Assembly of Standardized DNA Parts Using BioBrick Ends in E. coli

Ho-Shing, Olivia; Lau, Kin H.; Vernon, William; Eckdahl, Todd T.; Campbell, A. Malcolm

doi:10.1007/978-1-61779-564-0_6

Cited by 16 publications

(10 citation statements)

References 6 publications

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“…Finally, the betL * mutation in L. monocytogenes represents a double edged sword; from a food safety perspective, a single point mutation with the potential to induce such dramatic shifts in cell growth and survival at low a w and temperatures—making an already dangerous pathogen even more formidable—raises significant food-safety concerns which need to be addressed 1 , 35 . However, from a synthetic biology point of view, a boosted-stress resistance locus, such as betL *, represents a useful BioBrick 36 for the design of more physiologically robust pharmabiotic strains 37 - 42 …”

Section: Resultsmentioning

confidence: 99%

A single point mutation in the listerialbetLσ^A-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity

et al. 2013

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Betaine uptake in Listeria monocytogenes is mediated by three independent transport systems, the simplest of which in genetic terms is the secondary transporter BetL. Using a random mutagenesis approach, based on the E. coli XL1 Red mutator strain, we identified a single point mutation in a putative promoter region upstream of the BetL coding region which leads to a significant increase in betL transcript levels under osmo- and chill-stress conditions and a concomitant increase in stress tolerance. Furthermore, the mutation appears to counter the heretofore unreported “twisted” cell morphology observed for L. monocytogenes grown at elevated osmolarities in tryptone soy broth.

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Section: Resultsmentioning

confidence: 99%

A single point mutation in the listerialbetLσ^A-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity

et al. 2013

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“…The functional region of gene part BBa_K1218026, including the oligonucleotide sequences of interest, the BioBrick prefix and suffix, and the expression primers, was synthesized by Elim Biopharmaceuticals and cloned into plasmid backbone pSB1C3 (BioBricks Foundation, San Francisco, CA, USA) using an EcoRI-PstI (New England Biolabs, #E0546S) cloning protocol for BioBrick assembly 70 . Part BBa_K1218022 was synthesized by GeneBlocks (Integrated DNA Technologies) and cloned into pSB1C3 using the same protocol.…”

Section: Methodsmentioning

confidence: 99%

Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology

Vecchioni

Capece

Toomey

et al. 2019

Sci Rep

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DNA is an attractive candidate for integration into nanoelectronics as a biological nanowire due to its linear geometry, definable base sequence, easy, inexpensive and non-toxic replication and self-assembling properties. Recently we discovered that by intercalating Ag + in polycytosine-mismatch oligonucleotides, the resulting C-Ag + -C duplexes are able to conduct charge efficiently. To map the functionality and biostability of this system, we built and characterized internally-functionalized DNA nanowires through non-canonical, Ag + -mediated base pairing in duplexes containing cytosine-cytosine mismatches. We assessed the thermal and chemical stability of ion-coordinated duplexes in aqueous solutions and conclude that the C-Ag + -C bond forms DNA duplexes with replicable geometry, predictable thermodynamics, and tunable length. We demonstrated continuous ion chain formation in oligonucleotides of 11–50 nucleotides (nt), and enzyme ligation of mixed strands up to six times that length. This construction is feasible without detectable silver nanocluster contaminants. Functional gene parts for the synthesis of DNA- and RNA-based, C-Ag + -C duplexes in a cell-free system have been constructed in an Escherichia coli expression plasmid and added to the open-source BioBrick Registry, paving the way to realizing the promise of inexpensive industrial production. With appropriate design constraints, this conductive variant of DNA demonstrates promise for use in synthetic biological constructs as a dynamic nucleic acid component and contributes molecular electronic functionality to DNA that is not already found in nature. We propose a viable route to fabricating stable DNA nanowires in cell-free and synthetic biological systems for the production of self-assembling nanoelectronic architectures.

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“…For the last 10 years, the synthetic biology community has designed switches (Gardner 2000), biobricks (Ho-Shing et al 2012), oscillators (Purcell et al 2010), quorum sensing (Danino et al 2010), non-natural DNA (Pinheiro et al 2012) and minimal synthetic cell (Gibson et al 2010). In the next 10 years, we hope to see more publications on synthetic chromosomes, alternative genetic codes, several non-bio brick initiatives, genome scale engineering and faster methods to make synthetic cells.…”

Section: Critical Appraisal Of the Fieldmentioning

confidence: 99%

A Brief Introduction to Synthetic Biology

Patil

Dhar

2014

Systems and Synthetic Biology

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"What I cannot create, I do not understand." -Richard FeynmanOrganisms are complex systems that run massively parallel and interactive molecular processes. From an H-atom to the whole cell, cells manage information over at least six orders of magnitude in size. To understand a system that integrates contextual, temporal and spatial complexity by default, calls for innovative and massive data gathering efforts. Data gathered over the last two decades has revealed a huge inventory of molecular parts and contextual interactions. Still a good understanding of biology is lacking.In the early 2000, people asked: can one assemble biological systems from scratch from a standard inventory of parts, instead of relying upon the naturally evolved systems. One of the key foundational papers that hinted towards engineering approach to biology, was a three gene circuit called repressilator that was plugged into E.coli as a non-native applet and stably expressed (Elowitz and Leibler, Nature 403:335-338, 2000). This paper accelerated the thought process that we now know as synthetic biology.

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Assembly of Standardized DNA Parts Using BioBrick Ends in E. coli

Cited by 16 publications

References 6 publications

A single point mutation in the listerialbetLσ^A-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity

A single point mutation in the listerialbetLσ^A-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity

Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology

A Brief Introduction to Synthetic Biology

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Assembly of Standardized DNA Parts Using BioBrick Ends in E. coli

Cited by 16 publications

References 6 publications

A single point mutation in the listerialbetLσA-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity

A single point mutation in the listerialbetLσA-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity

Construction and characterization of metal ion-containing DNA nanowires for synthetic biology and nanotechnology

A Brief Introduction to Synthetic Biology

Contact Info

Product

Resources

About

A single point mutation in the listerialbetLσ^A-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity

A single point mutation in the listerialbetLσ^A-dependent promoter leads to improved osmo- and chill-tolerance and a morphological shift at elevated osmolarity