Publications
106 results found
Wright O, Stan G-B, Ellis T, 2013, Building-in biosafety for synthetic biology, MICROBIOLOGY-SGM, Vol: 159, Pages: 1221-1235, ISSN: 1350-0872
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- Citations: 82
Wu M, Su R-Q, Li X, et al., 2013, Engineering of regulated stochastic cell fate determination, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, Vol: 110, Pages: 10610-10615, ISSN: 0027-8424
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- Citations: 69
Weenink T, Ellis T, 2013, Creation and Characterization of Component Libraries for Synthetic Biology, SYNTHETI C BIOLOGY, Vol: 1073, Pages: 51-60, ISSN: 1064-3745
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- Citations: 1
Blount BA, Weenink T, Ellis T, 2012, Construction of synthetic regulatory networks in yeast, FEBS LETTERS, Vol: 586, Pages: 2112-2121, ISSN: 0014-5793
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- Citations: 50
Blount BA, Weenink T, Vasylechko S, et al., 2012, Rational Diversification of a Promoter Providing Fine-Tuned Expression and Orthogonal Regulation for Synthetic Biology, PLOS ONE, Vol: 7, ISSN: 1932-6203
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- Citations: 116
Brucoli F, Hawkins RM, James CH, et al., 2011, Novel C8-linked pyrrolobenzodiazepine (PBD)-heterocycle conjugates that recognize DNA sequences containing an inverted CCAAT box, BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, Vol: 21, Pages: 3780-3783, ISSN: 0960-894X
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- Citations: 17
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
Ellis T, Wang X, Collins JJ, 2009, Diversity-based, model-guided construction of synthetic gene networks with predicted functions, NATURE BIOTECHNOLOGY, Vol: 27, Pages: 465-471, ISSN: 1087-0156
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- Citations: 347
Ellis T, Wang X, Collins JJ, 2008, Diversity-Based Design of Synthetic Gene Networks with Desired Functions, Synthetic Biology 4.0
Constructing predictable gene networks with desired functions remains hampered by the lack of well-characterized components and the fact that assembled networks often require extensive, iterative retrofitting for optimization. Here we present an approach where network components are synthesized with random sequences incorporated into their design, giving rapid parallel production of component libraries with inherent diversity. When coupled with in silico modeling, libraries present a choice of characterized parts for gene network design, and those optimal for the desired function can be selected for network assembly, without the need for post-hoc tweaking. We validated our approach in yeast (S.cerevisiae) by synthesizing a regulatory promoter library and using it to construct negative feedforward loop networks with different, desired input-output characteristics. We then implemented the method to produce a synthetic gene network that acts as a timer, tunable by component choice. We utilize this network to control the timing of the yeast flocculation phenotype, which is crucial to brewing, illustrating a practical application of our approach.
Ellis T, Wang X, Collins JJ, 2008, Gene regulation: Hacking the network on a sugar high, MOLECULAR CELL, Vol: 30, Pages: 1-2, ISSN: 1097-2765
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- Citations: 1
Ellis T, Evans DA, Martin CRH, et al., 2007, A 96-well DNase I footprinting screen for drug-DNA interactions, Nucleic Acids Research, Vol: 35, Pages: 1-8, ISSN: 0305-1048
The established protocol for DNase I footprinting has been modified to allow multiple parallel reactions to be rapidly performed in 96-well microtitre plates. By scrutinizing every aspect of the traditional method and making appropriate modifications it has been possible to considerably reduce the time, risk of sample loss and complexity of footprinting, whilst dramatically increasing the yield of data (30-fold). A semi-automated analysis system has also been developed to present footprinting data as an estimate of the binding affinity of each tested compound to any base pair in the assessed DNA sequence, giving an intuitive ‘one compound–one line’ scheme. Here, we demonstrate the screening capabilities of the 96-well assay and the subsequent data analysis using a series of six pyrrolobenzodiazepine-polypyrrole compounds and human Topoisomerase II alpha promoter DNA. The dramatic increase in throughput, quantified data and decreased handling time allow, for the first time, DNase I footprinting to be used as a screening tool to assess DNA-binding agents.
Van Vliet LD, Ellis T, Foley PJ, et al., 2007, Molecular recognition of DNA by rigid [<i>n</i>]-polynorbornane-derived bifunctional intercalators:: Synthesis and evaluation of their binding properties, JOURNAL OF MEDICINAL CHEMISTRY, Vol: 50, Pages: 2326-2340, ISSN: 0022-2623
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- Citations: 39
Martin C, Ellis T, McGurk CJ, et al., 2005, Sequence-selective interaction of the minor-groove interstrand cross-linking agent SJG-136 with naked and cellular DNA: Footprinting and enzyme inhibition studies, BIOCHEMISTRY, Vol: 44, Pages: 4135-4147, ISSN: 0006-2960
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- Citations: 42
Bailly C, Kluza J, Martin C, et al., 2005, DNase I footprinting of small molecule binding sites on DNA., Methods Mol Biol, Vol: 288, Pages: 319-342, ISSN: 1064-3745
Nuclease footprinting techniques were initially developed to investigate protein-deoxyribonucleic acid (DNA) interactions but these tools of molecular biology have also become instrumental for probing sequence-selective binding of small molecules to DNA. Here, the method is described and technical details are given for performing deoxyribonuclease (DNase) I footprinting with DNA-binding drugs. An example is presented where DNase I is used (as well as DNase II and micrococcal nuclease) to probe the patterns of sequence-selective recognition of DNA by the anticancer antibiotic actinomycin D. DNase I is a convenient endonuclease for detecting and locating the position of actinomycin-binding sites within GC-rich sequences.
Waring MJ, Ben-Hadda T, Kotchevar AT, et al., 2002, 2,3-bifunctionalized quinoxalines: Synthesis, DNA interactions and evaluation of anticancer, anti-tuberculosis and antifungal activity, MOLECULES, Vol: 7, Pages: 641-656, ISSN: 1420-3049
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- Citations: 86
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