MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering

Mads Bonde, Michael Schantz Klausen, Mads Valdemar Anderson, Annika Nilsson Wallin, Harris H. Wang, Morten Otto Alexander Sommer

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Abstract

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.
Original languageEnglish
JournalNucleic Acids Research
Volume12
Issue numberW1
Pages (from-to)W408-W415
ISSN0305-1048
DOIs
Publication statusPublished - 2014

Cite this

Bonde, Mads ; Klausen, Michael Schantz ; Anderson, Mads Valdemar ; Nilsson Wallin, Annika ; Wang, Harris H. ; Sommer, Morten Otto Alexander. / MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. In: Nucleic Acids Research. 2014 ; Vol. 12, No. W1. pp. W408-W415.
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abstract = "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 combinatorialcell libraries. Manual design of oligonucleotides for these approaches can be tedious, time-consuming, and may not be practical for larger projects targetingmany 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, includingamino 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.",
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MODEST: a web-based design tool for oligonucleotide-mediated genome engineering and recombineering. / Bonde, Mads; Klausen, Michael Schantz; Anderson, Mads Valdemar; Nilsson Wallin, Annika; Wang, Harris H.; Sommer, Morten Otto Alexander.

In: Nucleic Acids Research, Vol. 12, No. W1, 2014, p. W408-W415.

Research output: Contribution to journalJournal articleResearchpeer-review

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AU - Bonde, Mads

AU - Klausen, Michael Schantz

AU - Anderson, Mads Valdemar

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AU - Wang, Harris H.

AU - Sommer, Morten Otto Alexander

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