Difference Between CRISPR and Cas9

The main difference between CRISPR and Cas9 is that CRISPR is a part of a bacterial defense system that consists of short palindromic sequences whereas Cas9 is an endonuclease produced by the CRISPR system that acts as molecular scissors. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats while Cas stands for CRISPR associated protein 9. The short palindromic repeats produce CRISPR RNA (crRNA) that is specific to the target sequence. Cas9 cuts the DNA sequence specified by the crRNA. 

CRISPR and Cas9 are two components of the CRISPR/Cas9 system, an important part of the immune system of bacteria, which defends against invading virus. At present,  CRISPR/Cas9 system is one of the faster, cheaper and more accurate genome editing tool with a wide range of applications. 

Key Areas Covered 

1. What is CRISPR
     – Definition, Structure, Genome Editing
2. What is Cas9
     – Definition, Facts, Genome Editing
3. What are the Similarities Between CRISPR and Cas9
     – Outline of Common Features
4. What is the Difference Between CRISPR and Cas9
     – Comparison of Key Differences

Key Terms

Cas9, CRISPR, CRISPR/Cas9, crRNA, Genome editing Difference Between CRISPR and Cas9 - Comparison Summary

What is CRISPR 

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a unit of the repeating sequence found in bacterial and archaeal genomes. It was first discovered in archaea by Francisco Mojica. The repeating sequences of CRISPR are interrupted by spacer sequences. These spacer sequences are the remnants from past invaders. Therefore, the system serves as the genetic memory for detecting and destroying the invading bacteriophage. The spacer sequences are transcribed into short RNA sequences called crRNAs, which guide the system to bind to the specific target sequences. Once bound to such sequence, an endonuclease encoded by the CRISPR system like Cas9 cuts the specified DNA by shutting it off.

Difference Between CRISPR and Cas9

Figure 1: CRISPR System

CRISPER/Cas9 is a naturally occurring genome editing system in bacteria. It is also used as a genome editing tool in the lab. Scientists artificially create small RNA molecules called guide RNA (gRNA) that bind to a target sequence of a genome. Once the target DNA sequence is snipped off by the activity of Cas9,  cellular mechanisms resynthesize the DNA. Or else, the removed part of DNA can be replaced with another DNA piece.  

What is Cas9 

Cas9 is an endonuclease that cut specific double-stranded DNA. It is encoded by the bacterial CRISPR system. The target DNA sequence is specified by the sycrRNA of the CRISPR system. By manipulating the target sequence, CRISPR system can be used to manipulate a particular DNA sequence in a genome. Therefore, CRISPR/Cas9 system is used to treat genetic disorders.

Main Difference - CRISPER and Cas9

Figure 2: Role of Cas in the CRISPR System

Another type of endonucleases that can work with CRISPR system is Cpf1.  

Similarities Between CRISPR and Cas9  

  • CRISPR and Cas9 are two components of the CRISPR/Cas9 system. 
  • Both play a vital role in the adaptive immune system of bacteria by identifying and snipping out viral DNA from the bacterial genome
  • CRISPR/Cas9 system is used as a genome editing tool. 

Difference Between CRISPR and Cas9  


CRISPR refers to a family of DNA sequences found in bacteria and archaea while Cas9 refers to an RNA-guided DNA endonuclease associated with the CRISPR

Stands for 

CRISPR stands clustered regularly interspaced short palindromic repeats while Cas stands for CRISPR associated protein. 


CRISPR is a cluster of short palindromic sequences while Cas9 is an endonuclease encoded within the CRISPR. 


CRISPR produces crRNA that specifically binds to a target sequence while Cas9 serves as a molecular scissor that cuts the DNA sequence specified by the crRNA. 


CRISPR is a cluster of short palindromic sequences found in the bacterial genome. It is important in preventing the invading bacteriophage. Cas9 is an endonuclease encoded by the CRISPR system. It cuts off the nucleotide sequence specified by the crRNA. The crRNA is produced by the transcription of the CRISPR array. The main difference between CRISPR and Cas9 is the function of each component in the CRISPR system. 


1. “What Is CRISPR-Cas9?” Facts, The Public Engagement Team at the Wellcome Genome Campus, 19 Dec. 2016, Available Here

Image Courtesy:

1. “crRNA-Cas9” By marius walter – Own work (CC BY-SA 4.0) via Commons Wikimedia
2. “Crispr” By James atmos – Own work (CC BY-SA 3.0) via Commons Wikimedia

About the Author: Lakna

Lakna, a graduate in Molecular Biology and Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things. She has a keen interest in writing articles regarding science.

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