4zt9 Citations

STRUCTURAL BIOLOGY. A Cas9-guide RNA complex preorganized for target DNA recognition.

Science 348 1477-81 (2015)
Cited: 273 times
EuropePMC logo PMID: 26113724

Abstract

Bacterial adaptive immunity uses CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR transcripts for foreign DNA degradation. In type II CRISPR-Cas systems, activation of Cas9 endonuclease for DNA recognition upon guide RNA binding occurs by an unknown mechanism. Crystal structures of Cas9 bound to single-guide RNA reveal a conformation distinct from both the apo and DNA-bound states, in which the 10-nucleotide RNA "seed" sequence required for initial DNA interrogation is preordered in an A-form conformation. This segment of the guide RNA is essential for Cas9 to form a DNA recognition-competent structure that is poised to engage double-stranded DNA target sequences. We construe this as convergent evolution of a "seed" mechanism reminiscent of that used by Argonaute proteins during RNA interference in eukaryotes.

Articles - 4zt9 mentioned but not cited (5)

  1. Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. Ma E, Harrington LB, O'Connell MR, Zhou K, Doudna JA. Mol Cell 60 398-407 (2015)
  2. Structure and Dynamics of Cas9 HNH Domain Catalytic State. Zuo Z, Liu J. Sci Rep 7 17271 (2017)
  3. Protein engineering through tandem transamidation. Thompson RE, Stevens AJ, Muir TW. Nat Chem 11 737-743 (2019)
  4. Nucleic Acid-Dependent Conformational Changes in CRISPR-Cas9 Revealed by Site-Directed Spin Labeling. Vazquez Reyes C, Tangprasertchai NS, Yogesha SD, Nguyen RH, Zhang X, Rajan R, Qin PZ. Cell Biochem Biophys 75 203-210 (2017)
  5. Identification and Analysis of Small Molecule Inhibitors of CRISPR-Cas9 in Human Cells. Yang Y, Li D, Wan F, Chen B, Wu G, Li F, Ren Y, Liang P, Wan J, Songyang Z. Cells 11 3574 (2022)


Reviews citing this publication (86)

  1. Genome editing with CRISPR-Cas nucleases, base editors, transposases and prime editors. Anzalone AV, Koblan LW, Liu DR. Nat Biotechnol 38 824-844 (2020)
  2. CRISPR-Cas9 Structures and Mechanisms. Jiang F, Doudna JA. Annu Rev Biophys 46 505-529 (2017)
  3. Biology and Applications of CRISPR Systems: Harnessing Nature's Toolbox for Genome Engineering. Wright AV, Nuñez JK, Doudna JA. Cell 164 29-44 (2016)
  4. CRISPR/Cas9 in Genome Editing and Beyond. Wang H, La Russa M, Qi LS. Annu Rev Biochem 85 227-264 (2016)
  5. Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases. Tsai SQ, Joung JK. Nat Rev Genet 17 300-312 (2016)
  6. CRISPR/Cas9 Platforms for Genome Editing in Plants: Developments and Applications. Ma X, Zhu Q, Chen Y, Liu YG. Mol Plant 9 961-974 (2016)
  7. Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity. Tycko J, Myer VE, Hsu PD. Mol Cell 63 355-370 (2016)
  8. RNA-based recognition and targeting: sowing the seeds of specificity. Gorski SA, Vogel J, Doudna JA. Nat Rev Mol Cell Biol 18 215-228 (2017)
  9. The New State of the Art: Cas9 for Gene Activation and Repression. La Russa MF, Qi LS. Mol Cell Biol 35 3800-3809 (2015)
  10. A CRISPR toolbox to study virus-host interactions. Puschnik AS, Majzoub K, Ooi YS, Carette JE. Nat Rev Microbiol 15 351-364 (2017)
