doi: 10.1093/nar/gkw1254.

8.

Reconstruction of bacterial transcription-coupled repair at single-molecule resolution.

Fan J, Leroux-Coyau M, Savery NJ, Strick TR.

Nature. 2016 Aug 11;536(7615):234-7. Epub 2016 Aug 3.

PMID:
27487215
9.

Length heterogeneity at conserved sequence block 2 in human mitochondrial DNA acts as a rheostat for RNA polymerase POLRMT activity.

Tan BG, Wellesley FC, Savery NJ, Szczelkun MD.

Nucleic Acids Res. 2016 Sep 19;44(16):7817-29. doi: 10.1093/nar/gkw648. Epub 2016 Jul 19.

10.

Stalled transcription complexes promote DNA repair at a distance.

Haines NM, Kim YI, Smith AJ, Savery NJ.

Proc Natl Acad Sci U S A. 2014 Mar 18;111(11):4037-42. doi: 10.1073/pnas.1322350111. Epub 2014 Feb 19.

11.

The conserved C-terminus of the PcrA/UvrD helicase interacts directly with RNA polymerase.

Gwynn EJ, Smith AJ, Guy CP, Savery NJ, McGlynn P, Dillingham MS.

PLoS One. 2013 Oct 16;8(10):e78141. doi: 10.1371/journal.pone.0078141. eCollection 2013.

12.

Modelling emergence of oscillations in communicating bacteria: a structured approach from one to many cells.

Mina P, di Bernardo M, Savery NJ, Tsaneva-Atanasova K.

J R Soc Interface. 2013 Jan 6;10(78):20120612. doi: 10.1098/rsif.2012.0612.

13.

Initiation of transcription-coupled repair characterized at single-molecule resolution.

Howan K, Smith AJ, Westblade LF, Joly N, Grange W, Zorman S, Darst SA, Savery NJ, Strick TR.

Nature. 2012 Oct 18;490(7420):431-4. doi: 10.1038/nature11430. Epub 2012 Sep 9.

14.

BSim: an agent-based tool for modeling bacterial populations in systems and synthetic biology.

Gorochowski TE, Matyjaszkiewicz A, Todd T, Oak N, Kowalska K, Reid S, Tsaneva-Atanasova KT, Savery NJ, Grierson CS, di Bernardo M.

PLoS One. 2012;7(8):e42790. doi: 10.1371/journal.pone.0042790. Epub 2012 Aug 24.

15.

Multipartite control of the DNA translocase, Mfd.

Smith AJ, Pernstich C, Savery NJ.

Nucleic Acids Res. 2012 Nov 1;40(20):10408-16. doi: 10.1093/nar/gks775. Epub 2012 Aug 16.

16.

Temperature dependence of ssrA-tag mediated protein degradation.

Purcell O, Grierson CS, Bernardo Md, Savery NJ.

J Biol Eng. 2012 Jul 23;6(1):10. doi: 10.1186/1754-1611-6-10.

17.

The conflict between DNA replication and transcription.

McGlynn P, Savery NJ, Dillingham MS.

Mol Microbiol. 2012 Jul;85(1):12-20. doi: 10.1111/j.1365-2958.2012.08102.x. Epub 2012 May 31. Review.

18.

A multi-functional synthetic gene network: a frequency multiplier, oscillator and switch.

Purcell O, di Bernardo M, Grierson CS, Savery NJ.

PLoS One. 2011 Feb 17;6(2):e16140. doi: 10.1371/journal.pone.0016140.

19.

Regulation and rate enhancement during transcription-coupled DNA repair.

Manelyte L, Kim YI, Smith AJ, Smith RM, Savery NJ.

Mol Cell. 2010 Dec 10;40(5):714-24. doi: 10.1016/j.molcel.2010.11.012.

20.

A comparative analysis of synthetic genetic oscillators.

Purcell O, Savery NJ, Grierson CS, di Bernardo M.

J R Soc Interface. 2010 Nov 6;7(52):1503-24. doi: 10.1098/rsif.2010.0183. Epub 2010 Jun 30. Review.

