ArticlePloS one2012
Transformation with oligonucleotides creating clustered changes in the yeast genome.
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 10 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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
10 citing papers in PubMed.
- Genome editing outcomes reveal mycobacterial NucS participates in a short-patch repair of DNA mismatches.Nucleic acids research · 2024Article
- Genome Editing Outcomes Reveal Mycobacterial NucS Participates in a Short-Patch Repair of DNA Mismatches.bioRxiv : the preprint server for biology · 2023Article
- Extensive trimming of short single-stranded DNA oligonucleotides during replication-coupled gene editing in mammalian cells.PLoS genetics · 2020Article
- Precise Editing at DNA Replication Forks Enables Multiplex Genome Engineering in Eukaryotes.Cell · 2017Article
- 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
- Significance of stem cell markerOncology letters · 2016Article
- Replicative DNA polymerase δ but not ε proofreads errors in Cis and in Trans.PLoS genetics · 2015Article
- Yeast oligo-mediated genome engineering (YOGE).ACS synthetic biology · 2013Article
- Different roles of eukaryotic MutS and MutL complexes in repair of small insertion and deletion loops in yeast.PLoS genetics · 2013Article
- In vivo bypass of 8-oxodG.PLoS genetics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
We have studied single-strand oligonucleotide (oligo) transformation of yeast by using 40-nt long oligos that create multiple base changes to the yeast genome spread throughout the length of the oligos, making it possible to measure the portions of an oligo that are incorporated during transformation. Although the transformation process is greatly inhibited by DNA mismatch repair (MMR), the pattern of incorporation is essentially the same in the presence or absence of MMR, whether the oligo anneals to the leading or lagging strand of DNA replication, or whether phosphorothioate linkages are used at either end. A central core of approximately 15 nt is incorporated with a frequency of >90%; the ends are incorporated with a lower frequency, and loss of the two ends appears to be by different mechanisms. Bases that are 5-10 nt from the 5' end are generally lost with a frequency of >95%, likely through a process involving flap excision. On the 3' end, bases 5-10 nt from the 3' end are lost about 1/3 of the time. These results indicate that oligos can be used to create multiple simultaneous changes to the yeast genome, even in the presence of MMR.
Indexed as
Identifiers
What OpenQuestion holds
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.