Researchers have developed a novel computational tool to help design single guide RNAs (sgRNAs) for DNA deletion using the CRISPR-Cas system. The new tool, CRISPETa, was reported in PLOS Computational Biology recently.
Since its initial discovery and subsequent development throughout the last decade, CRISPR has become known as a powerful tool in genomic experiments, both for trying to understand the genome and attempting to treat genetic disorders. Several variants of the system have been developed, such as CRISPRi to influence gene expression at a transcription level and dCas9 to bind to the DNA without cleaving the strand. In 2015, Professor Rory Johnson and his team developed another CRISPR variant, known as DECKO, which was designed specifically to facilitate the removal of selected DNA sequences from the genome.
DECKO uses two distinct sgRNAs to guide the cleavage protein Cas9 to the correct sites in the genome on either side of the material being deleted. When the nuclease cleaves the DNA at both sites, the sequence between the two loci is removed completely from the genome with high accuracy. The nature of CRISPR means that DECKO can be used to remove both coding and non-coding material and as a result has become a popular tool among researchers.
During the initial development of DECKO, the team noticed that one of the most time-consuming parts of their experiments was the sgRNA design process because there was no pre-made design software available. Now, Master’s student Carlos Pulido may have created the solution to this problem with a novel software pipeline called CRISPETa, which can suggest sgRNAs based on the intended target region.