Publications
66 results found
Cehovin A, Simpson PJ, McDowell MA, et al., 2013, Specific DNA recognition mediated by a type IV pilin, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 3065-3070, ISSN: 0027-8424
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- Citations: 112
Lu D, Silhan J, MacDonald JT, et al., 2012, Structural basis for the recognition and cleavage of abasic DNA in <i>Neisseria meningitidis</i>, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 109, Pages: 16852-16857, ISSN: 0027-8424
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- Citations: 16
Silhan J, Nagorska K, Zhao Q, et al., 2012, Specialization of an Exonuclease III family enzyme in the repair of 3' DNA lesions during base excision repair in the human pathogen Neisseria meningitidis, Nucleic Acids Research, Vol: 40, Pages: 2065-2075, ISSN: 1362-4962
We have previously demonstrated that the twoExonuclease III (Xth) family members presentwithin the obligate human pathogen Neisseriameningitidis, NApe and NExo, are important forsurvival under conditions of oxidative stress. Ofthese, only NApe possesses AP endonucleaseactivity, while the primary function of NExoremained unclear. We now reveal further functionalspecialization at the level of 30-PO4 processing forNExo. We demonstrate that the bi-functional meningococcalglycosylases Nth and MutM can performstrand incisions at abasic sites in addition to NApe.However, no such functional redundancy existsfor the 30-phosphatase activity of NExo, and thecytotoxicity of 30-blocking lesions is reflectedin the marked sensitivity of a mutant lackingNExo to oxidative stress, compared to strainsdeficient in other base excision repair enzymes. Ahistidine residue within NExo that is responsiblefor its lack of AP endonuclease activity isalso important for its 30-phosphatase activity,demonstrating an evolutionary trade off in enzymefunction at the single amino acid level. This specializationof two Xth enzymes for the 30-end processingand strand-incision reactions has notpreviously been observed and provides a newparadigm within the prokaryotic world for separationof these critical functions during baseexcision repair.
Nagorska K, Silhan J, Li Y, et al., 2012, A network of enzymes involved in repair of oxidative DNA damage in Neisseria meningitidis, MOLECULAR MICROBIOLOGY, Vol: 83, Pages: 1064-1079, ISSN: 0950-382X
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- Citations: 20
Sheppard C, Camara B, Shadrin A, et al., 2011, Inhibition of <i>Escherichia coli</i> RNAp by T7 Gp2 Protein: Role of Negatively Charged Strip of Amino Acid Residues in Gp2, JOURNAL OF MOLECULAR BIOLOGY, Vol: 407, Pages: 623-632, ISSN: 0022-2836
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- Citations: 9
Grippon S, Zhao Q, Robinson T, et al., 2011, Differential modes of DNA binding by mismatch uracil DNA glycosylase from Escherichia coli: implications for abasic lesion processing and enzyme communication in the base excision repair pathway, Nucleic Acids Research, Vol: 39, Pages: 2593-2603, ISSN: 1362-4962
Mismatch uracil DNA glycosylase (Mug) fromEscherichia coli is an initiating enzyme in thebase-excision repair pathway. As with other DNAglycosylases, the abasic product is potentiallymore harmful than the initial lesion. Since Mug isknown to bind its product tightly, inhibitingenzyme turnover, understanding how Mug bindsDNA is of significance when considering how Muginteracts with downstream enzymes in the baseexcisionrepair pathway. We have demonstrateddifferential binding modes of Mug between its substrateand abasic DNA product using both band shiftand fluorescence anisotropy assays. Mug binds itsproduct cooperatively, and a stoichiometric analysisof DNA binding, catalytic activity and saltdependenceindicates that dimer formation is offunctional significance in both catalytic activity andproduct binding. This is the first report ofcooperativity in the uracil DNA glycosylase superfamilyof enzymes, and forms the basis of productinhibition in Mug. It therefore provides a new perspectiveon abasic site protection and the findingsare discussed in the context of downstream lesionprocessing and enzyme communication in the baseexcision repair pathway.
