ArticleNucleic acids research2011
Modified bases enable high-efficiency oligonucleotide-mediated allelic replacement via mismatch repair evasion.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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46 citing papers in PubMed, 75 citations in OpenAlex.
- Do Chemically Modified Oligonucleotide Therapeutics Require Environmental Risk Assessment?Environmental science & technology · 2026Article
- Advances in Decoding Bacterial N-Terminal Proteoforms: Technologies, Challenges, and Functional Insights.Microorganisms · 2026Review
- ORBIT for E. coli: kilobase-scale oligonucleotide recombineering at high throughput and high efficiency.Nucleic acids research · 2024Article
- Proteins à la carte: riboproteogenomic exploration of bacterial N-terminal proteoform expression.mBio · 2024Article
- Recent advances in genome-scale engineering inEngineering microbiology · 2024Review
- Strategies to identify and edit improvements in synthetic genome segments episomally.Nucleic acids research · 2023Article
- Recombineering and MAGE.Nature reviews. Methods primers · 2021Article
- Extensive trimming of short single-stranded DNA oligonucleotides during replication-coupled gene editing in mammalian cells.PLoS genetics · 2020Article
- Bacterial Genetic Engineering by Means of Recombineering for Reverse Genetics.Frontiers in microbiology · 2020Review
- A versatile platform strain for high-fidelity multiplex genome editing.Nucleic acids research · 2019Article
- Synthetic biology for evolutionary engineering: from perturbation of genotype to acquisition of desired phenotype.Biotechnology for biofuels · 2019Review
- Directed evolution of multiple genomic loci allows the prediction of antibiotic resistance.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Article
- Efficient engineering of chromosomal ribosome binding site libraries in mismatch repair proficient Escherichia coli.Scientific reports · 2017Article
- Rewriting the Genetic Code.Annual review of microbiology · 2017Review
- A 'Semi-Protected Oligonucleotide Recombination' Assay for DNA Mismatch Repair in vivo Suggests Different Modes of Repair for Lagging Strand Mismatches.Nucleic acids research · 2017Article
- λ Recombination and Recombineering.EcoSal Plus · 2016Review
- LNA modification of single-stranded DNA oligonucleotides allows subtle gene modification in mismatch-repair-proficient cells.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Leveraging modern DNA assembly techniques for rapid, markerless genome modification.Biology methods & protocols · 2016Article
- A highly precise and portable genome engineering method allows comparison of mutational effects across bacterial species.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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Authors and funding
4 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome engineering using single-stranded oligonucleotides is an efficient method for generating small chromosomal and episomal modifications in a variety of host organisms. The efficiency of this allelic replacement strategy is highly dependent on avoidance of the endogenous mismatch repair (MMR) machinery. However, global MMR inactivation generally results in significant accumulation of undesired background mutations. Here, we present a novel strategy using oligos containing chemically modified bases (2'-Fluoro-Uridine, 5-Methyl-deoxyCytidine, 2,6-Diaminopurine or Iso-deoxyGuanosine) in place of the standard T, C, A or G to avoid mismatch detection and repair, which we tested in Escherichia coli. This strategy increases transient allelic-replacement efficiencies by up to 20-fold, while maintaining a 100-fold lower background mutation level. We further show that the mismatched bases between the full length oligo and the chromosome are often not incorporated at the target site, probably due to nuclease activity at the 5' and 3' termini of the oligo. These results further elucidate the mechanism of oligo-mediated allelic replacement (OMAR) and enable improved methodologies for efficient, large-scale engineering of genomes.
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