Synthetic Biology
Support and Educational Content

CRISPR and Cas9 for flexible genome editing

Note: This article was originally published in 2013. It contains useful general information about CRISPR and genome editing. However, it does not reflect the development of CRISPR tools such as the IDT Alt-R™ CRISPR-Cas9 and Alt-R CRISPR-Cpf1 Systems, which provide improved efficacy and ease of use, reduced off-target effects, and a quicker route to publication. Learn more about the Alt-R CRISPR products.

CRISPR RNAs make targeted gene editing easy

CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats) are sequences found naturally in bacteria and archaea that are part of an adaptive defense mechanism. CRISPRs, in conjunction with CRISPR associated (Cas) proteins, are able to recognize and cleave complementary DNA sequences, protecting the cells from foreign sequences [1].

Following the discovery of CRISPRs, it was shown that the S. pyogenes Cas9 nuclease could be directed to cleave specific DNA sequences when used in conjunction with a small CRISPR associated RNA (crRNA) and a separate transactivating RNA (tracrRNA). The crRNA contains a target-specific protospacer of 20–40 bases, and a repeat motif that is recognized and bound by the tracrRNA. The crRNA is processed so that the protospacer recognizes 20 bases of the target sequence, which must also contain a protospacer adjacent motif (PAM) [2]. The PAM sequence is not included in the guide RNA sequence, but is found next to to the target sequence on the non-target strand. The GG bases of the PAM site are recognized by a major groove interaction with Cas9 [2, 3]. When the crRNA and tracrRNA come together, they direct Cas9 to DNA sequences that are complementary to the protospacer, and Cas9 creates a double-stranded break (DSB) [2].

Figure 1 shows how the CRISPR/Cas9 system can be used to create a DSB at a sequence-specific target site. More recently, it has been shown that Cas9 can be targeted to desired gene locations in a variety of organisms, from E. coli to humans, with a chimeric single-guide RNA (sgRNA) that contains both the crRNA and tracrRNA elements [4,5].

 Figure 1.  Examples of CRISPR/Cas9 designs using gBlocks® Gene Fragments. The tracrRNA and crRNA required to guide Cas9 to a target sequence can be combined into a chimeric sgRNA (yellow). The sgRNA, including a U6 promoter, can be ordered as a single gBlocks Gene Fragment. The ~4.1 kb, S. pyogenes Cas9 sequence can be codon-optimized and assembled from 6–7 gBlocks Gene Fragments, depending on design (green). Single plasmid, plasmid-Cas9 + gBlocks sgRNA, and in vitro RNA translation are some of the methods used to introduce CRISPR/Cas9 elements into cells. Cas9 creates a double-stranded break (DSB) 3 bases from the NGG sequence that makes up the PAM site of S. pyogenes. Note that the PAM site is not included in the sgRNA, but must be present in the target. S. pyogenes Cas9 recognizes the two GG bases of the PAM sequence, on the non-target strand, by means of a major groove interaction [3]. DSB repair will produce a deletion by non-homologous end joining (NHEJ) in most cases. Mutations or insertions can be created by homologous repair (HR), by adding a donor sequence that has homologous overlaps to the DSB site—typically 100–1000 bp of overlap is used.

In most eukaryotic cells, the DSB created by Cas9 is repaired by non-homologous end joining (NHEJ), which results in small deletions or insertions that disrupt genes where the break occurred. This mechanism can be used to achieve gene silencing at the genome level. Alternatively, in some cells, and in presence of donor DNA that contains homologous overlaps with DNA on either side of the DSB, endogenous DNA repair mechanisms can integrate “foreign” DNA into the cell’s genome by homologous recombination. The ability to introduce foreign sequences at specific genomic loci can be used to obtain targeted changes to genes or add genes or molecular pathways to genomes by incorporating synthetic sequences [5,6].

Most importantly, the CRISPR/Cas9 system is relatively easy to implement compared to other editing approaches as a means to create either targeted gene disruptions in a variety of organisms and cell types, or to insert sequence changes to targeted genomic regions [4].

Improving the accuracy of Cas9

One of the reported limitations of the CRISPR/Cas9 system is that it can also recognize sequences with up to 5 mismatched bases, especially at the 5′ end of the target sequence. This means that off-target effects may occur at a rate higher than other methods of genome editing [6,7,8].

A potential solution to increase specificity of CRISPR induced changes has recently been demonstrated independently by the labs of Dr George Church at Harvard University and Dr Feng Zhang at Massachusetts Institute of Technology. By altering the amino acid sequence at 1 of the 2 catalytic sites within Cas9, they have created Cas9 mutants that nick only 1 strand of DNA per sgRNA target. Using this Cas9 “nickase”, DSBs can only be made by creating 2 targeting CRISPR complexes with 2 independent sgRNAs. Each sgRNA is designed to recognize a sequence in close proximity to the other, one targeting the sense and the other the antisense strand of the desired genome location. The dual specificity of this method is thought to greatly reduce the off-target effects [9,10]. Other yet to be identified Cas9 improvements, or enzymes from sources other than S. pyogenes may further improve the overall efficacy and/or specificity of the system.