  11. The Revolution Continues: Newly Discovered Systems Expand the CRISPR-Cas Toolkit. Murugan K, Babu K, Sundaresan R, Rajan R, Sashital DG. Mol Cell 68 15-25 (2017)
  12. Cas9 versus Cas12a/Cpf1: Structure-function comparisons and implications for genome editing. Swarts DC, Jinek M. Wiley Interdiscip Rev RNA 9 e1481 (2018)
  13. Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery. Bolukbasi MF, Gupta A, Wolfe SA. Nat Methods 13 41-50 (2016)
  14. CRISPR-Cas12a: Functional overview and applications. Paul B, Montoya G. Biomed J 43 8-17 (2020)
  15. Current and future prospects for CRISPR-based tools in bacteria. Luo ML, Leenay RT, Beisel CL. Biotechnol Bioeng 113 930-943 (2016)
  16. Type II-C CRISPR-Cas9 Biology, Mechanism, and Application. Mir A, Edraki A, Lee J, Sontheimer EJ. ACS Chem Biol 13 357-365 (2018)
  17. CRISPR-Cas orthologues and variants: optimizing the repertoire, specificity and delivery of genome engineering tools. Cebrian-Serrano A, Davies B. Mamm Genome 28 247-261 (2017)
  18. CRISPR/cas systems redefine nucleic acid detection: Principles and methods. Wang M, Zhang R, Li J. Biosens Bioelectron 165 112430 (2020)
  19. Imaging Specific Genomic DNA in Living Cells. Chen B, Guan J, Huang B. Annu Rev Biophys 45 1-23 (2016)
  20. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. Synth Syst Biotechnol 3 135-149 (2018)
  21. Engineering Nanoparticles for Targeted Delivery of Nucleic Acid Therapeutics in Tumor. Xiao Y, Shi K, Qu Y, Chu B, Qian Z. Mol Ther Methods Clin Dev 12 1-18 (2019)
  22. Lessons from Enzyme Kinetics Reveal Specificity Principles for RNA-Guided Nucleases in RNA Interference and CRISPR-Based Genome Editing. Bisaria N, Jarmoskaite I, Herschlag D. Cell Syst 4 21-29 (2017)
  23. Diversity of CRISPR-Cas immune systems and molecular machines. Barrangou R. Genome Biol 16 247 (2015)
  24. Structures and mechanisms of CRISPR RNA-guided effector nucleases. Nishimasu H, Nureki O. Curr Opin Struct Biol 43 68-78 (2017)
  25. CRISPR-Cas in Streptococcus pyogenes. Le Rhun A, Escalera-Maurer A, Bratovič M, Charpentier E. RNA Biol 16 380-389 (2019)
  26. Optimization of genome editing through CRISPR-Cas9 engineering. Zhang JH, Adikaram P, Pandey M, Genis A, Simonds WF. Bioengineered 7 166-174 (2016)
  27. CRISPR/Cas9 in insects: Applications, best practices and biosafety concerns. Taning CNT, Van Eynde B, Yu N, Ma S, Smagghe G. J Insect Physiol 98 245-257 (2017)
  28. Class 2 CRISPR-Cas RNA-guided endonucleases: Swiss Army knives of genome editing. Stella S, Alcón P, Montoya G. Nat Struct Mol Biol 24 882-892 (2017)
  29. Conformational regulation of CRISPR-associated nucleases. Jackson RN, van Erp PB, Sternberg SH, Wiedenheft B. Curr Opin Microbiol 37 110-119 (2017)
  30. CRISPR-Cas9 genome engineering: Treating inherited retinal degeneration. Burnight ER, Giacalone JC, Cooke JA, Thompson JR, Bohrer LR, Chirco KR, Drack AV, Fingert JH, Worthington KS, Wiley LA, Mullins RF, Stone EM, Tucker BA. Prog Retin Eye Res 65 28-49 (2018)
  31. Progress and Challenges for Live-cell Imaging of Genomic Loci Using CRISPR-based Platforms. Wu X, Mao S, Ying Y, Krueger CJ, Chen AK. Genomics Proteomics Bioinformatics 17 119-128 (2019)
