Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE
journal contributionposted on 07.04.2016, 00:00 by Michael Quintin, Natalie J. Ma, Samir Ahmed, Swapnil Bhatia, Aaron Lewis, Farren J Isaacs, Douglas Densmore
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.
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design requirementsrecombination efficiencyMAGE experimentsresult validationAvrII restriction sitesprimer sequencesDNAMAGE Genome engineering technologiesMerlin oligoLarge Scale Genome EngineeringEscherichia coli genomePCRprimer design proceduresorganism genotypegenome engineeringMAGE cyclesexperiment planningallelic replacement ratesBLASTenergy calculation