Edit-R synthetic crRNA negative controls

Gene editing
Gene editing reagents
Edit-R Synthetic crRNA negative controls

Edit-R synthetic crRNA negative controls

Bioinformatically designed to not target any gene in human or mouse genomes

Synthetic guide RNAs for efficient gene knockout & unparalleled specificity

Transfection-ready RNAs eliminate cloning and in vitro transcription steps
Chemically modified for improved nuclease resistance

Reminder: Synthetic crRNA must be paired with synthetic tracrRNA to form the full guide RNA complex that targets Cas9 editing.

AAVS1/Rosa26 cutting controls are designed to target regions of the genome that do not result in functional knockout of a protein or known phenotypic changes. These regions are sometimes known as safe harbor regions. These guides are validated for mismatch detection assays and are recommended for screening applications as an additional control that results in Cas9 cutting without a phenotypic readout.

Non-targeting Controls are recommended as negative controls for experiments using crRNAs in human or mouse cells. All Edit-R Non-targeting Controls are designed to have a minimum of three mismatches or gaps to all potential PAM-adjacent targets in human and mouse genomes. Changes in viability or gene expression levels in cells treated with these controls likely reflect a baseline cellular response that can be compared to the levels in cells treated with target-specific crRNAs.

Remember to order tracrRNA for use with your controls!

How much crRNA & tracrRNA do I need?

This table provides the approximate number of experiments that can be carried out for lipid transfection methods at the recommended crRNA:tracrRNA working concentration (25 nM:25nM) in various plate/well formats. Calculations do not account for pipetting errors.

crRNA nmol	tracrRNA nmol	96-well plate 100 µL reaction volume	24-well plate 500 µL reaction volume	12-well plate 1000 µL reaction volume	6-well plate 2500 µL reaction volume
2	2	800	160	80	32
5	5	2000	400	200	80
10	10	4000	800	400	160
20	20	8000	1600	800	320

High percentage of gene editing using the T7E1 assay to determine indel formation of the Edit-R AAVS1 cutting controls

Jurkat cells (250,000/96w) were nucleofected with (SE buffer, program CL-120) 50 pmol of RNP (40 µM NLS-Cas9 + 80 µM sgRNA) in triplicate. U2OS cells hEF1α-Cas9 were transfected using 0.15 µL Dharmafect 4/96w + 50 µM sgRNA (incubated at room temperature for 20 minutes in MEM solution).

After 72 hours cells were harvested for direct lysis (+ Rnase + proteinase K). Primers per spacer region were used to amplify 450-800 bp genomic amplicon from the edited and unedited samples. A hot-start Phusion II touch-down PCR program was used to generate amplicons for each sample (Tm ~65 for each). PCRs were directly incubated with T7 endonuclease I and ran on a 2% agarose SyberSafe gel @ 80V for 90 minutes.

TIDE analysis confirms high efficiency of indel formation using Edit-R AAVS1 cutting control guides

Jurkat cells (250,000/96w) were nucleofected with 50 pmol of RNP (40 µM NLS-Cas9 + 80 µM sgRNA) in SE buffer and program CL-120, in triplicate. U2OS cells were transfected using 0.15 µL Dharmafect 4/96w + 50 µM sgRNA (incubated at room temperature for 20 minutes in MEM solution).

After 72 hours cells were harvested for direct lysis. Primers per spacer region were used to amplify 450-800 bp genomic amplicon from the edited and unedited samples. A hot-start Phusion II touch-down PCR program was used to generate amplicons for each sample. PCRs were sent for Sanger sequencing. Sequencing files were analyzed by tracking of indels by decomposition (TIDE).

Efficient CRISPR-Cas9 gene editing achieved with synthetic sgRNA and synthetic crRNA:tracrRNA

CRISPR cas9 Synthetic sgRNA

The synthetic sgRNA for target gene editing resulted in high editing efficiency (data shown are from two experiments; (A), and high editing efficiency was also achieved for synthetic crRNA:tracrRNA (B).

High efficiency of indel generation using Edit-R Rosa26 cutting controls by T7EI

NIH/3T3 Cas9 stable cells were plated at 10,000 cells/well in a 96 well plate and transfected using 0.2 µL Dharmafect 1 with 25 nM sgRNA (incubated at room temperature for 20 minutes in MEM solution). Cells were harvested at 72 hours post-transfection for direct cell lysis. Primers per spacer region were used to amplify 450-800 bp genomic amplicon from the edited and unedited samples. A hot-start Phusion II touch-down PCR program was used to generate amplicons for each sample. PCR samples were directly incubated with T7 endonuclease I and ran on a 2% agarose SyberSafe gel @ 80V for 90 minutes.

High efficiency of indel generation using Edit-R Rosa26 cutting controls by TIDE

rosa26 cutting sgrna tide graph

NIH/3T3 Cas9 stable cells were plated at 10,000 cells/well in a 96 well plate and transfected using 0.2 µL Dharmafect 1 with 25 nM sgRNA (incubated at room temperature for 20 minutes in MEM solution). Cells were harvested at 72 hours post-transfection for direct cell lysis. Primers per spacer region were used to amplify 450-800 bp genomic amplicon from the edited and unedited samples. A hot-start Phusion II touch-down PCR program was used to generate amplicons for each sample. PCR samples were sent for Sanger sequencing. Sequencing files were analyzed by tracking of indels by decomposition.

Yes, these controls have the 2xMS modification pattern, as described in the Stabilizing modifications on Edit-R crRNA and tracrRNA blog article.

Our neutral cutting controls target an inactive region of the genome to provide a quantitative measure of cutting efficiency by mismatch detection assays, while maintaining a negative or negligible phenotype.

The neutral cutting controls target safe harbor genomic loci: human AAVS1 located on chromosome 19 and mouse Rosa26 on chromosome 6. Safe harbor loci are well-characterized, widely accepted, inactive genomic regions.

Our non-targeting control guide RNAs do not target any region in the genome. Non-targeting designs control for phenotypic changes that may be caused by the delivery of the CRISPR-Cas9 reagents in the absence of cutting. However, the non-targeting controls cannot indicate changes caused by Cas9 cutting because they do not result in cutting by the Cas9 enzyme.

Our positive controls target established housekeeping genes to offer insight into phenotypic changes that might be due to Cas9 cutting but are not specific to cutting within the gene of interest. However, there may be cell types or culture conditions under which cutting at the housekeeping gene locus could result in a phenotype, or experimental situations where disrupting a gene is not desired. To overcome this potentially confounding effect, the neutral cutting control can be included to provide more robust results and increased confidence in the phenotypes observed following editing of the target gene.

Neutral cutting controls can be helpful if there is concern that an observed phenotype is not gene-specific. In particular, neutral cutting controls are helpful as an additional control in screening applications and when a phenotype is observed with a positive control guide RNA. Additionally, this guide can be used in discovery settings where disruption of a gene could affect downstream phenotypes and results.