  32. Chemical Biology Approaches to Genome Editing: Understanding, Controlling, and Delivering Programmable Nucleases. Hu JH, Davis KM, Liu DR. Cell Chem Biol 23 57-73 (2016)
  33. CRISPR-Cas Targeting of Host Genes as an Antiviral Strategy. Chen S, Yu X, Guo D. Viruses 10 E40 (2018)
  34. CRISPR Tools To Control Gene Expression in Bacteria. Vigouroux A, Bikard D. Microbiol Mol Biol Rev 84 e00077-19 (2020)
  35. CRISPR-Cas Technologies and Applications in Food Bacteria. Stout E, Klaenhammer T, Barrangou R. Annu Rev Food Sci Technol 8 413-437 (2017)
  36. Minimizing off-Target Mutagenesis Risks Caused by Programmable Nucleases. Ishida K, Gee P, Hotta A. Int J Mol Sci 16 24751-24771 (2015)
  37. Why Argonaute is needed to make microRNA target search fast and reliable. Klein M, Chandradoss SD, Depken M, Joo C. Semin Cell Dev Biol 65 20-28 (2017)
  38. Structural biology of CRISPR-Cas immunity and genome editing enzymes. Wang JY, Pausch P, Doudna JA. Nat Rev Microbiol 20 641-656 (2022)
  39. Understanding the mechanistic basis of non-coding RNA through molecular dynamics simulations. Palermo G, Casalino L, Magistrato A, Andrew McCammon J. J Struct Biol 206 267-279 (2019)
  40. Using Synthetically Engineered Guide RNAs to Enhance CRISPR Genome Editing Systems in Mammalian Cells. Allen D, Rosenberg M, Hendel A. Front Genome Ed 2 617910 (2020)
  41. Harnessing "A Billion Years of Experimentation": The Ongoing Exploration and Exploitation of CRISPR-Cas Immune Systems. Klompe SE, Sternberg SH. CRISPR J 1 141-158 (2018)
  42. The rapidly advancing Class 2 CRISPR-Cas technologies: A customizable toolbox for molecular manipulations. Wang J, Zhang C, Feng B. J Cell Mol Med 24 3256-3270 (2020)
  43. Applications of the CRISPR-Cas9 system in kidney research. Higashijima Y, Hirano S, Nangaku M, Nureki O. Kidney Int 92 324-335 (2017)
  44. Allosteric regulation of CRISPR-Cas9 for DNA-targeting and cleavage. Zuo Z, Liu J. Curr Opin Struct Biol 62 166-174 (2020)
  45. CRISPR RNA-guided autonomous delivery of Cas9. Wilkinson RA, Martin C, Nemudryi AA, Wiedenheft B. Nat Struct Mol Biol 26 14-24 (2019)
  46. CRISPR/Cas-Based Modifications for Therapeutic Applications: A Review. Bharathkumar N, Sunil A, Meera P, Aksah S, Kannan M, Saravanan KM, Anand T. Mol Biotechnol 64 355-372 (2022)
  47. How bacteria control the CRISPR-Cas arsenal. Leon LM, Mendoza SD, Bondy-Denomy J. Curr Opin Microbiol 42 87-95 (2018)
  48. The tracrRNA in CRISPR Biology and Technologies. Liao C, Beisel CL. Annu Rev Genet 55 161-181 (2021)
  49. CRISPR-associated nucleases: the Dawn of a new age of efficient crop improvement. Ghogare R, Williamson-Benavides B, Ramírez-Torres F, Dhingra A. Transgenic Res 29 1-35 (2020)
  50. CRISPR/Cas9 System: A Bacterial Tailor for Genomic Engineering. Lone BA, Karna SKL, Ahmad F, Shahi N, Pokharel YR. Genet Res Int 2018 3797214 (2018)
  51. The Use of CRISPR/Cas9 as a Tool to Study Human Infectious Viruses. Lin H, Li G, Peng X, Deng A, Ye L, Shi L, Wang T, He J. Front Cell Infect Microbiol 11 590989 (2021)
  52. Single-Molecule View of Small RNA-Guided Target Search and Recognition. Globyte V, Kim SH, Joo C. Annu Rev Biophys 47 569-593 (2018)
