Since its launch, Nature Methods has seen many papers that have influenced the Synthetic Biology community. As a supplement to our May Focus on Synthetic Biology we take a nostalgic trip through the highlights of our papers in this area for different aspects of synthetic biology.
Cloning
In 2007 Stephen Elledge and Mamie Li developed SLIC (sequence and ligation-independent cloning) a strategy that uses homologous recombination to assembly many DNA fragments in vitro in a single reaction. Later the same year Mitsuhiro Itaya and colleagues also used homologous recombination in their bottom up assembly to unite larger DNA pieces to genomes of ~ 140kb size.
In 2009 Daniel Gibson and colleagues presented their one-pot enzymatic reaction that successfully assembled genomes 100s of kilobases and has since been dubbed ‘Gibson Assembly’. The method reached fame on Youtube when the Cambridge iGEM team for 2010 created a music video showing how Gibson Assembly saves frustrated scientists:
Gene and genome synthesis
In 2007, to improve error-free DNA synthesis, Duhee Bang and George Church developed circular assembly amplification that eliminated error-containing oligonucleotides from the assembly. A few years later Jay Shendure and colleagues introduced their dial-out PCR to retrieve desired DNA molecules from a library for gene assembly.
For an in depth review on the topic of DNA synthesis, error correction and gene assembly visit Sriram Kosuri and George Church’s review in our Focus issue.
In 2010, on the heels of their breakthrough with Mycoplasma mycoides JCVI-syn1.0 – the first chemically synthesized bacterial genome (Gibson D, et al Science 329, 2010) - Gibson et al. published the chemical synthesis of the mouse mitochondrial genome in our pages. They adapted Gibson Assembly to begin at the oligonucleotide level to rapidly make larger fragments that were then combined into the desired genome, exclusively in vitro. Once synthesized a bacterial genome might need to be further modified, but to do so in an organism other than E. coli proved challenging. In 2013 Bogumil Karas et al, showed that whole genomes, as large as 1.8 megabases can be directly transferred from bacteria to yeast where genetic manipulation is routine.
In our current Focus issue Gibson reviews the state of the art in genome assembly techniques , compares strategies and discusses what the future may hold.
Genome modification
To quickly generate large libraries of promoters in targeted regions of a bacterial chromosome George Church and colleagues presented coselection MAGE (multiplex automated genome engineering) in 2012. The increasingly popular CRISPR system can also rapidly edit genomes with few off-target effects when Cas9 is used as a nickase as William Skarnes and colleagues showed earlier this year.
Gene activation can be tuned by targeting transcription factors via the CRISPR-Cas9 system as Charles Gersbach demonstrated in 2013.
Circuit design
To ease construction of complex circuits Adam Arkin and colleagues adapted known translational regulators to control transcriptional elongation in 2012. A bit later the same year Jim Collins and colleagues showed that an iterative plug-and-play method makes use of a large repository of genetic components when designing circuits. This year Jeff Tabor and colleagues showed how gene circuit dynamics can be controlled with light. On April 28 Douglas Densmore and his team introduced Raven , software that calculates assembly plans for complex circuits.
Parts characterization
To be successful in any of the above applications one needs reliable and well characterized parts. Last year Drew Endy, Adam Arkin and colleagues presented a method to quantify the performance of genetic elements and in a companion paper they introduced a library of standardized transcription and translation initiation elements available through biofab.
Towards the end of 2013 Christopher Voigt and colleagues expanded the designer’s toolbox with over 500 well characterized transcriptional terminators. Robert Landick discussed how these ‘better stop signs’ as he termed them provide insight into the mechanism of termination.
UPDATE: There is now a joint special on Synthetic Biology at nature.com/synbio with articles from Nature, Nature Reviews Microbiology and Nature Methods.
Enjoy reading. The papers mentioned above are listed below in chronological order.