A quantitative model for the dynamics of target recognition and off-target rejection by the CRISPR-Cas Cascade complex
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DOI: 10.1038/s41467-022-35116-5
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- Benjamin P. Kleinstiver & Vikram Pattanayak & Michelle S. Prew & Shengdar Q. Tsai & Nhu T. Nguyen & Zongli Zheng & J. Keith Joung, 2016. "High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects," Nature, Nature, vol. 529(7587), pages 490-495, January.
- Behrouz Eslami-Mossallam & Misha Klein & Constantijn V. D. Smagt & Koen V. D. Sanden & Stephen K. Jones & John A. Hawkins & Ilya J. Finkelstein & Martin Depken, 2022. "A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
- Robert R. F. Machinek & Thomas E. Ouldridge & Natalie E. C. Haley & Jonathan Bath & Andrew J. Turberfield, 2014. "Programmable energy landscapes for kinetic control of DNA strand displacement," Nature Communications, Nature, vol. 5(1), pages 1-9, December.
- Samuel H. Sternberg & Benjamin LaFrance & Matias Kaplan & Jennifer A. Doudna, 2015. "Conformational control of DNA target cleavage by CRISPR–Cas9," Nature, Nature, vol. 527(7576), pages 110-113, November.
- Janice S. Chen & Yavuz S. Dagdas & Benjamin P. Kleinstiver & Moira M. Welch & Alexander A. Sousa & Lucas B. Harrington & Samuel H. Sternberg & J. Keith Joung & Ahmet Yildiz & Jennifer A. Doudna, 2017. "Enhanced proofreading governs CRISPR–Cas9 targeting accuracy," Nature, Nature, vol. 550(7676), pages 407-410, October.
- Blake Wiedenheft & Gabriel C. Lander & Kaihong Zhou & Matthijs M. Jore & Stan J. J. Brouns & John van der Oost & Jennifer A. Doudna & Eva Nogales, 2011. "Structures of the RNA-guided surveillance complex from a bacterial immune system," Nature, Nature, vol. 477(7365), pages 486-489, September.
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- Pierre Aldag & Marius Rutkauskas & Julene Madariaga-Marcos & Inga Songailiene & Tomas Sinkunas & Felix Kemmerich & Dominik Kauert & Virginijus Siksnys & Ralf Seidel, 2023. "Dynamic interplay between target search and recognition for a Type I CRISPR-Cas system," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
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