  53. Targeting cancer epigenetics with CRISPR-dCAS9: Principles and prospects. Rahman MM, Tollefsbol TO. Methods 187 77-91 (2021)
  54. CRISPR/Cas9: a historical and chemical biology perspective of targeted genome engineering. Singh A, Chakraborty D, Maiti S. Chem Soc Rev 45 6666-6684 (2016)
  55. Functional Features and Current Applications of the RNA-Targeting Type VI CRISPR-Cas Systems. Perčulija V, Lin J, Zhang B, Ouyang S. Adv Sci (Weinh) 8 2004685 (2021)
  56. Inhibition of RNA-binding proteins with small molecules. Wu P. Nat Rev Chem 4 441-458 (2020)
  57. CRISPR/Cas9 therapeutics: progress and prospects. Li T, Yang Y, Qi H, Cui W, Zhang L, Fu X, He X, Liu M, Li PF, Yu T. Signal Transduct Target Ther 8 36 (2023)
  58. The CRISPR-Cas9 system in Neisseria spp. Zhang Y. Pathog Dis 75 (2017)
  59. Tips, Tricks, and Potential Pitfalls of CRISPR Genome Editing in Saccharomyces cerevisiae. Antony JS, Hinz JM, Wyrick JJ. Front Bioeng Biotechnol 10 924914 (2022)
  60. Advances in engineering CRISPR-Cas9 as a molecular Swiss Army knife. Meaker GA, Hair EJ, Gorochowski TE. Synth Biol (Oxf) 5 ysaa021 (2020)
  61. Chemical Modifications of CRISPR RNAs to Improve Gene-Editing Activity and Specificity. Rozners E. J Am Chem Soc 144 12584-12594 (2022)
  62. Adaptation by Type III CRISPR-Cas Systems: Breakthrough Findings and Open Questions. Zhang X, An X. Front Microbiol 13 876174 (2022)
  63. Disease modeling and stem cell immunoengineering in regenerative medicine using CRISPR/Cas9 systems. Antao AM, Karapurkar JK, Lee DR, Kim KS, Ramakrishna S. Comput Struct Biotechnol J 18 3649-3665 (2020)
  64. Dynamics and mechanisms of CRISPR-Cas9 through the lens of computational methods. Saha A, Arantes PR, Palermo G. Curr Opin Struct Biol 75 102400 (2022)
  65. Exploiting DNA Endonucleases to Advance Mechanisms of DNA Repair. Thompson MK, Sobol RW, Prakash A. Biology (Basel) 10 530 (2021)
  66. CRISPR-Based Approaches for Gene Regulation in Non-Model Bacteria. Call SN, Andrews LB. Front Genome Ed 4 892304 (2022)
  67. Current updates of CRISPR/Cas9-mediated genome editing and targeting within tumor cells: an innovative strategy of cancer management. Allemailem KS, Alsahli MA, Almatroudi A, Alrumaihi F, Alkhaleefah FK, Rahmani AH, Khan AA. Cancer Commun (Lond) 42 1257-1287 (2022)
  68. Gene editing innovations and their applications in cardiomyopathy research. Kyriakopoulou E, Monnikhof T, van Rooij E. Dis Model Mech 16 dmm050088 (2023)
  69. The CRISPR revolution and its potential impact on global health security. Watters KE, Kirkpatrick J, Palmer MJ, Koblentz GD. Pathog Glob Health 115 80-92 (2021)
  70. Type II anti-CRISPR proteins as a new tool for synthetic biology. Zhang Y, Marchisio MA. RNA Biol 18 1085-1098 (2021)
  71. Application of CRISPR/Cas9 Technology in Cancer Treatment: A Future Direction. Rabaan AA, AlSaihati H, Bukhamsin R, Bakhrebah MA, Nassar MS, Alsaleh AA, Alhashem YN, Bukhamseen AY, Al-Ruhimy K, Alotaibi M, Alsubki RA, Alahmed HE, Al-Abdulhadi S, Alhashem FA, Alqatari AA, Alsayyah A, Farahat RA, Abdulal RH, Al-Ahmed AH, Imran M, Mohapatra RK. Curr Oncol 30 1954-1976 (2023)