Ellis T, Adie T, Baldwin GS, 2011, DNA assembly for synthetic biology: from parts to pathways and beyond, INTEGRATIVE BIOLOGY, Vol: 3, Pages: 109-118, ISSN: 1757-9694
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- Citations: 207
Ivanov AP, Instuli E, McGilvery C, et al., 2010, DNA tunneling detector embedded in a nanopore, Nano Letters, Vol: 11, Pages: 279-285, ISSN: 1530-6992
We report on the fabrication and characterization of a DNA nanopore detector with integrated tunneling electrodes. Functional tunneling devices were identified by tunneling spectroscopy in different solvents and then used in proof-of-principle experiments demonstrating, for the first time, concurrent tunneling detection and ionic current detection of DNA molecules in a nanopore platform. This is an important step toward ultrafast DNA sequencing by tunneling.
Robinson T, Manning HB, Dunsby C, et al., 2010, Investigating fast enzyme-DNA kinetics using multidimensional fluorescence imaging and microfluidics, Conference on Microfluidics, BioMEMS, and Medical Microsystems VIII, Publisher: SPIE-INT SOC OPTICAL ENGINEERING, ISSN: 0277-786X
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- Citations: 1
Ayub M, Ivanov A, Instuli E, et al., 2010, Nanopore/electrode structures for single-molecule biosensing, Electrochimica Acta, Vol: 55, Pages: 8237-8243
Baldwin GS, Brooks NJ, Robson RE, et al., 2009, DNA Double Helices Recognize Mutual Sequence Homology in a Protein Free Environment, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, Vol: 26, Pages: 880-880, ISSN: 0739-1102
Robinson T, Schaerli Y, Wootton R, et al., 2009, Removal of background signals from fluorescence thermometry measurements in PDMS microchannels using fluorescence lifetime imaging, LAB ON A CHIP, Vol: 9, Pages: 3437-3441, ISSN: 1473-0197
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- Citations: 29
Robinson T, Valluri P, Manning HB, et al., 2008, Three-dimensional molecular mapping in a microfluidic mixing device using fluorescence lifetime imaging, OPTICS LETTERS, Vol: 33, Pages: 1887-1889, ISSN: 0146-9592
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- Citations: 19
Briggs LC, Baldwin GS, Miyata N, et al., 2008, Analysis of nucleotide binding to p97 reveals the properties of a tandem AAA hexameric ATPase, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 283, Pages: 13745-13752
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- Citations: 64
Baldwin GS, Brooks NJ, Robson RE, et al., 2008, DNA double helices recognize mutual sequence homology in a protein free environment, J. Phys. Chem. B, Vol: 112, Pages: 1060-1064
Di Noia JM, Williams GT, Chan DTY, et al., 2007, Dependence of antibody gene diversification on uracil excision, Journal of Experimental Medicine, Vol: 204, Pages: 3209-3219, ISSN: 1540-9538
Activation-induced deaminase (AID) catalyses deamination of deoxycytidine to deoxyuridinewithin immunoglobulin loci, triggering pathways of antibody diversifi cation that arelargely dependent on uracil-DNA glycosylase (uracil- N -glycolase [UNG]). Surprisinglyeffi cient class switch recombination is restored to ung / B cells through retroviraldelivery of active-site mutants of UNG, stimulating discussion about the need for UNG ’ suracil-excision activity. In this study, however, we fi nd that even with the overexpressionachieved through retroviral delivery, switching is only mediated by UNG mutants thatretain detectable excision activity, with this switching being especially dependent onMSH2. In contrast to their potentiation of switching, low-activity UNGs are relativelyineffective in restoring transversion mutations at C:G pairs during hypermutation, or inrestoring gene conversion in stably transfected DT40 cells. The results indicate that UNGdoes, indeed, act through uracil excision, but suggest that, in the presence of MSH2,effi cient switch recombination requires base excision at only a small proportion of theAID-generated uracils in the S region. Interestingly, enforced expression of thymine-DNAglycosylase (which can excise U from U:G mispairs) does not (unlike enforced UNG orSMUG1 expression) potentiate effi cient switching, which is consistent with a need eitherfor specifi c recruitment of the uracil-excision enzyme or for it to be active on singlestrandedDNA.
