Synthetic Biology Projects tRNA

Synthetic Biology Projects

The purpose of this page is to provide a resource for our growing community contributing to synthetic biology, oligonucleotide assembly, in vitro translation, mini-genomes, ribosome display, etc. Some of the links below are inactive until after approval by the publisher. -- Updated 9-May-2009 by gmc. (Belorussian translation)

(1) Synthetic Genomics: DNA from chips, error correction & assembly

Tian J, Gong H, Sheng N, Zhou X, Gulari E, Gao X, & Church GM (2004) Accurate Multiplex Gene Synthesis from Programmable DNA Chips.
May-2001 Minigenome/ BioSpice project start.
01-Feb-04 list#1: Oligos used for synthesis of 21 E.coli small subunit ribosomal proteins =minigenome subset; promoter, SD, his-tags added during gene PCR (918 oligos from a 4K-format Xeotron/Atactic oligo array).
25-Mar-04 list#2: Oligos for synthesis of a 125Kbp minigenome & 777kbp M. mobile genome. (95376 oligos from a 191K Nimblegen array format).
Supplementary tables 1 & 2 and images for a 14,593 bp operon of 21 ribosomal genes (accession AY773199) and assembly of one gene (s19) from 95376 oligos (6.7 Mbases).
Industrial-strength spin-off : Gen9-2009 (aka Engeneos-2001, Codon Devices-2005)

(2) Bio-security & Surveillance technologies

  • 18-Jun-2004: A Synthetic Biohazard Non-proliferation Proposal.
  • International Association Synthetic Biology (IASB), International Consortium for Polynucleotide Synthesis (ICPS)
  • Sloan Foundation working group.
  • DNA design with select agent filtering : SynBioSIS.
  • Bio-weathermap using 'next generation' sequencing technologies.

    (3) Engineering microbial genomic chassis for safer biotechnology.

    Synthetic Biology Engineering Research Center SynBERC. See: Safeguarding Biology (2009)

    (4) rE.coli project to make new in vivo genetic codes

    Farren Isaacs, Harris Wang, Zach Sun, Resmi Charalel (with Peter Carr et al. in Joe Jacobson's group). We have changed all 314 UAG stop codons to UAA and will next try to knock-out the prfA gene (encoding release factor RF1). See: Nature 2009.

    (5) Mirror-image biopolymers

    Duhee Bang is ligating synthetic peptides to make a mirror DNA Polymerase (Sulfolobus solfataricus P2 DNA polymerase IV -- Dpo4) for mirror-PCR. See also 2001 DARPA grant for mirror protein synthesis construction plan. With this in mind, in 2007, Mike Jewett began working on effcient in vitro protein synthesis of translation factors and ribosomal proteins. (see also item #9 below). See also: Wired 2010 Mirror life article

    (6) iGEM and other training

    Check here for our role in iGEM an international Genetically Engineered Machine competition. Our 2004 iGEM project was an integrase-based "counter" done in collaboration with Jim Collins's group at BU. (Published in Science 2009) Two 2005 iGEM projects were BioWire & BioSketch. The Fall & Spring course MCB 100 has contributing in interesting ways with Harvard iGEM teams e.g. 2006 , 2007 , 2008 , 2009 , 2010 , 2011 .

    (7) Microbial and Plant engineering for converting Photons to Biofuels

    See our DOE Genomes to Life Center. Spin off companies: Joule Unlimited , LS9.com

    (8) DNA-nanostructures

    This project is to design complex 3D nanostructures using single-stranded and double-stranded DNA building blocks (e.g. M13 circles and oligos) Shawn Douglas in collaboration with William Shih and Peng Yin. Open Source software: caDNAno

    (9) Minimal Genomes & Synthetic Cells

    This began as a Biophysics problem set question in 1992 and in 2001 became a DARPA-funded project.

    Forster, AC & Church, GM Nature EMBO MSB Aug-2006 : Toward synthesis of a minimal cell.
    Forster, AC & Church, GM Genome Research 17(1):1-6. Dec-2006 Synthetic biology projects in vitro.
    The image below (and on the cover of Genome Research and BBC video) was generated using grid.pl.

    A "3D parts-list" figure encoded by an E.coli based minigenome of 150 macromolecules (plus 45 small molecules) is below (derived from 3D structures in the table developed for the above MSB paper). 2.7 kbp of the full 113 kbp minigenome is shown. The colors reflect those of Fig 1 & 2 (blue DNA to red RNA to purple proteins). The layout reflects the 4x4x4 genetic code in figure 3, the 20 aminoacids (aa) in single-letter format. Only one tRNA-synthetase complex is shown per aa even if more than one tRNA exists for that aa. The 'extra' tRNAs are shown bound to modification enzymes or free, hence those enzymes are clustered near their main substrate tRNAs in the code layout. Translation factors end in F: initiation (IF), elongation(EF), and release (RF). Note that many of these proteins resemble tRNA in shape. fM= formyl-Met-tRNA with the Fmt formylase. Some of the molecules are not yet displayed (Qm=RF Gln methylase, TilS, PrfC) and some are rough homology models (e.g. some tRNAs). More than one copy of a molecule is shown when the function of the complex requires it, e.g. GroE = 14 copies of GroEL (60kd) and 7 copies of GroES (10kd).

    in vitro genetic code