Stabilizing modifications on Edit-R crRNA and tracrRNA

Evolution of the first synthetic CRISPR RNA product line

When development of the Edit-R predesigned crRNA product line began back in 2013, our goal was to design and manufacture an optimal, predesigned, genome-wide product line for CRISPR-mediated knockout. One major accomplishment towards this goal was our development of a data-driven algorithm for selecting guide RNAs more likely to cause functional protein knockout, not just create a double-strand break. For 2017, we are drawing on our RNA synthesis expertise to further improve experimental outcomes for our customers.

Modifications for nuclease resistance

With the advent of Cas9 mRNA and protein reagents, we found that CRISPR efficiency in some applications, especially co-electroporation with Cas9 mRNA, could be improved when the crRNA and tracrRNA were modified for improved stability (nuclease-resistance). RNA modifications to resist degradation are not new to the field, nor to Dharmacon products. Our siSTABLE™ siRNA modification pattern and Accell™ siRNA reagents both include modified bases and backbone linkages for improved nuclease resistance.

We systematically tested modifications on the 2ʹ position of the sugar and phosphate backbone of both crRNA and tracrRNA. We found several positions on both the crRNA and tracrRNA where modifications were not well-tolerated and led to a decrease in editing efficiency. In addition, we found that having more than two 2’-O-methyl bases and phosphorothioate linkages in specific patterns on the crRNA and tracrRNA were very toxic in some cell types. When our selected pattern of stabilizing modifications is applied to the single-strand region of the crRNA:tracrRNA complex (Figure 1) co-electroporation results with Cas9 mRNA (Figure 2A) are greatly improved, and to some degree, Cas9 protein co-electroporation results are also improved (Figure 2B).

Position of stabilizing modifications on Edit-R synthetic crRNA and tracrRNA


Figure 1: Edit-R synthetic guide RNA are modified with two 2’ O-methyl and backbone phosphorothioates (MS) on the 5’ end of the crRNA (green strand) and on the 3’ end of the tracrRNA (blue strand). One to three MS modifications in all combinations of the 5’, 3’ or both ends of the RNA strands were tested.


A. Co-electroporation of crRNA:tracrRNA w/ Cas9
mRNA in K562 cells
Co-electroporation of crRNA:tracrRNA with Cas9 mRNA in K562 cells
B. Co-electroporation of crRNA:tracrRNA w/ Cas9
protein in K562 cells
Co-electroporation of crRNA:tracrRNA with Cas9 protein in K562 cells

Figure 2: A
. Stabilizing modifications are required for successful co-electroporation of Cas9 mRNA and crRNA:tracrRNA. Use of unmodified crRNA and tracrRNA to achieve gene editing requires a sequential electroporation protocol. B. Co-electroporation of Cas9 protein and crRNA:tracrRNA does not require stabilizing modifications, but results may be improved with their addition.

Improved DNA-free gene editing applications

Table 1 illustrates the overall benefit to stabilized synthetic crRNA and tracrRNA across different CRISPR-Cas9 gene editing applications. Virtually no difference in editing efficiency is detected when Cas9 is stably expressed or co-transfected with Cas9 protein as an RNP complex. However, co-transfection and co-electroporation with Cas9 mRNA are improved by the nuclease resistant properties of these modifications.

Table 1: Common CRISPR-Cas9 applications and the observed impact of 2xMS stabilizing modifications on crRNA:tracrRNA
Application Editing efficiency
  Unmodified crRNA:tracrRNA Modified for nuclease resistance
Transfection into Cas9-expressing cells ++ ++
Transfection of RNP (Cas9 protein) ++ ++
Electroporation of RNP ++ ++
Typically, the same or better
Co-transfection with Cas9 mRNA or plasmid ++ ++
Typically, the same or better
Co-electroporation with Cas9 mRNA -
Sequential delivery is required
What does this mean for you?

As of February 2017, all Edit-R predesigned crRNA and tracrRNA will carry these modifications for nuclease resistance with no change in price! Custom crRNA designed and ordered with the CRISPR Design Tool will also be modified by default, but unmodified is still an option. Edit-R tracrRNA (Cat # U-002005-xx) will carry the 3ʹ modification for nuclease resistance with no change in price. If you currently have some unmodified crRNA or tracrRNA (Cat# U-002000-xx) in your freezer, not to worry! Unless you are working with an application that requires nuclease stability (see Table 1), you can use any combination of modified or unmodified Edit-R crRNA and tracrRNA.

If you have any questions about using Edit-R CRISPR RNA in your lab, please contact our Scientific Support team.

Additional Resources
Publications with Dharmacon Edit-R CRISPR-Cas9 reagents - Recommended Reading
  • These publications demonstrate Edit-R CRISPR-Cas9 genome editing reagents for target gene knockout or precise knock-in in a variety of applications.
Edit-R predesigned crRNA
  • Guaranteed to edit your target! Algorithm-optimized crRNA for genome-wide coverage of human, mouse, or rat genes. Modifications for nuclease resistance improve DNA-free editing. Simply search for your gene!
CRISPR Design Tool
  • Place a custom order, or design and order your own crRNA or lentiviral sgRNA with our easy-to-use interface.