Abstract
CRISPR-associated nuclease (Cas) has been widely applied to modify the genomes of various cell types. As RNA-guided endonucleases, Cas enzymes can target different genomic sequences simply by changing the guide sequence of the CRISPR RNA (crRNA) or single guide RNA (sgRNA). Recent studies have demonstrated that DNA-RNA chimeric crRNA or sgRNA can efficiently guide the Cas9 protein for genome editing with reduced off-target effects. This chapter aims to describe a procedure for using chimeric RNA to modify the genomes of mammalian cells.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Jinek M, Chylinski K, Fonfara I et al (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821
Jinek M, East A, Cheng A et al (2013) RNA-programmed genome editing in human cells. elife 2:e00471
Mali P, Yang L, Esvelt KM et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826
Cong L, Ran FA, Cox D et al (2013) Multiplex genome engineering using CRISPR/Cas systems. Science 339:819–823
Cox DB, Platt RJ, Zhang F (2015) Therapeutic genome editing: prospects and challenges. Nat Methods 21:121–131
Zetsche B, Gootenberg JS, Abudayyeh OO et al (2015) Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163:759–771
Yin H, Kauffman KJ, Anderson DG (2017) Delivery technologies for genome editing. Nat Rev Drug Discov 16:387–399
Slaymaker IM, Gao LY, Zetsche B et al (2016) Rationally engineered Cas9 nucleases with improved specificity. Science 351:84–88
Kleinstiver BP, Pattanayak V, Prew MS et al (2016) High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Nature 529:490–495
Chen JS, Dagdas YS, Kleinstiver BP et al (2017) Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature 550:407–410
Yin H, Song CQ, Suresh S et al (2018) Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Nat Chem Biol 14:311–316
Hendel A, Bak RO, Clark JT et al (2015) Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells. Nat Biotechnol 33:985–989
Yin H, Song CQ, Suresh S et al (2017) Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Nat Biotechnol 35:1179–1187
Koo T, Lee J, Kim JS (2015) Measuring and reducing off-target activities of programmable nucleases including CRISPR-Cas9. Mol Cells 38:475–481
Kim S, Koo T, Jee HG et al (2018) CRISPR RNAs trigger innate immune responses in human cells. Genome Res 28:367–373
Wienert B, Shin J, Zelin E et al (2018) In vitro-transcribed guide RNAs trigger an innate immune response via the RIG-I pathway. PLoS Biol 16:e2005840
Mu W, Tang N, Cheng C et al (2019) In vitro transcribed sgRNA causes cell death by inducing interferon release. Protein Cell 10(6):461–465
Jakimo N, Chatterjee P, Jacobson JM (2017) Chimeric CRISPR guides enhance Cas9 target specificity. bioRxiv:147686
Rueda FO, Bista M, Newton MD et al (2017) Mapping the sugar dependency for rational generation of a DNA-RNA hybrid-guided Cas9 endonuclease. Nat Commun 8:1610
Schofield A, O’Reilly D, Malek-Adamian E et al (2018) Extensive CRISPR RNA modification reveals chemical compatibility and structure-activity relationships for Cas9 biochemical activity. Nucleic Acids Res 47:546–558
Jiang F, Zhou K, Ma L et al (2015) A Cas9–guide RNA complex preorganized for target DNA recognition. Science 348:1477–1481
Nishimasu H, Ran FA, Hsu PD et al (2014) Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156:935–949
Ryan DE, Taussig D, Steinfeld I et al (2018) Improving CRISPR-Cas specificity with chemical modifications in single-guide RNAs. Nucleic Acids Res 46:792–803
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Lu, S., Zhang, Y., Yin, H. (2021). Chimeric DNA–RNA Guide RNA Designs. In: Fulga, T.A., Knapp, D.J.H.F., Ferry, Q.R.V. (eds) CRISPR Guide RNA Design. Methods in Molecular Biology, vol 2162. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0687-2_6
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0687-2_6
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0686-5
Online ISBN: 978-1-0716-0687-2
eBook Packages: Springer Protocols