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Synthetic Biology

A list of tools, databases and methods for synthetic biology.

Antibiotics and Secondary Metabolite Analysis Shell (antiSMASH)

http://antismash.secondarymetabolites.org/

A tool which allows the user to search through up to a whole genome and find secondary metabolite synthesis genes. It works on plant, bacterial and fungal sequences.

From the abstract: The first comprehensive pipeline capable of identifying biosynthetic loci covering the whole range of known secondary metabolite compound classes (polyketides, non-ribosomal peptides, terpenes, aminoglycosides, aminocoumarins, indolocarbazoles, lantibiotics, bacteriocins, nucleosides, beta-lactams, butyrolactones, siderophores, melanins and others). It aligns the identified regions at the gene cluster level to their nearest relatives from a database containing all other known gene clusters, and integrates or cross-links all previously available secondary-metabolite specific gene analysis methods in one interactive view.

CRISPR/Cas genome editing

http://www.addgene.org/CRISPR/plant/

CRISPR/Cas technology is described on this website.

Three papers demonstrating CRISPR-Cas genome editing technology in plants were published back-to-back in Nature Vol. 31 Issue 8 (2013). 

CRISPR/Cas constructs for plant science are available on Addgene

Earlham Institute BioFoundry

http://www.earlham.ac.uk/earlham-dna-foundry

The field of bioengineering is underpinned by our ability to assembly bespoke and complex DNA molecules at scale.  We are working to push the limits of the size and scale of DNA assembly and have recently automated the fabrication of large DNA assemblies in sub-microliter volumes at the Earlham DNA Foundry. This has been coupled to validation using next-generation sequencing technologies.

Gibson Assembly

http://www.srcf.ucam.org/~wac26/gibson/

An online manual for Gibson Isothermal Assembly, including an explanation of the chemistry, a clear workflow, and advice on sourcing materials. 

Gibson Assembly was first published in Gibson et al. 2009, Nature Methods DOI:10.1038/NMETH.1318

Golden Gate, Golden Braid, and MoClo

http://j5.jbei.org/j5manual/pages/23.html

The Golden Gate DNA assembly method offers standardized, quasi-scarless, multi-part DNA assembly, and is an excellent choice for combinatorial library construction. For background and links, see: http://j5.jbei.org/j5manual/pages/23.html

The parts for Golden Gate assembly are now available on Addgene

Golden Gate was originally published in Engler C et al., 2008. A One Pot, One Step, Precision Cloning Method with High Throughput Capability. PLoS ONE 3(11): e3647. doi:10.1371/journal.pone.0003647

The Golden Braid method is adapted from Golden Gate. It is published in Sarrion-Perdigones A et al., 2011. GoldenBraid: An Iterative Cloning System for Standardized Assembly of Reusable Genetic Modules. PLoS ONE 6(7): e21622. doi:10.1371/journal.pone.0021622

 

GoldenBraid DNA Assembly

https://gbcloning.upv.es/

GoldenBraid is a modular cloning technique. The GB Cloning website includes protocols and a digital tool to help with assembly. Users can request a starter kit containing the parts required for GB cloning.

GoldenBraid 2.0 was published in: Sarrion-Perdigones A, Vazquez-Vilar M, Palací J, Castelijns B, Forment J, Ziarsolo P, Blanca J, Granell A, Orzaez D. (2013) GoldenBraid 2.0: A Comprehensive DNA Assembly Framework for Plant Synthetic Biology. Plant Physiol. 2013 162: 1618-1631.

Infobiotics.org

http://www.infobiotics.org/

Infobiotics workbench is a computational framework implementing a synergy between executable biology, multi-compartmental stochastic simulations, formal model analysis and structural/parameter model optimisation for computational systems and synthetic biology. 

Infobiotics.org was first published in 

Blakes et al. 2011. The Infobiotics Workbench: an integrated in silico modelling platform for Systems and Synthetic Biology. Bioinformatics doi: 10.1093/bioinformatics/btr571

 

International Genetically Engineered Machine (iGEM)

https://gbcloning.upv.es/

The iGEM Foundation is an independent, non-profit organization dedicated to the advancement of synthetic biology, education and competition, and the development of an open community and collaboration. This is done by fostering an open, cooperative community and friendly competition.

 

iGEM’s main program is the iGEM Competition. The iGEM competition gives students the opportunity to push the boundaries of synthetic biology by tackling everyday issues facing the world. Made up of primarily university students, multidisciplinary teams work together to design, build, test, and measure a system of their own design using interchangeable biological parts and standard molecular biology techniques. Every year nearly 6,000 people dedicate their summer to iGEM and then come together in the fall to present their work and compete at the annual Jamboree.

Liverpool GeneMill

http://genemill.liv.ac.uk

The Liverpool GeneMill has been funded by the BBSRC with an initial investment of £3M to establish a facility for the rapid high throughput construction and testing of synthetic DNA constructs. Liverpool GeneMill removes complexity for the end user, providing end-to-end design, construction and phenotypic validation of libraries of gene constructs for academic and industrial applications.

  • construct design
  • DNA synthesis (sequence verified); from plasmid libraries to artificial chromosomes
  • genome editing tools e.g. CRISPR/Cas9 and TALENs
  • protein design and expression systems (including bacteria, yeast, plant, mammalian and cell-free systems)
  • protein expression and function prototyping
  • scalable fermentation analysis
  • metabolomic / proteomic analyses.

OpenPlant

http://openplant.org/

BBSRC funded Synethtic Biology hub. Collaboration between University of Cambridge and the Sainsbury laboratory in Norwich.

Providing open technologies for plant synethtic biology. Many available resources.

Pcomp

http://coiledcoils.chm.bris.ac.uk/pcomp/

From the website: Pcomp is a database of rationally designed Peptide components for synthetic biology. Entries in Pcomp are tectons that form self-assembled units. These have the potential to combine into functional assemblies and further organised or encapsulated into systems.

Plasmids from The Sainsbury Laboratory

http://synbio.tsl.ac.uk/?page_id=52

This database contains a list of molecular parts (plasmids) in use at SynBio@TSL. The database currently contains 95 backbones and tools and 135 standard parts for plants.

Many plasmids in the database are available from the non-profit organisation, AddGene. Unpublished plasmids not available through AddGene are available but may not have been tested. 

SynBio@TSL

http://synbio.tsl.ac.uk/

The SynBio@TSL pages are a rich source of information for all things synthetic biology. They include introductions to the field and to specific techniques, guides to synbio tools and resources, and protocols. 

SynBio@TSL YouTube Channel

https://www.youtube.com/channel/UCUOR6ZqMFxUJlm8VLtmKIEA/feed

YouTube channel from SynBio@TSL, featuring a series of videos on parallel gene cloning methods GoldenGate and MoClo.

Synthetic Biology Open Language

http://www.sbolstandard.org/

From the website: Synthetic Biology Open Language (SBOL) is a software standard for the electronic exchange of specifications and descriptions of genetic parts, devices, modules, systems, and engineered genomes.

Synthetic biology videos

http://www.youtube.com/playlist?list=PLylDstki6x-p3LHwkTKldrdQBgvWzc6W0

A selection of synthetic biology experts present their research and their idea of synthetic biology at the 2012 New Phytologist workshop on Synthetic Biology.