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In molecular biology, CRISPR-associated endonuclease in Prevotella and Francisella 1[a] or Cpf1 is a single RNA-guided endonuclease lacking a small trans-encoded RNA, a tracrRNA, and it utilizes a T-rich protospacer-adjacent motif[4] of 2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system,[5] also known as PAM.[6] It recognizes a T-rich PAM, TTTN, but on the 5' side of the guide. Cpf1 cleaves DNA via a staggered DNA double-stranded break.[7]

Genome editing[edit]

Out of 16 Cpf1-family proteins, scientists identified two candidate enzymes from Acidaminococcus and Lachnospiraceae, with efficient genome-editing activity in human cells.[8] Cpf1 was introduced with features that SpCas9 is lacking. Cpf1 requires only a 42-nt short CRISPR RNA (crRNA) to find its target, instead of the ~100-nt guide RNA for SpCas9, and it recognizes a protospacer-adjacent motif (PAM) that is 5′ instead of 3′ of the target site.[9]

Cas9 vs. Cpf1[edit]

Feature Cas9 Cpf1
Structure Two RNA required (Or 1 fusion transcript (crRNA+tracrRNA=gRNA) One RNA required
Cutting mechanism Blunt end cuts Staggered end cuts
Cutting site Proximal to recognition site Distal from recognition site
Target sites G-rich PAM T-rich PAM

See also[edit]


  1. ^ Pollard, T.D. (2007). Cell Biology. Philadelphia: Saunders. pp. 200–203. ISBN 978-1-4160-2255-8.
  2. ^ Latchman DS (Dec 1997). "Transcription factors: an overview". The International Journal of Biochemistry & Cell Biology. 29 (12): 1305–12. doi:10.1016/S1357-2725(97)00085-X. PMC 2002184. PMID 9570129.
  3. ^ Karin M (Feb 1990). "Too many transcription factors: positive and negative interactions". The New Biologist. 2 (2): 126–31. PMID 2128034.
  4. ^ http://www.cell.com/abstract/S0092-8674(15)01200-3 Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
  5. ^ Shah SA, Erdmann S, Mojica FJ, Garrett RA (2013). "Protospacer recognition motifs: mixed identities and functional diversity". RNA Biology. 10 (5): 891–899. doi:10.4161/rna.23764. PMC 3737346. PMID 23403393.
  6. ^ Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F (2015). "Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System". Cell. 163 (3): 759–771. doi:10.1016/j.cell.2015.09.038.
  7. ^ Using Cpf1 for CRISPR published by "Benchling" (2015)
  8. ^ Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells by Benjamin P Kleinstiver, Shengdar Q Tsai, Michelle S Prew, Nhu T Nguyen, Moira M Welch, Jose M Lopez, Zachary R McCaw, Martin J Aryee & J Keith Joung in "Nature Biotechnology" 34, 869–874 (2016) doi:10.1038/nbt.3620 Published online 27 June 2016
  9. ^ Showdown between Cas9 and Cpf1 by Nature Methods 13, 714 - (2016) doi:10.1038/nmeth.3979 Published online 30 August 2016
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