A Cpf1-based genome editing system is also available for use with AT-rich sequence situations.

Advancing CRISPR research with gBlocks® Gene Fragments

Several research publications describe how scientists have taken advantage of the sequence and application flexibility of IDT gBlocks Gene Fragments to explore CRISPR and Cas9 function. The custom-made, synthetic gBlocks Gene Fragments have been used to create codon-optimized versions of Cas9, constructed for efficient expression in various host cells [5,6,11]. It is also simple to make variants, such as the Cas9 nickases described by the Church and Zhang labs, or to add motifs like nuclear localization signals that direct translated Cas9 enzyme into the nucleus for genome targeting.

Along with the various Cas9 constructs, chimeric sgRNAs also need to be generated. Typical sgRNA designs are ~150 bp in length, and a complete design that includes a human U6 promoter can be made with ~450 bp of DNA sequence, which means these can be easily ordered as a single gBlocks Gene Fragment, making them ideal for generating synthetic sgRNAs quickly and inexpensively [5,9,11]. The sgRNA constructs and promoter can then be cloned into an expression vector, introduced directly into cells, or in vitro transcribed into RNA. Figure 1 illustrates some popular CRISPR/Cas9 designs that can be generated using gBlocks Gene Fragments.

Including the Cas9 and sgRNA on the same plasmid simplifies the experimental procedure, while keeping the sgRNA and Cas9 separate has the advantage of allowing tight dosage control of these individual components. Choosing the correct construction method for your experiments will depend on the specific aims of your research design. In addition to controlling dosage, the duration of the Cas9 and sgRNA can be regulated by using in vitro transcribed RNA for transfer into cells. While DNA is relatively stable when transfected or injected into cells, transcribed RNA is quickly degraded, meaning that the CRISPR/Cas9 elements will be short-lived. Their short lifespan ensures that the artificial constructs will not be incorporated into genomic DNA and passed on to daughter cells [12].

Additional research demonstrating CRISPR/Cas9 designs can be found by clicking on the Citations link at

As an alternative to assembly of your own reagents, IDT provides a kit, the Alt-R CRISPR-Cas9 System, that includes all of the components needed for successful genome editing. See the Product focus sidebar, below, for more information.


  1. Makarova KS, Grishin NV, et al. (2006) A putative RNA-interference-based immune system in prokaryotes: computational analysis of the predicted enzymatic machinery, functional analogies with eukaryotic RNAi, and hypothetical mechanisms of action. Biol Direct, 1(7).
  2. Jinek M, Chylinski K, et al. (2012) A programmable dual-RNA–guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096): 816–821.
  3. Anders C, Niewoehner O, et al. (2014) Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease. Nature. 513(7519):569–573.
  4. Mussolino C, Cathomen T. (2013) RNA guides genome engineering. Nat Biotechnol, 31(3):208–209.
  5. Cong L, Ran FA, et al. (2013) Multiplex genome engineering using CRISPR/Cas systems. Science, 339(6121):819–23.
  6. Mali P, Yang L, et al. (2013) RNA-guided human genome engineering via Cas9. Science, 336(6121):823–826.
  7. Pattanayak V, Lin S, et al. (2013) High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol, 31(9):839–843.
  8. Hsu PD, Scott DA, et al (2013) DNA targeting specificity of RNA-guided Cas9 nucleases. Nat Biotechnol, 31(9):827–832.
  9. Mali P, Aach J, et al. (2013) CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering. Nat Biotechnol, 31(9):833–838.
  10. Ran FA, Hsu PD, et al. (2013) Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell, 154(6):1380–1389.
  11. Dickinson DJ, Ward JD, et al. (2013) Engineering the Caenorhabditis elegansgenome using Cas9-triggered homologous recombination. Nat Methods, 10(10):1028–1034.
  12. Yang H, Haoyi W, et al. (2013) One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell, 6(154):1370–1379.

Product Focus—dsDNA fragments and genome editing reagents

gBlocks® Gene Fragments are double-stranded, sequence-verified genomic blocks 125 to 2000 bp in length that ship quickly for affordable and easy gene construction or modification. gBlocks Gene Fragments are synthesized using the same industry-leading, high-fidelity synthesis chemistry developed by IDT for Ultramer® oligonucleotides, and are sequence verified prior to shipping.

Learn more about gBlocks Gene Fragments.

