DNA assembly and standardisation of biological components
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The use of standardised components is found in all fields of engineering, where it allows the benefits of abstraction, decoupling and insulation from unnecessary detail in the design of complex systems. The ability to construct new DNA sequences has far outpaced our capacity to design the genetic circuits that these might encode. Synthetic Biology promises simplified design using modular standardised DNA components.
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Publication Date: 2011 Dec 28 PMID: 22209624 Authors: Ma, S. - Saaem, I. - Tian, J. Journal: Trends Biotechnol Accurate, economical and high-throughput gene and genome synthesis is essential to the development of synthetic biology and biotechnology. New large-scale gene synthesis methods harnessing the power of DNA microchips have recently been demonstrated. Yet, the technology is still...
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Publication Date: 2012 Mar 9 PMID: 22403384 Authors: Paige, J. S. - Nguyen-Duc, T. - Song, W. - Jaffrey, S. R. Journal: Science Genetically encoded sensors are powerful tools for imaging intracellular metabolites and signaling molecules. However, developing sensors is challenging because they require proteins that undergo conformational changes upon binding the desired target molecule. We...
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J Biol Eng. 2012 Feb 28;6(1):1
Authors: Chen J, Densmore D, Ham TS, Keasling JD, Hillson NJ
Abstract ABSTRACT: BACKGROUND: Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must...
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Methods Mol Biol. 2012;852:197-213
Authors: Villalobos A, Welch M, Minshull J
Abstract The promise of synthetic biology lies in the creation of novel function from the proper combination of genetic elements. De novo gene synthesis has become a cost-effective method for building virtually any conceptualized genetic construct, removing the constraints of extant sequences, and greatly...
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Methods Mol Biol. 2012;852:11-21
Authors: Gibson DG
Abstract The yeast Saccharomyces cerevisiae can take up and assemble at least 38 overlapping single-stranded oligonucleotides and a linear double-stranded vector in one transformation event. These oligonucleotides can overlap by as few as 20 bp and can be as long as 200 nucleotides in length to produce kilobase-sized synthetic DNA molecules....
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Methods Mol Biol. 2012;852:151-63
Authors: Linshiz G, Yehezkel TB, Shapiro E
Abstract Making faultless complex objects from potentially faulty building blocks is a fundamental challenge in computer engineering, nanotechnology, and synthetic biology. We developed an error-correcting recursive construction procedure that attempts to address this challenge. Making DNA molecules from synthetic...
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Scientists have discovered how bacteriophages - viruses that infect bacteria - manage to pierce the bacterial membrane: with an iron spike.
When they crystallized this smaller protein fragment, the x-rays were finally able to resolve its structure, and from this the team had the very first picture of the tip of the spike: a single iron atom held ...
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At the Advances in Genome Biology and Technology 2012 conference (AGBT), Oxford Nanopore Technologies Ltd. announced it is entering the gene-sequencing battle with a disposable DNA sequencer that will sell for under $900 in the second half of 2012. The USB-size sequencer is called the MinION (min-ion), and has already demonstrated the potential to bring genome sequencing and personalized...
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rsTagRFP is the first monomeric red fluorescent protein (FP) with reversibly photoswitchable absorbance spectra. The switching is realized by irradiation of rsTagRFP with blue (440 nm) and yellow (567 nm) light, turning the protein fluorescence ON and OFF, respectively. It is perhaps the most useful probe in this color class that has yet been reported. Because of the photoswitchable absorbance,...
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Copepods are the dominant taxa in zooplankton communities of the ocean world-wide. Although bioluminescence of certain copepods has been known for more than a hundred years, there is very limited information about the structure and evolutionary history of copepod luciferase genes. Here we report the cDNA sequences of 11 copepod luciferases isolated from the superfamily Augaptiloidea in the order...
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Large-insert BAC (bacterial artificial chromosome) and BIBAC (binary BAC) libraries are essential for modern genomics research for all organisms. We helped pioneer the BAC and BIBAC technologies, and by using them we have constructed hundreds of BAC and BIBAC libraries for different species of plants,
Construction of BIBAC and BAC libraries from a variety of organisms for advanced genomics...
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Megabase-sized DNA is crucial to modern genomics research of all organisms. Among the preparation methods developed, the nuclei method is the simplest and most widely used for preparing high-quality megabase-sized DNA from divergent organisms. In this method, nuclei are first isolated by physically grinding the...
Preparation of megabase-sized DNA from a variety of organisms using the nuclei...
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Protein expression in Escherichia coli at 15-25 degrees C is widely used to increase the solubility of recombinant proteins. However, many recombinant proteins are insolubly expressed even at those low temperatures. Here, we show that recombinant proteins can be expressed as soluble forms by simply lowering temperature to 6-10 degrees C without cold adapted chaperon systems. By using E. coli...
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This shows a model of the "threading tetra-intercalator " bound up in the double helix of a DNA sequence. Chemists at The University of Texas at Austin have created a molecule that's so good at tangling itself inside the double helix of a DNA sequence that it can stay there for up to 16 days before the DNA liberates itself, much longer than any other molecule reported.
New molecule can tangle...
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New England Biolabs, Inc. (NEB) and Synthetic Genomics, Inc. (SGI) jointly announce that they have entered into a licensing agreement whereby NEB will introduce a master mix based on Gibson Assembly™, a revolutionary technology developed by Dr. Daniel Gibson and his colleagues at the J. Craig Venter Institute (JCVI) as part of a program sponsored by SGI.
Gibson Assembly enables the rapid...
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Tobacco etch virus (TEV) protease is widely used to remove tags from recombinant fusion proteins because of its stringent sequence specificity. It is generally accepted that the high concentrations of salts or other special agents in most protein affinity chromatography buffers can affect enzyme activity, including that of TEV protease. Consequently, tedious desalination or the substitution of...
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In bacteria, many small regulatory RNAs (sRNAs) are induced in response to specific environmental signals or stresses and act by base-pairing with mRNA targets to affect protein translation or mRNA stability. In Escherichia coli, the gene for the sRNA IS061/IsrA, here renamed McaS, was predicted to reside in an intergenic region between abgR, encoding a transcription regulator and ydaL, encoding...
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Xenogeneic silencing proteins facilitate horizontal gene transfer by silencing expression of AT-rich sequences. By virtue of their activity these proteins serve as master regulators of a variety of important functions including motility, drug resistance, and virulence. Three families of silencers have been identified to date: the H-NS like proteins of Gram-negative bacteria, the MvaT like...
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Quorum-sensing systems mediate chemical communication between bacterial cells, coordinating cell-density-dependent processes like biofilm formation and virulence-factor expression. In the proteobacterial LuxI/LuxR quorum sensing paradigm, a signaling molecule generated by an enzyme (LuxI) diffuses between cells and allosterically stimulates a transcriptional regulator (LuxR) to activate its...
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ABSTRACT: BACKGROUND: In many laboratories, researchers store experimental data on their own workstation using spreadsheets. However, this approach poses a number of problems, ranging from sharing issues to inefficient data-mining. Standard spreadsheets are also error-prone as data do not undergo any validation process. To overcome spreadsheets inherent limitations, a number of proprietary...
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