  72. Approaches to Enhance Precise CRISPR/Cas9-Mediated Genome Editing. Denes CE, Cole AJ, Aksoy YA, Li G, Neely GG, Hesselson D. Int J Mol Sci 22 8571 (2021)
  73. CRISPR/Cas9 assisted stem cell therapy in Parkinson's disease. Pinjala P, Tryphena KP, Prasad R, Khatri DK, Sun W, Singh SB, Gugulothu D, Srivastava S, Vora L. Biomater Res 27 46 (2023)
  74. Genome editing technologies, mechanisms and improved production of therapeutic phytochemicals: Opportunities and prospects. Mitra S, Anand U, Ghorai M, Kant N, Kumar M, Radha, Jha NK, Swamy MK, Proćków J, de la Lastra JMP, Dey A. Biotechnol Bioeng 120 82-94 (2023)
  75. Regulating CRISPR/Cas9 Function through Conditional Guide RNA Control. Brown W, Zhou W, Deiters A. Chembiochem 22 63-72 (2021)
  76. Advances and challenges in CRISPR-based real-time imaging of dynamic genome organization. Thuma J, Chung YC, Tu LC. Front Mol Biosci 10 1173545 (2023)
  77. CRISP Points on Establishing CRISPR-Cas9 In Vitro Culture Experiments in a Resource Constraint Haematology Oncology Research Lab. Das J, Bhatia P, Singh A. Indian J Hematol Blood Transfus 35 208-214 (2019)
  78. CRISPR/Cas9 genome editing for neurodegenerative diseases. Nouri Nojadeh J, Bildiren Eryilmaz NS, Ergüder BI. EXCLI J 22 567-582 (2023)
  79. HIV infection detection using CRISPR/Cas systems: Present and future prospects. Deng B, Xue J. Comput Struct Biotechnol J 21 4409-4423 (2023)
  80. Insights into the Mechanism of CRISPR/Cas9-Based Genome Editing from Molecular Dynamics Simulations. Bhattacharya S, Satpati P. ACS Omega 8 1817-1837 (2023)
  81. Putting CRISPR-Cas system in action: a golden window for efficient and precise genome editing for crop improvement. Tariq A, Mushtaq M, Yaqoob H, Bhat BA, Zargar SM, Raza A, Ali S, Charagh S, Mubarik MS, Zaman QU, Prasad PV, Mir RA. GM Crops Food 14 1-27 (2023)
  82. Recent advances in therapeutic CRISPR-Cas9 genome editing: mechanisms and applications. Zhou L, Yao S. Mol Biomed 4 10 (2023)
  83. Targeting miRNA by CRISPR/Cas in cancer: advantages and challenges. Hussen BM, Rasul MF, Abdullah SR, Hidayat HJ, Faraj GSH, Ali FA, Salihi A, Baniahmad A, Ghafouri-Fard S, Rahman M, Glassy MC, Branicki W, Taheri M. Mil Med Res 10 32 (2023)
  84. The Many (Inter)faces of Anti-CRISPRs: Modulation of CRISPR-Cas Structure and Dynamics by Mechanistically Diverse Inhibitors. Belato HB, Lisi GP. Biomolecules 13 264 (2023)
  85. Twisting and swiveling domain motions in Cas9 to recognize target DNA duplexes, make double-strand breaks, and release cleaved duplexes. Wang J, Arantes PR, Ahsan M, Sinha S, Kyro GW, Maschietto F, Allen B, Skeens E, Lisi GP, Batista VS, Palermo G. Front Mol Biosci 9 1072733 (2022)
  86. gRNA Design: How Its Evolution Impacted on CRISPR/Cas9 Systems Refinement. Motoche-Monar C, Ordoñez JE, Chang O, Gonzales-Zubiate FA. Biomolecules 13 1698 (2023)

Articles citing this publication (182)

  1. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F. Cell 163 759-771 (2015)
  2. High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects. Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK. Nature 529 490-495 (2016)
  3. Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA. Nature 550 407-410 (2017)
