Build Your CRISPR Vocabulary

By Emily P. Bentley

Emily P. Bentley July 02, 2024

CRISPR is a sleek acronym for a real mouthful of a phrase: Clustered Regularly Interspaced Short Palindromic Repeats. That contrast of simplicity and complexity is reflected in the biology, too. CRISPR is an elegant bacterial immune system and an efficient gene editing tool… but boy does it have a lot of parts!

If you’re still a bit confused by CRISPR acronyms, this post is for you. We’ll cover the common terminology for the proteins, DNA, and RNA used in CRISPR.

Figure 1: Overview of the parts of CRISPR. The bacterial chromosome encodes a tracrRNA (in some systems including Cas9), Cas proteins, and a CRISPR array. The CRISPR array is composed of identical repeat sequences and variable spacer sequences. The array is transcribed and processed into crRNAs, each including one repeat and one spacer. In bacteria, these crRNAs are bound by Cas proteins (Cas9 shown here). The repeat sequence base pairs with the tracrRNA, and the spacer sequence is used to target complementary DNA sequences. In laboratory settings, an sgRNA includes the crRNA and tracrRNA sequences in a “single-guide RNA” that performs both functions. Cas9 cuts both the target and nontarget DNA strands upstream of the PAM site found in the nontarget strand.

Protein

Cas: Different CRISPR systems involve different proteins, but many of them are called Cas, short for “CRISPR-associated.” The most famous of these proteins is Cas9 nuclease, but there are many other Cas proteins as well, both natural and engineered. What these proteins all have in common is the ability to use an RNA guide to target other nucleic acids—usually DNA—to cut, nick, or bind.

DNA

CRISPR array: The section of the bacterial chromosome that stores a genetic record of previously encountered foreign nucleic acids. The unusual sequence of these arrays, with alternating spacers and repeats, was the original impetus for studying CRISPR.

Spacers: Copies of foreign nucleic acid sequences in the CRISPR array that will become guides for future targeted degradation. Before integration into the array, these sequences are called protospacers.

Repeats: Bacterial DNA that appears between each spacer in the CRISPR array, distinguishing the foreign sequences and keeping the array organized.

Target strand: The strand of foreign DNA that Cas proteins recognize using an RNA guide.

Non-target strand: The paired strand of foreign DNA cut by Cas9, whose sequence is not checked. Assuming full complementarity, its sequence matches the guide sequence.

PAM: The “protospacer-adjacent motif” present in the non-target strand of DNA to be cut, which varies between CRISPR systems. Cas proteins won’t cut DNA that doesn’t have their specific PAM, which is how they avoid chopping up their own CRISPR arrays. On the other hand, viruses can evolve to evade CRISPR by mutating these sequences.

Pro tip! Various labs have created Cas9 enzymes with looser PAM requirements, which are available from Addgene!

RNA

crRNA: “CRISPR RNAs” are transcribed from the CRISPR array and include a spacer and a repeat sequence. The spacer sequence is the RNA guide, like a wanted poster that Cas9 uses to track down its suspect—the target DNA.

tracrRNA: A “trans-activating CRISPR RNA” base pairs to the repeat section of the crRNA, forming the repeat:antirepeat duplex. tracrRNAs also contain multiple stem loops that are recognized by the Cas9 protein from the appropriate species. Some Cas proteins, like LbCas12a or AsCas12a, do not require a tracrRNA.

sgRNA: “Single-guide RNAs” were invented by synthetic biologists. An sgRNA combines a crRNA and a tracrRNA into a single strand that folds back on itself, simplifying the CRISPR-Cas9 system for laboratory applications. At Addgene, we sometimes refer to the programmable guide sequence as the spacer and the remaining sequence as the scaffold.

gRNA: "Guide RNA" is a general term referring to the RNAs used by Cas proteins, either a crRNA + tracrRNA pair or an sgRNA. It is often used interchangeably with the term sgRNA.

Seed sequence: The 8-10 bases on the 3’ end of an RNA guide (either crRNA or sgRNA). Cas9 requires perfect complementarity in this region between the guide and target in order to cut DNA, whereas some mismatches can be tolerated outside this region.