MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering.
Recombineering and multiplex automated genome engineering (MAGE) offer the possibility to rapidly modify multiple genomic or plasmid sites at high efficiencies. This enables efficient creation of genetic variants including both single mutants with specifically targeted modifications as well as combinatorial cell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targeting many genomic sites. At present, the change from a desired phenotype (e.g. altered expression of a specific protein) to a designed MAGE oligo, which confers the corresponding genetic change, is performed manually. To address these challenges, we have developed the MAGE Oligo Design Tool (MODEST). This web-based tool allows designing of MAGE oligos for (i) tuning translation rates by modifying the ribosomal binding site, (ii) generating translational gene knockouts and (iii) introducing other coding or non-coding mutations, including amino acid substitutions, insertions, deletions and point mutations. The tool automatically designs oligos based on desired genotypic or phenotypic changes defined by the user, which can be used for high efficiency recombineering and MAGE. MODEST is available for free and is open to all users at http://modest.biosustain.dtu.dk.
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark msom@bio.dtu.dk.
Mads T
MT
Bonde
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark.
Michael S
MS
Klausen
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark.
Mads V
MV
Anderson
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark.
Annika I N
AI
Wallin
Department of Systems Biology, Columbia University College of Physicians and Surgeons, NY 10032, USA msom@bio.dtu.dk.
Harris H
HH
Wang
Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2970 Hørsholm, Denmark Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark msom@bio.dtu.dk.
Morten O A
MO
Sommer
D055786:Gene Knockout Techniques; D005818:Genetic Engineering / Q000379:methods*; D016678:Genome; D023281:Genomics / Q000379:methods; D020407:Internet; D009154:Mutation; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000737:chemistry*; D014176:Protein Biosynthesis; D011995:Recombination, Genetic; D012984:Software; D001616:beta-Galactosidase / Q000235:genetics / Q000378:metabolism
D009841:Oligonucleotides; D001616:beta-Galactosidase