The CRISPR-Cpf1 nuclease is the best alternative to the commonly used Cas9 for genome editing. Cpf1 recognizes a protospacer adjacent motif (PAM) sequence of TTTV, which differs from the Cas9 PAM sequence, NGG. Having Cpf1 as a second option increases the likelihood of editing as close as possible to your desired target site. In this presentation, Dr Rolf Turk introduces the optimized Alt-R™ CRISPR-Cpf1 System and explains how it can be used as a powerful new tool for your genome editing research. Dr Turk presents the basics of the system, as well as protocols for getting started in genome editing.
4. Cas9 genome editing
• RNA-guided endonuclease
• PAM site (NGG)
• crRNA and tracrRNA
• Blunt-ended cut sites
4
5. Cpf1 genome editing
• RNA-guided endonuclease
• Cpf1: CRISPR from Prevotella and Francisella 1
• Class II, type V
• Cpf1 editing in mammalian cells
• Acidaminococcus sp. BV3L6
• Lachnospiraceae bacterium ND2006
• Single guide RNA (crRNA, 41–44 nt)
• Double-stranded break with staggered ends
• PAM site is thymidine-rich
• Preferentially uses TTTV
5
Zetsche B, Gootenberg JS, et al. (2015) Cpf1 is a single RNA-guided
Endonuclease of a class 2 CRISPR-Cas system. Cell, 163:759–771.
6. Cpf1 structure and function
66
Yamano T, Nishimasu H, et al. (2016) Crystal structure of cpf1 in
complex with guide RNA and target DNA. Cell, 165(4):949–962.
8. Low off-target editing with Cpf1
8
Kim D, Kim J, et al. (2016) Genome-wide analysis reveals specificities of
Cpf1 endonucleases in human cells. Nat Biotech, 34(8):863–868.
9. Lower off-target effects with Cpf1 RNP vs. plasmid
9
Kim D, Kim J, et al. (2016) Genome-wide analysis reveals specificities of
cpf1 endonucleases in human cells. Nat Biotech, 34(8):863–868.
28. Positive controls for genome editing using the
Alt-R™ CRISPR-Cpf1 System
28
0
10
20
30
40
50
60
70
80
90
100
Hs - HEK 293 Mm - Hepa1-6 Rn - RAT2
T7EItotaleditingefficiency(%)
5 µM RNP—3 µM Enhancer
Amaxa® Nucleofector® System
29. Comparison of genome editing using SpCas9 vs. AsCpf1
29
* Molecular weight of
Alt-R™ Nuclease
† N = any base
V = A, C, or GTTTV
30. Alt-R™ CRISPR-Cpf1 System
Core components:
• Alt-R CRISPR-Cpf1 crRNA
• Alt-R A.s. Cpf1 Nuclease 2 NLS
• Alt-R Cpf1 Electroporation Enhancer
Sequences for positive and negative crRNA controls for human, mouse, and
rat are available at www.idtdna.com/CRISPR-Cpf1.
Also see our highly effective Alt-R CRISPR-Cas9 System at
www.idtdna.com/CRISPR-Cas9.
30
32. Questions?
TALK TO A PERSON.
Our experts are available for consultation.
“The people
at @idtdna are
awesome. A+ for
customer service.”
Nikolai Braun
Contact us by web chat, email, or phone.
Find local contact details at: www.idtdna.com
“Best tech support
ever, @idtdna!”
Lauren Sakowski
32