Alt-R CRISPR-Cas9 System includes all the reagents needed for successful genome editing. Based on the natural S. pyogenes CRISPR-Cas9 system, the Alt-R CRISPR-Cas9 System offers numerous advantages over alternative methods:

  • Higher on-target potency than other CRISPR systems
  • Precision control with delivery of Cas9 ribonucleoprotein (RNP)
  • Efficient delivery of the RNP with lipofection or electroporation
  • No toxicity or innate immune response activation, in contrast to in vitro transcribed Cas9 mRNA and sgRNAs

Learn more about the Alt-R CRISPR-Cas9 System.

Alt-R CRISPR-Cpf1 System allows targeting of AT-rich regions, only requires a crRNA bound to the Cpf1 nuclease to form an active ribonucleoprotein (RNP), and produces a staggered cut with a 5′ overhang. The Cpf1 protospacer adjacent motif (PAM: TTTN) allows for new CRISPR target sites that are not available with the CRISPR-Cas9 System. These reagents:

  • Enable genome editing in organisms with AT-rich genomes
  • Allow interrogation of additional genomic regions compared to Cas9
  • Require simply complexing the crRNA with the Cpf1 protein—no tracrRNA needed
  • Permit efficient delivery of the RNP into cells by electroporation

Learn more about the Alt-R CRISPR-Cpf1 System.

Additional CRISPR support tools extend the ease-of-use and performance of the Alt-R system through options for fluorescent visualization, enhanced nuclease transfection, and genome editing detection.

Find out more about IDT’s entire line of CRISPR products.

Related reading

Improve your genome editing with the Alt-R™ S.p. Cas9 Nuclease 3NLS and modified crRNAs—Product Spotlight: Methods for CRISPR-Cas9 genome editing are diverse, but not all of them perform equally well. Learn about the Alt-R™ S.p. Cas9 Nuclease 3NLS that, when used in combination the optimized Alt-R CRISPR crRNA and tracrRNA, provides a highly effective editing solution that is also easy to use.

6 pieces of data that will change how you set up your CRISPR-Cas9 experiments—To improve the efficiency of CRISPR-Cas9 genome editing, IDT scientists evaluated several factors—Cas9 delivery, crRNA and tracrRNA length, which gRNA formats provide the most efficient on-target editing and elicit the least toxicity, the importance of protospacer size and site selection—that influence how we design and perform genome editing experiments. Review the data and results for 6 important factors that were addressed. These experimental findings resulted in a set of potent CRISPR tools that are now offered as the Alt-R™ CRISPR-Cas9 System.

CRISPR guide RNA format affects genome editing outcomes—Learn how the use of different formats for CRISPR guide RNAs can lead to different genome editing outcomes. The optimized, short RNA oligos that make up the crRNA and tracrRNA components of the Alt-R™ CRISPR-Cas9 System outperform other CRISPR guide RNA formats. In addition to their improved editing efficiency, these short RNA oligos are unable to incorporate into the target genome, avoiding a common problem associated with DNA constructs, to provide cleaner editing results.

CRISPR genome editing: 5 considerations for target site selection—Read how your genome editing experiments can be improved with 5 quick tips for target selection and with reagents from the Alt-R™ CRISPR-Cas9 System.

Review other DECODED Online newsletter articles on CRISPR in genome editing applications or on gBlocks Gene Fragment use in synthetic biology applications.

You can also browse our DECODED Online newsletter for additional application reviews, lab tips, and citation summaries to facilitate your research.

Author: Hans Packer, PhD, is a scientific writer at IDT.

© 2013, 2016, 2017 Integrated DNA Technologies. All rights reserved. Trademarks contained herein are the property of Integrated DNA Technologies, Inc. or their respective owners. For specific trademark and licensing information, see

gBlocks® Gene Fragments

Double-stranded DNA up to 3,000 kb—great for easy gene construction, CRISPR genome editing, and more.

Learn how ≫

Related Articles

CRISPR and Cas9 for Flexible Genome Editing

Applications of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) for targeted gene editing or removal of sequences.

Read more ≫

Cloning Strategies Part 3: Blunt-End Cloning

Tips and tricks for blunt-end cloning.

Read more ≫

Building Biological Factories for Renewable and Sustainable Products

Amyris uses genetic engineering and screening technologies to design microorganisms that convert plant-sourced sugars into target molecules, including pharmaceuticals, biofuels, polymers, flavors, and fragrances.

Read more ≫

iGEM Students Engineer Biological Tools for a Better World

iGEM teams show how non-standard natural and synthetic amino acids can be used in 1) peptide synthesis, and 2) disease monitoring and treatment. Both projects make use of gBlocks® Gene Fragments to speed construct assembly.

Read more ≫

Creating a Synthetic Immune System for Optimized Immune Profiling

A high-throughput method for sequencing and quantification of rearranged antigen receptors on T- and B-cells using gBlocks Gene Fragments to create a “gold standard synthetic immune system.”

Read more ≫