21.

DNA cleavage and methylation specificity of the single polypeptide restriction-modification enzyme LlaGI.

Smith RM, Diffin FM, Savery NJ, Josephsen J, Szczelkun MD.

Nucleic Acids Res. 2009 Nov;37(21):7206-18. doi: 10.1093/nar/gkp790.

22.

The unstructured C-terminal extension of UvrD interacts with UvrB, but is dispensable for nucleotide excision repair.

Manelyte L, Guy CP, Smith RM, Dillingham MS, McGlynn P, Savery NJ.

DNA Repair (Amst). 2009 Nov 2;8(11):1300-10. doi: 10.1016/j.dnarep.2009.08.005. Epub 2009 Sep 16.

23.

An N-terminal clamp restrains the motor domains of the bacterial transcription-repair coupling factor Mfd.

Murphy MN, Gong P, Ralto K, Manelyte L, Savery NJ, Theis K.

Nucleic Acids Res. 2009 Oct;37(18):6042-53. doi: 10.1093/nar/gkp680. Epub 2009 Aug 21.

24.

Effects of the bacterial transcription-repair coupling factor during transcription of DNA containing non-bulky lesions.

Smith AJ, Savery NJ.

DNA Repair (Amst). 2008 Oct 1;7(10):1670-9. doi: 10.1016/j.dnarep.2008.06.020. Epub 2008 Sep 10.

PMID:
18707026
25.

The molecular mechanism of transcription-coupled DNA repair.

Savery NJ.

Trends Microbiol. 2007 Jul;15(7):326-33. Epub 2007 Jun 14.

PMID:
17572090
26.

Transcription coupled nucleotide excision repair in Escherichia coli can be affected by changing the arginine at position 529 of the beta subunit of RNA polymerase.

Ganesan AK, Smith AJ, Savery NJ, Zamos P, Hanawalt PC.

DNA Repair (Amst). 2007 Oct 1;6(10):1434-40. Epub 2007 May 25.

27.

Controlling the motor activity of a transcription-repair coupling factor: autoinhibition and the role of RNA polymerase.

Smith AJ, Szczelkun MD, Savery NJ.

Nucleic Acids Res. 2007;35(6):1802-11. Epub 2007 Feb 28.

28.

Structural basis for bacterial transcription-coupled DNA repair.

Deaconescu AM, Chambers AL, Smith AJ, Nickels BE, Hochschild A, Savery NJ, Darst SA.

Cell. 2006 Feb 10;124(3):507-20.

29.

RNA polymerase mutants defective in the initiation of transcription-coupled DNA repair.

Smith AJ, Savery NJ.

Nucleic Acids Res. 2005 Feb 1;33(2):755-64. Print 2005.

30.

A DNA translocation motif in the bacterial transcription--repair coupling factor, Mfd.

Chambers AL, Smith AJ, Savery NJ.

Nucleic Acids Res. 2003 Nov 15;31(22):6409-18.

31.

Characterisation of the Escherichia coli mfd promoter.

Stanley LK, Savery NJ.

Arch Microbiol. 2003 May;179(5):381-5. Epub 2003 Mar 26.

PMID:
12658334
32.
33.

UP element-dependent transcription at the Escherichia coli rrnB P1 promoter: positional requirements and role of the RNA polymerase alpha subunit linker.

Meng W, Belyaeva T, Savery NJ, Busby SJ, Ross WE, Gaal T, Gourse RL, Thomas MS.

Nucleic Acids Res. 2001 Oct 15;29(20):4166-78.

35.
37.

Transcription activation at Class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase alpha subunit.

Savery NJ, Lloyd GS, Kainz M, Gaal T, Ross W, Ebright RH, Gourse RL, Busby SJ.

EMBO J. 1998 Jun 15;17(12):3439-47.

40.

Transcription activation at class II CRP-dependent promoters: the role of different activating regions.

Rhodius VA, West DM, Webster CL, Busby SJ, Savery NJ.

Nucleic Acids Res. 1997 Jan 15;25(2):326-32.

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