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For use in genome engineering, the Streptococcus pyogenes system was simplified to two components: the Cas9 nuclease and a single chimeric guide RNA (gRNA).
The relaxation of sequence specificity of the RNA-guided endonuclease system remains the biggest challenge so far for its use in genome engineering (Jinek et al., 2014; Sternberg et al., 2014).
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These pre-existing genomic sequences paired with the evolved recombinase variants can be then used in genome engineering experiments.
Although eight yeast site-specific tyrosine recombinases are known, only Flp is actively used in genome engineering.
The serine recombinase family is large and includes many other proteins besides ϕC31 integrase with the potential to be widely used in genome engineering.
We discuss the unanswered questions posed by genome engineering experiments in a variety of systems in which the serine recombinases have been used and finally describe more recently discovered serine recombinases that have the potential to be used in genome engineering.
To expand use of the Flp/FRT system in genome engineering, variants of Flp recombinase can be evolved to recognize pre-existing genomic sequences that resemble FRT and thus can serve as recombination sites.
We have attempted to distil these lessons into the proposed considerations in Box 1. Introduction of the multiple alleles that will be necessary to adequately dissect lncRNA in vivo function will be greatly aided by recent advances in genome engineering using designer site-specific nucleases such as CRISPR/Cas9 and TALENs.
Recent advances in genome engineering using CRISPR/Cas9, an ancient bacterial immune-like system, have revolutionized cancer genetics.
It now sees widespread application in genome engineering workflows, especially using the Streptococcus pyogenes endonuclease Cas9.
The recent advances in genome engineering (such as the use of the CRISPR technology) may enable synthetic biologists to produce large insertions, deletions or inversions in the genome [ 28].
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