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 6-Aug-2006 by gmc.

(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 : Codon Devices

(2) Bio-security & Surveillance technologies

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

    (3) Engineering genomic Chassis for safe therapeutic bacteria

    Synthetic Biology Engineering Research Center SynBERC

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

    Farren Isaacs, Resmi Charalel (with Peter Carr et al. in Joe Jacobson's group)

    (5) Mirror-image biopolymers

    Duhee Bang is ligating synthetic peptides to make novel DNA Polymerases.

    (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. Two 2005 iGEM projects were BioWire & BioSketch. MCB 100 is contributing in interesting ways with Harvard iGEM teams e.g. 2006.

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

    See our DOE Genomes to Life Center

    (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 Paul Rothemund.

    (9) Minimal Genomes & Synthetic Cells

    Nature EMBO MSB Aug-2006 : Forster, AC & Church, GM Toward synthesis of a minimal cell. Genome Res. 17(1):1-6. Dec-2006 Synthetic biology projects in vitro.

    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 table 1 in 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