Single-Base Resolution: Increasing the Specificity of the CRISPR-Cas System in Gene Editing

Roy Rabinowitz, Daniel Offen*

*Corresponding author for this work

Research output: Contribution to journalReview articlepeer-review

11 Scopus citations


The CRISPR-Cas system holds great promise in the treatment of diseases caused by genetic variations. The Cas protein, an RNA-guided programmable nuclease, generates a double-strand break at precise genomic loci. However, the use of the clustered regularly interspersed short palindromic repeats (CRISPR)-Cas system to distinguish between single-nucleotide variations is challenging. The promiscuity of the guide RNA (gRNA) and its mismatch tolerance make allele-specific targeting an elusive goal. This review presents a meta-analysis of previous studies reporting position-dependent mismatch tolerance within the gRNA. We also examine the conservativity of the seed sequence, a region within the gRNA with stringent sequence dependency, and propose the existence of a subregion within the seed sequence with a higher degree of specificity. In addition, we summarize the reports on high-fidelity Cas nucleases with improved specificity and compare the standard gRNA design methodology to the single-nucleotide polymorphism (SNP)-derived protospacer adjacent motif (PAM) approach, an alternative method for allele-specific targeting. The combination of the two methods may be advantageous in designing CRISPR-based therapeutics and diagnostics for heterozygous patients. In this review, Rabinowitz and Offen describe and compare the methods to improve the specificity of the CRISPR-Cas system, including high-fidelity synthetic enzymes, SNP-derived PAM and other methodologies. Furthermore, a meta-analysis of SpCas9 specificity profiles by several studies is presented to investigate the stringency of the gRNA seed sequence.

Original languageEnglish
Pages (from-to)937-948
Number of pages12
JournalMolecular Therapy
Issue number3
StatePublished - 3 Mar 2021


FundersFunder number
Aufzien Family Center for the Prevention and Treatment of Parkinson’s Disease
Prajs-Drimmer Institute for the Development of Anti-Degenerative Drugs


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