ArticlePloS one2012
Stable gene targeting in human cells using single-strand oligonucleotides with modified bases.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 32 citations in OpenAlex.
- Removal of TREX1 activity enhances CRISPR-Cas9-mediated homologous recombination.Nature biotechnology · 2025Article
- Cleavage efficiency of CRISPR/Cas9 system with G-quadruplex-capped single-guide RNA motifs in RNase II and RNase R.3 Biotech · 2025Article
- Extensive trimming of short single-stranded DNA oligonucleotides during replication-coupled gene editing in mammalian cells.PLoS genetics · 2020Article
- Editing the Sickle Cell Disease Mutation in Human Hematopoietic Stem Cells: Comparison of Endonucleases and Homologous Donor Templates.Molecular therapy : the journal of the American Society of Gene Therapy · 2019Article
- High fidelity CRISPR/Cas9 increases precise monoallelic and biallelic editing events in primordial germ cells.Scientific reports · 2018Article
- Efficient Delivery and Nuclear Uptake Is Not Sufficient to Detect Gene Editing in CD34+ Cells Directed by a Ribonucleoprotein Complex.Molecular therapy. Nucleic acids · 2018Article
- DNA mismatch repair and oligonucleotide end-protection promote base-pair substitution distal from a CRISPR/Cas9-induced DNA break.Nucleic acids research · 2018Article
- CRISPR-DirectedThe CRISPR journal · 2018Article
- Article
- Beyond editing to writing large genomes.Nature reviews. Genetics · 2017Article
- To cleave or not to cleave: therapeutic gene editing with and without programmable nucleases.Nature reviews. Drug discovery · 2017Article
- 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
- Oligonucleotide-Mediated Genome Editing Provides Precision and Function to Engineered Nucleases and Antibiotics in Plants.Plant physiology · 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
- Oligonucleotide-directed mutagenesis for precision gene editing.Plant biotechnology journal · 2016Review
- Replicative DNA polymerase δ but not ε proofreads errors in Cis and in Trans.PLoS genetics · 2015Article
- Synthetic biology in mammalian cells: next generation research tools and therapeutics.Nature reviews. Molecular cell biology · 2014Review
- Optimization of scarless human stem cell genome editing.Nucleic acids research · 2013Article
- Genome-scale engineering for systems and synthetic biology.Molecular systems biology · 2013Review
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Recent advances allow multiplexed genome engineering in E. coli, employing easily designed oligonucleotides to edit multiple loci simultaneously. A similar technology in human cells would greatly expedite functional genomics, both by enhancing our ability to test how individual variants such as single nucleotide polymorphisms (SNPs) are related to specific phenotypes, and potentially allowing simultaneous mutation of multiple loci. However, oligo-mediated targeting of human cells is currently limited by low targeting efficiencies and low survival of modified cells. Using a HeLa-based EGFP-rescue reporter system we show that use of modified base analogs can increase targeting efficiency, in part by avoiding the mismatch repair machinery. We investigate the effects of oligonucleotide toxicity and find a strong correlation between the number of phosphorothioate bonds and toxicity. Stably EGFP-corrected cells were generated at a frequency of ~0.05% with an optimized oligonucleotide design combining modified bases and reduced number of phosphorothioate bonds. We provide evidence from comparative RNA-seq analysis suggesting cellular immunity induced by the oligonucleotides might contribute to the low viability of oligo-corrected cells. Further optimization of this method should allow rapid and scalable genome engineering in human cells.
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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.