  4. The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA. Fonfara I, Richter H, Bratovič M, Le Rhun A, Charpentier E. Nature 532 517-521 (2016)
  5. Applications of CRISPR technologies in research and beyond. Barrangou R, Doudna JA. Nat Biotechnol 34 933-941 (2016)
  6. Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O. Cell 165 949-962 (2016)
  7. Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage. Jiang F, Taylor DW, Chen JS, Kornfeld JE, Zhou K, Thompson AJ, Nogales E, Doudna JA. Science 351 867-871 (2016)
  8. Conformational control of DNA target cleavage by CRISPR-Cas9. Sternberg SH, LaFrance B, Kaplan M, Doudna JA. Nature 527 110-113 (2015)
  9. Crystal Structure of Staphylococcus aureus Cas9. Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O. Cell 162 1113-1126 (2015)
  10. Structural Basis for Guide RNA Processing and Seed-Dependent DNA Targeting by CRISPR-Cas12a. Swarts DC, van der Oost J, Jinek M. Mol Cell 66 221-233.e4 (2017)
  11. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. Nat Biotechnol 34 528-530 (2016)
  12. Structure-guided chemical modification of guide RNA enables potent non-viral in vivo genome editing. Yin H, Song CQ, Suresh S, Wu Q, Walsh S, Rhym LH, Mintzer E, Bolukbasi MF, Zhu LJ, Kauffman K, Mou H, Oberholzer A, Ding J, Kwan SY, Bogorad RL, Zatsepin T, Koteliansky V, Wolfe SA, Xue W, Langer R, Anderson DG. Nat Biotechnol 35 1179-1187 (2017)
  13. Structure and Engineering of Francisella novicida Cas9. Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O. Cell 164 950-961 (2016)
  14. The crystal structure of Cpf1 in complex with CRISPR RNA. Dong D, Ren K, Qiu X, Zheng J, Guo M, Guan X, Liu H, Li N, Zhang B, Yang D, Ma C, Wang S, Wu D, Ma Y, Fan S, Wang J, Gao N, Huang Z. Nature 532 522-526 (2016)
  15. CRISPR/Cas9-Derived Mutations Both Inhibit HIV-1 Replication and Accelerate Viral Escape. Wang Z, Pan Q, Gendron P, Zhu W, Guo F, Cen S, Wainberg MA, Liang C. Cell Rep 15 481-489 (2016)
  16. Disabling Cas9 by an anti-CRISPR DNA mimic. Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA. Sci Adv 3 e1701620 (2017)
  17. The Molecular Architecture for RNA-Guided RNA Cleavage by Cas13a. Liu L, Li X, Ma J, Li Z, You L, Wang J, Wang M, Zhang X, Wang Y. Cell 170 714-726.e10 (2017)
  18. Two Distant Catalytic Sites Are Responsible for C2c2 RNase Activities. Liu L, Li X, Wang J, Wang M, Chen P, Yin M, Li J, Sheng G, Wang Y. Cell 168 121-134.e12 (2017)
  19. A conformational checkpoint between DNA binding and cleavage by CRISPR-Cas9. Dagdas YS, Chen JS, Sternberg SH, Doudna JA, Yildiz A. Sci Adv 3 eaao0027 (2017)
  20. How to measure and evaluate binding affinities. Jarmoskaite I, AlSadhan I, Vaidyanathan PP, Herschlag D. Elife 9 e57264 (2020)
  21. PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease. Yang H, Gao P, Rajashankar KR, Patel DJ. Cell 167 1814-1828.e12 (2016)
  22. Structural basis of CRISPR-SpyCas9 inhibition by an anti-CRISPR protein. Dong, Guo M, Wang S, Zhu Y, Wang S, Xiong Z, Yang J, Xu Z, Huang Z. Nature 546 436-439 (2017)
  23. Mechanistic Insights into the cis- and trans-Acting DNase Activities of Cas12a. Swarts DC, Jinek M. Mol Cell 73 589-600.e4 (2019)
