Conformational control of DNA target cleavage by CRISPR-Cas9

Nature

Volumn 527, Issue 7576, 2015, Pages 110-113

  Sternberg, Samuel H ^a   Lafrance, Benjamin ^a   Kaplan, Matias ^a,c   Doudna, Jennifer A ^a,b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c Stanford University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE STRANDED DNA; NUCLEASE; BACTERIAL PROTEIN; CRISPR ASSOCIATED PROTEIN; DNA; ENDONUCLEASE; GUIDE RNA;

BIOENGINEERING; CATALYSIS; DNA; ENZYME ACTIVITY; GENOME; IMMUNE SYSTEM; MOLECULAR ANALYSIS; RECOGNITION;

ALLOSTERISM; ARTICLE; BASE PAIRING; CONFORMATIONAL TRANSITION; CRISPR CAS SYSTEM; DNA CLEAVAGE; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME SPECIFICITY; FLUORESCENCE RESONANCE ENERGY TRANSFER; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DOUBLE STRANDED DNA BREAK; GENETIC ENGINEERING; METABOLISM; STREPTOCOCCUS PYOGENES;

ANIMALIA; BACTERIA (MICROORGANISMS);

ALLOSTERIC REGULATION; BACTERIAL PROTEINS; BASE PAIRING; BINDING SITES; CATALYTIC DOMAIN; CRISPR-ASSOCIATED PROTEINS; CRISPR-CAS SYSTEMS; DNA; DNA BREAKS, DOUBLE-STRANDED; DNA CLEAVAGE; ENDONUCLEASES; FLUORESCENCE RESONANCE ENERGY TRANSFER; GENETIC ENGINEERING; MODELS, MOLECULAR; RNA, GUIDE; STREPTOCOCCUS PYOGENES;

EID: 84946215320     PISSN: 00280836     EISSN: 14764687     Source Type: Journal    
DOI: 10.1038/nature15544     Document Type: Article

References (31)

1. van der Oost, J., Westra, E. R., Jackson, R. N. & Wiedenheft, B. Unravelling the structural and mechanistic basis of CRISPR-Cas systems. Nature Rev. Microbiol. 12, 479-492 (2014).
2. Barrangou, R. & Marraffini, L. A. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol. Cell 54, 234-244 (2014).
3. Jinek, M. et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337, 816-821 (2012).
4. Hsu, P. D., Lander, E. S. & Zhang, F. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278 (2014).
5. Doudna, J. A. & Charpentier, E. Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science 346, 1258096 (2014).
6. Sternberg, S. H. & Doudna, J. A. Expanding the biologist's toolkit with CRISPR-Cas9. Mol. Cell 58, 568-574 (2015).
7. Wu, X., Kriz, A. J. & Sharp, P. A. Target specificity of the CRISPR-Cas9 system. Quant. Biol. 2, 59-70 (2014).
8. Gori, J. L. et al. Delivery and specificity of CRISPR-Cas9 genome editing technologies for human gene therapy. Hum. Gene Ther. 26, 443-451 (2015).
9. Wu, X. et al. Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. Nature Biotechnol. 32, 670-676 (2014).
10. Tsai, S. Q. et al. GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases. Nature Biotechnol. 33, 187-197 (2015).
11. Ran, F. A. et al. In vivo genome editing using Staphylococcus aureus Cas9. Nature 520, 186-191 (2015).
12. Sternberg, S. H., Redding, S., Jinek, M., Greene, E. C. & Doudna, J. A. DNA interrogation by the CRISPR RNA-guided endonuclease Cas9. Nature 507, 62-67 (2014).
13. Jinek, M. et al. Structures of Cas9 endonucleases reveal RNA-mediated conformational activation. Science 343, 1247997 (2014).
14. Jiang, F., Zhou, K., Ma, L., Gressel, S. & Doudna, J. A. A Cas9-guide RNA complex preorganized for target DNA recognition. Science 348, 1477-1481 (2015).
15. Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935-949 (2014).
16. Anders, C., Niewoehner, O., Duerst, A. & Jinek, M. Structural basis of PAMdependent target DNA recognition by the Cas9 endonuclease. Nature 513, 569-573 (2014).
17. Hou, Z. et al. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc. Natl Acad. Sci. USA 110, 15644-15649 (2013).
18. Majumdar, Z. K., Hickerson, R., Noller, H. F. & Clegg, R. M. Measurements of internal distance changes of the 30S ribosome using FRET with multiple donor-acceptor pairs: quantitative spectroscopic methods. J. Mol. Biol. 351, 1123-1145 (2005).
19. Clegg, R. M. Fluorescence resonance energy transfer and nucleic acids. Methods Enzymol. 211, 353-388 (1992).
20. Wright, A. V. et al. Rational design of a split-Cas9 enzyme complex. Proc. Natl Acad. Sci. USA 112, 2984-2989 (2015).
21. Biertümpfel, C., Yang, W. & Suck, D. Crystal structure of T4 endonuclease VII resolving a Holliday junction. Nature 449, 616-620 (2007).
22. Szczelkun, M. D. et al. Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes. Proc. Natl Acad. Sci. USA 111, 9798-9803 (2014).
23. Cencic, R. et al. Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage. PLoS One 9, e109213 (2014).
24. Fu, Y., Sander, J. D., Reyon, D., Cascio, V. M. & Joung, J. K. Improving CRISPRCas nuclease specificity using truncated guide RNAs. Nature Biotechnol. 32, 279-284 (2014).
25. Gasiunas, G., Barrangou, R., Horvath, P. & Siksnys, V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc. Natl Acad. Sci. USA 109, E2579-E2586 (2012).
26. Nishimasu, H. et al. Crystal structure of Staphylococcus aureus Cas9. Cell 162, 1113-1126 (2015).
27. Rutkauskas, M. et al. Directional R-loop formation by the CRISPR-Cas surveillance complex cascade provides efficient off-target site rejection. Cell Reports 10, 1534-1543 (2015).
28. Briner, A. E. et al. Guide RNA functional modules direct Cas9 activity and orthogonality. Mol. Cell 56, 333-339 (2014).
29. Robert, X. & Gouet, P. Deciphering key features in protein structures with the new ENDscript server. Nucleic Acids Res. 42, W320-W324 (2014).
30. Sternberg, S. H., Haurwitz, R. E. & Doudna, J. A. Mechanism of substrate selection by a highly specific CRISPR endoribonuclease. RNA 18, 661-672 (2012).
31. Ashkenazy, H., Erez, E., Martz, E., Pupko, T. & Ben-Tal, N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res. 38, W529-W533 (2010).