ArticleNucleic acids research2012
Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
32 citing papers in PubMed, 63 citations in OpenAlex.
- High-throughput analyses of a reconstituted diversity-generating retroelement identify intrinsic and extrinsic determinants of diversification.PLoS genetics · 2026Article
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- Coselection of BAC for Escherichia coli chromosomal DNA multiplex automated genome engineering.Biotechnology letters · 2024Article
- Engineering the Signal Resolution of a Paper-Based Cell-Free Glutamine Biosensor with Genetic Engineering, Metabolic Engineering, and Process Optimization.Sensors (Basel, Switzerland) · 2024Article
- Past, Present, and Future of Genome Modification inMicroorganisms · 2022Review
- A multifunctional system for genome editing and large-scale interspecies gene transfer.Nature communications · 2022Article
- A versatile genetic engineering toolkit for E. coli based on CRISPR-prime editing.Nature communications · 2021Article
- High-throughput functional variant screens via in vivo production of single-stranded DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Improved bacterial recombineering by parallelized protein discovery.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Structure and mechanism of the Red recombination system of bacteriophage λ.Progress in biophysics and molecular biology · 2019Review
- A versatile platform strain for high-fidelity multiplex genome editing.Nucleic acids research · 2019Article
- 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
- Molecular Mechanisms That Contribute to Horizontal Transfer of Plasmids by the Bacteriophage SPP1.Frontiers in microbiology · 2017Article
- DNA annealing by Redβ is insufficient for homologous recombination and the additional requirements involve intra- and inter-molecular interactions.Scientific reports · 2016Article
- Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- λ Recombination and Recombineering.EcoSal Plus · 2016Review
- Seven gene deletions in seven days: Fast generation of Escherichia coli strains tolerant to acetate and osmotic stress.Scientific reports · 2015Article
- Systems analysis of methylerythritol-phosphate pathway flux in E. coli: insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite.Microbial cell factories · 2015Article
- Rapid prototyping of microbial cell factories via genome-scale engineering.Biotechnology advances · 2015Review
- The no-SCAR (Scarless Cas9 Assisted Recombineering) system for genome editing in Escherichia coli.Scientific reports · 2015Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Disrupting the interaction between primase and helicase in Escherichia coli increases Okazaki fragment (OF) length due to less frequent primer synthesis. We exploited this feature to increase the amount of ssDNA at the lagging strand of the replication fork that is available for λ Red-mediated Multiplex Automatable Genome Engineering (MAGE). Supporting this concept, we demonstrate that MAGE enhancements correlate with OF length. Compared with a standard recombineering strain (EcNR2), the strain with the longest OFs displays on average 62% more alleles converted per clone, 239% more clones with 5 or more allele conversions and 38% fewer clones with 0 allele conversions in 1 cycle of co-selection MAGE (CoS-MAGE) with 10 synthetic oligonucleotides. Additionally, we demonstrate that both synthetic oligonucleotides and accessible ssDNA targets on the lagging strand of the replication fork are limiting factors for MAGE. Given this new insight, we generated a strain with reduced oligonucleotide degradation and increased genomic ssDNA availability, which displayed 111% more alleles converted per clone, 527% more clones with 5 or more allele conversions and 71% fewer clones with 0 allele conversions in 1 cycle of 10-plex CoS-MAGE. These improvements will facilitate ambitious genome engineering projects by minimizing dependence on time-consuming clonal isolation and screening.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.