  24. Type V CRISPR-Cas Cpf1 endonuclease employs a unique mechanism for crRNA-mediated target DNA recognition. Gao P, Yang H, Rajashankar KR, Huang Z, Patel DJ. Cell Res 26 901-913 (2016)
  25. Nucleosome breathing and remodeling constrain CRISPR-Cas9 function. Isaac RS, Jiang F, Doudna JA, Lim WA, Narlikar GJ, Almeida R. Elife 5 e13450 (2016)
  26. Minimal PAM specificity of a highly similar SpCas9 ortholog. Chatterjee P, Jakimo N, Jacobson JM. Sci Adv 4 eaau0766 (2018)
  27. Profiling of engineering hotspots identifies an allosteric CRISPR-Cas9 switch. Oakes BL, Nadler DC, Flamholz A, Fellmann C, Staahl BT, Doudna JA, Savage DF. Nat Biotechnol 34 646-651 (2016)
  28. Significant enhancement of fatty acid composition in seeds of the allohexaploid, Camelina sativa, using CRISPR/Cas9 gene editing. Jiang WZ, Henry IM, Lynagh PG, Comai L, Cahoon EB, Weeks DP. Plant Biotechnol J 15 648-657 (2017)
  29. Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O. Mol Cell 67 633-645.e3 (2017)
  30. Improving CRISPR-Cas specificity with chemical modifications in single-guide RNAs. Ryan DE, Taussig D, Steinfeld I, Phadnis SM, Lunstad BD, Singh M, Vuong X, Okochi KD, McCaffrey R, Olesiak M, Roy S, Yung CW, Curry B, Sampson JR, Bruhn L, Dellinger DJ. Nucleic Acids Res 46 792-803 (2018)
  31. Structure of the Cpf1 endonuclease R-loop complex after target DNA cleavage. Stella S, Alcón P, Montoya G. Nature 546 559-563 (2017)
  32. CRISPR-Cas9 nuclear dynamics and target recognition in living cells. Ma H, Tu LC, Naseri A, Huisman M, Zhang S, Grunwald D, Pederson T. J Cell Biol 214 529-537 (2016)
  33. Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim WA, Huang B. Nucleic Acids Res 44 e75 (2016)
  34. Structural Plasticity of PAM Recognition by Engineered Variants of the RNA-Guided Endonuclease Cas9. Anders C, Bargsten K, Jinek M. Mol Cell 61 895-902 (2016)
  35. Synthetic CRISPR RNA-Cas9-guided genome editing in human cells. Rahdar M, McMahon MA, Prakash TP, Swayze EE, Bennett CF, Cleveland DW. Proc Natl Acad Sci U S A 112 E7110-7 (2015)
  36. RNA-dependent RNA targeting by CRISPR-Cas9. Strutt SC, Torrez RM, Kaya E, Negrete OA, Doudna JA. Elife 7 e32724 (2018)
  37. Real-space and real-time dynamics of CRISPR-Cas9 visualized by high-speed atomic force microscopy. Shibata M, Nishimasu H, Kodera N, Hirano S, Ando T, Uchihashi T, Nureki O. Nat Commun 8 1430 (2017)
  38. Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9. Yang H, Patel DJ. Mol Cell 67 117-127.e5 (2017)
  39. Partial DNA-guided Cas9 enables genome editing with reduced off-target activity. Yin H, Song CQ, Suresh S, Kwan SY, Wu Q, Walsh S, Ding J, Bogorad RL, Zhu LJ, Wolfe SA, Koteliansky V, Xue W, Langer R, Anderson DG. Nat Chem Biol 14 311-316 (2018)
  40. Aptazyme-embedded guide RNAs enable ligand-responsive genome editing and transcriptional activation. Tang W, Hu JH, Liu DR. Nat Commun 8 15939 (2017)
  41. A CRISPR-Cas9-triggered strand displacement amplification method for ultrasensitive DNA detection. Zhou W, Hu L, Ying L, Zhao Z, Chu PK, Yu XF. Nat Commun 9 5012 (2018)
  42. Internal guide RNA interactions interfere with Cas9-mediated cleavage. Thyme SB, Akhmetova L, Montague TG, Valen E, Schier AF. Nat Commun 7 11750 (2016)
