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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 of 2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system, also known as PAM. 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.
Out of 16 Cpf1-family proteins, scientists identified two candidate enzymes from Acidaminococcus and Lachnospiraceae, with efficient genome-editing activity in human cells. 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.
Cas9 vs. 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|
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- Using Cpf1 for CRISPR published by "Benchling" (2015)
- 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
- Showdown between Cas9 and Cpf1 by Nature Methods 13, 714 - (2016) doi:10.1038/nmeth.3979 Published online 30 August 2016
- The centromere is the part of a chromosome that links sister chromatids or a dyad. During mitosis, spindle fibers attach to the centromere via the kinetochore.
- A transcription factor or promoter factor is a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence.