ArticleBMC bioinformatics2022
PrimedSherlock: a tool for rapid design of highly specific CRISPR-Cas12 crRNAs.
Article in BMC bioinformatics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 22 citations in OpenAlex.
- Biosensors for the detection of arthropod-borne veterinary viruses: A comprehensive review.Veterinary and animal science · 2026Review
- A Modular and Programmable Cas13d Platform for RNA Single Nucleotide Variant Detection.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- The CRISPR-Cas toolkit for mosquito-borne virus surveillance: detection, tracing, and discovery.Frontiers in cellular and infection microbiology · 2026Review
- Applications and Challenges of CRISPR-Cas Technology for the Detection of Antimicrobial Resistance Genes.Infection and drug resistance · 2026Review
- Important applications of DNA nanotechnology combined with CRISPR/Cas systems in biotechnology.RSC advances · 2025Review
- PathoGD: an integrative genomics approach to primer and guide RNA design for CRISPR-based diagnostics.Communications biology · 2025Article
- CRISPR-epigenetic crosstalk: From bidirectional regulation to therapeutic potential.Computational and structural biotechnology journal · 2025Review
- Article
- Krisp: A Python package to aid in the design of CRISPR and amplification-based diagnostic assays from whole genome sequencing data.PLoS computational biology · 2024Article
- Review
- Advancements in Airborne Viral Nucleic Acid Detection with Wearable Devices.Advanced sensor research · 2024Article
- Point-of-care testing diagnosis of African swine fever virus by targeting multiple genes with enzymatic recombinase amplification and CRISPR/Cas12a System.Frontiers in cellular and infection microbiology · 2024Article
- Integrating Genomic Data with the Development of CRISPR-Based Point-of-Care-Testing for Bacterial Infections.Current clinical microbiology reports · 2024Review
- Article
- Point-of-Care Testing for Infectious Diseases Based on Class 2 CRISPR/Cas Technology.Diagnostics (Basel, Switzerland) · 2023Review
- Latest Advances in Arbovirus Diagnostics.Microorganisms · 2023Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundCRISPR-Cas based diagnostic assays provide a portable solution which bridges the benefits of qRT-PCR and serological assays in terms of portability, specificity and ease of use. CRISPR-Cas assays are rapidly fieldable, specific and have been rigorously validated against a number of targets, including HIV and vector-borne pathogens. Recently, CRISPR-Cas12 and CRISPR-Cas13 diagnostic assays have been granted FDA approval for the detection of SARS-CoV-2. A critical step in utilizing this technology requires the design of highly-specific and efficient CRISPR RNAs (crRNAs) and isothermal primers. This process involves intensive manual curation and stringent parameters for design in order to minimize off-target detection while also preserving detection across divergent strains. As such, a single, streamlined bioinformatics platform for rapidly designing crRNAs for use with the CRISPR-Cas12 platform is needed. Here we offer PrimedSherlock, an automated, computer guided process for selecting highly-specific crRNAs and primers for targets of interest.
resultsUtilizing PrimedSherlock and publicly available databases, crRNAs were designed against a selection of Flavivirus genomes, including West Nile, Zika and all four serotypes of Dengue. Using outputs from PrimedSherlock in concert with both wildtype A.s Cas12a and Alt-R Cas12a Ultra nucleases, we demonstrated sensitive detection of nucleic acids of each respective arbovirus in in-vitro fluorescence assays. Moreover, primer and crRNA combinations facilitated the detection of their intended targets with minimal off-target background noise.
conclusionsPrimedSherlock is a novel crRNA design tool, specific for CRISPR-Cas12 diagnostic platforms. It allows for the rapid identification of highly conserved crRNA targets from user-provided primer pairs or PrimedRPA output files. Initial testing of crRNAs against arboviruses of medical importance demonstrated a robust ability to distinguish multiple strains by exploiting polymorphisms within otherwise highly conserved genomic regions. As a freely-accessible software package, PrimedSherlock could significantly increase the efficiency of CRISPR-Cas12 diagnostics. Conceptually, the portability of detection kits could also be enhanced when coupled with isothermal amplification technologies.
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