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Clustered Regularly Interspaced Short Palindromic Repeats

CRISPR is a natural DNA sequence in bacteria (such as E. coli) that helps to defend against viruses.

CRISPR in Bacterial Defences

  • Bacteriophage inserts its nucleic acids (DNA or RNA) into the bacterium.
  • The bacterium takes a portion of the viral nucleic acid and stores it in its own genome (in areas called spacers).
  • When the same virus attacks again, the bacterium transcribes the stored viral DNA and forms a complex structure with an endonuclease called Cas-9.
  • The transcribed strand is complementary to the viral nucleic acids, and helps Cas9 to recognise the viral sequence and cut it.


CRISPR-Cas9 genome editing includes two key components: a single-guide RNA (gRNA) and a CRISPR-associated endonuclease (Cas).

  • Cas9: It is an endonuclease enzyme which functions as a pair of molecular scissors to cut the target DNA sequence.
  • sgRNA: Single-guide RNA is the combination of tracrRNA and crRNA.
  • crRNA contains two main parts, the spacer sequence that directs the complex to the target DNA and a region that binds to tracrRNA. When tracrRNA binds to crRNA, a functional guide RNA (gRNA) is formed for Cas9 to recognize.

crRNA (CRISPR RNA) consists of a spacer and a repeat, which are transcribed and cleaved to produce the imprint for Cas9 to cut DNA. tracrRNA (trans-activating RNA) is complementary to crRNA which allows the two molecules to form the final structure of the gRNA (guide RNA) complex. tracrRNA binds tightly with Cas9 to build the CRISPR-Cas9 complex.