Abstract:
:Genome engineering technologies now enable precise manipulation of organism genotype, but can be limited in scalability by their design requirements. Here we describe Merlin ( http://merlincad.org ), an open-source web-based tool to assist biologists in designing experiments using multiplex automated genome engineering (MAGE). Merlin provides methods to generate pools of single-stranded DNA oligonucleotides (oligos) for MAGE experiments by performing free energy calculation and BLAST scoring on a sliding window spanning the targeted site. These oligos are designed not only to improve recombination efficiency, but also to minimize off-target interactions. The application further assists experiment planning by reporting predicted allelic replacement rates after multiple MAGE cycles, and enables rapid result validation by generating primer sequences for multiplexed allele-specific colony PCR. Here we describe the Merlin oligo and primer design procedures and validate their functionality compared to OptMAGE by eliminating seven AvrII restriction sites from the Escherichia coli genome.
journal_name
ACS Synth Bioljournal_title
ACS synthetic biologyauthors
Quintin M,Ma NJ,Ahmed S,Bhatia S,Lewis A,Isaacs FJ,Densmore Ddoi
10.1021/acssynbio.5b00219subject
Has Abstractpub_date
2016-06-17 00:00:00pages
452-8issue
6issn
2161-5063journal_volume
5pub_type
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journal_title:ACS synthetic biology
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journal_title:ACS synthetic biology
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abstract::Lactams are an important class of commodity chemicals used in the manufacture of nylons, with millions of tons produced every year. Biological production of lactams could be greatly improved by high-throughput sensors for lactam biosynthesis. To identify biosensors of lactams, we applied a chemoinformatic approach ins...
journal_title:ACS synthetic biology
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doi:10.1021/acssynbio.6b00136
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journal_title:ACS synthetic biology
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