Carpenter EP, Corbett A, Thomson H, et al., 2007, AP endonuclease paralogues with distinct activities in DNA repair and bacterial pathogenesis, EMBO JOURNAL, Vol: 26, Pages: 1363-1372, ISSN: 0261-4189
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- Citations: 39
Bellamy SRW, Krusong K, Baldwin GS, 2007, A rapid reaction analysis of uracil DNA glycosylase indicates an active mechanism of base flipping, Nucleic Acids Research, Vol: 35, Pages: 1478-1487, ISSN: 1362-4962
Uracil DNA glycosylase (UNG) is the primary enzymefor the removal of uracil from the genome of manyorganisms. A key question is how the enzyme isable to scan large quantities of DNA in search ofaberrant uracil residues. Central to this is themechanism by which it flips the target nucleotideout of the DNA helix and into the enzyme-active site.Both active and passive mechanisms have beenproposed. Here, we report a rapid kinetic analysisusing two fluorescent chromophores to temporallyresolve DNA binding and base-flipping with DNAsubstrates of different sequences. This studydemonstrates the importance of the protein–DNAinterface in the search process and indicates anactive mechanism by which UNG glycosylasesearches for uracil residues.
Krusong K, Carpenter EP, Bellamy SRW, et al., 2006, A comparative study of uracil-DNA glycosylases from human and herpes simplex virus type 1, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 281, Pages: 4983-4992
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- Citations: 49
O'Neill RJ, Vorob'eva OV, Shahbakhti H, et al., 2003, Mismatch uracil glycosylase from <i>Escherichia coli</i> -: A general mismatch or a specific DNA glycosylase?, JOURNAL OF BIOLOGICAL CHEMISTRY, Vol: 278, Pages: 20526-20532, ISSN: 0021-9258
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- Citations: 50
Bellamy SRW, Baldwin GS, 2001, A kinetic analysis of substrate recognition by uracil-DNA glycosylase from herpes simplex virus type 1, NUCLEIC ACIDS RESEARCH, Vol: 29, Pages: 3857-3863, ISSN: 0305-1048
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- Citations: 39
Baldwin GS, Gormley NA, Halford SE, 2000, Manganese(II) as a probe for the mechanism and specificity of restriction endonucleases, Publisher: MARCEL DEKKER
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- Citations: 5
Thomas MP, Brady RL, Halford SE, et al., 1999, Structural analysis of a mutational hot-spot in the <i>Eco</i>RV restriction endonuclease:: a catalytic role for a main chain carbonyl group, NUCLEIC ACIDS RESEARCH, Vol: 27, Pages: 3438-3445, ISSN: 0305-1048
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- Citations: 22
Baldwin GS, Sessions RB, Erskine SG, et al., 1999, DNA cleavage by the <i>Eco</i>RV restriction endonuclease:: Roles of divalent metal ions in specificity and catalysis, JOURNAL OF MOLECULAR BIOLOGY, Vol: 288, Pages: 87-103, ISSN: 0022-2836
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- Citations: 70
Stanford NP, Halford SE, Baldwin GS, 1999, DNA cleavage by the <i>Eco</i>RV restriction endonuclease:: pH dependence and proton transfers in catalysis, JOURNAL OF MOLECULAR BIOLOGY, Vol: 288, Pages: 105-116, ISSN: 0022-2836
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- Citations: 44
Hurd PJ, Whitmarsh AJ, Baldwin GS, et al., 1999, Mechanism-based inhibition of C5-cytosine DNA methyltransferases by 2-H pyrimidinone, JOURNAL OF MOLECULAR BIOLOGY, Vol: 286, Pages: 389-401, ISSN: 0022-2836
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- Citations: 63
Erskine SG, Baldwin GS, Halford SE, 1997, Rapid-reaction analysis of plasmid DNA cleavage by the EcoRV restriction endonuclease, BIOCHEMISTRY, Vol: 36, Pages: 7567-7576, ISSN: 0006-2960
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- Citations: 66
Vipond IB, Baldwin GS, Oram M, et al., 1995, A general assay for restriction endonucleases and other DNA-modifying enzymes with plasmid substrates, MOLECULAR BIOTECHNOLOGY, Vol: 4, Pages: 259-268, ISSN: 1073-6085
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- Citations: 23
BALDWIN GS, VIPOND IB, HALFORD SE, 1995, RAPID REACTION ANALYSIS OF THE CATALYTIC CYCLE OF THE ECORV RESTRICTION-ENDONUCLEASE, BIOCHEMISTRY, Vol: 34, Pages: 705-714, ISSN: 0006-2960
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- Citations: 79
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