  43. C2c1-sgRNA Complex Structure Reveals RNA-Guided DNA Cleavage Mechanism. Liu L, Chen P, Wang M, Li X, Wang J, Yin M, Wang Y. Mol Cell 65 310-322 (2017)
  44. CRISPR-Cas9 conformational activation as elucidated from enhanced molecular simulations. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. Proc Natl Acad Sci U S A 114 7260-7265 (2017)
  45. Synthetically modified guide RNA and donor DNA are a versatile platform for CRISPR-Cas9 engineering. Lee K, Mackley VA, Rao A, Chong AT, Dewitt MA, Corn JE, Murthy N. Elife 6 e25312 (2017)
  46. Structural Basis for the Altered PAM Specificities of Engineered CRISPR-Cas9. Hirano S, Nishimasu H, Ishitani R, Nureki O. Mol Cell 61 886-894 (2016)
  47. Direct observation of DNA target searching and cleavage by CRISPR-Cas12a. Jeon Y, Choi YH, Jang Y, Yu J, Goo J, Lee G, Jeong YK, Lee SH, Kim IS, Kim JS, Jeong C, Lee S, Bae S. Nat Commun 9 2777 (2018)
  48. DNA-binding-domain fusions enhance the targeting range and precision of Cas9. Bolukbasi MF, Gupta A, Oikemus S, Derr AG, Garber M, Brodsky MH, Zhu LJ, Wolfe SA. Nat Methods 12 1150-1156 (2015)
  49. Crossing enhanced and high fidelity SpCas9 nucleases to optimize specificity and cleavage. Kulcsár PI, Tálas A, Huszár K, Ligeti Z, Tóth E, Weinhardt N, Fodor E, Welker E. Genome Biol 18 190 (2017)
  50. Development of Light-Activated CRISPR Using Guide RNAs with Photocleavable Protectors. Jain PK, Ramanan V, Schepers AG, Dalvie NS, Panda A, Fleming HE, Bhatia SN. Angew Chem Int Ed Engl 55 12440-12444 (2016)
  51. Incorporation of bridged nucleic acids into CRISPR RNAs improves Cas9 endonuclease specificity. Cromwell CR, Sung K, Park J, Krysler AR, Jovel J, Kim SK, Hubbard BP. Nat Commun 9 1448 (2018)
  52. Striking Plasticity of CRISPR-Cas9 and Key Role of Non-target DNA, as Revealed by Molecular Simulations. Palermo G, Miao Y, Walker RC, Jinek M, McCammon JA. ACS Cent Sci 2 756-763 (2016)
  53. Cryo-EM structures reveal coordinated domain motions that govern DNA cleavage by Cas9. Zhu X, Clarke R, Puppala AK, Chittori S, Merk A, Merrill BJ, Simonović M, Subramaniam S. Nat Struct Mol Biol 26 679-685 (2019)
  54. Cas9-catalyzed DNA Cleavage Generates Staggered Ends: Evidence from Molecular Dynamics Simulations. Zuo Z, Liu J. Sci Rep 5 37584 (2016)
  55. Structure and specificity of the RNA-guided endonuclease Cas9 during DNA interrogation, target binding and cleavage. Josephs EA, Kocak DD, Fitzgibbon CJ, McMenemy J, Gersbach CA, Marszalek PE. Nucleic Acids Res 43 8924-8941 (2015)
  56. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips. Jung C, Hawkins JA, Jones SK, Xiao Y, Rybarski JR, Dillard KE, Hussmann J, Saifuddin FA, Savran CA, Ellington AD, Ke A, Press WH, Finkelstein IJ. Cell 170 35-47.e13 (2017)
  57. NmeCas9 is an intrinsically high-fidelity genome-editing platform. Amrani N, Gao XD, Liu P, Edraki A, Mir A, Ibraheim R, Gupta A, Sasaki KE, Wu T, Donohoue PD, Settle AH, Lied AM, McGovern K, Fuller CK, Cameron P, Fazzio TG, Zhu LJ, Wolfe SA, Sontheimer EJ. Genome Biol 19 214 (2018)
  58. Profiling single-guide RNA specificity reveals a mismatch sensitive core sequence. Zheng T, Hou Y, Zhang P, Zhang Z, Xu Y, Zhang L, Niu L, Yang Y, Liang D, Yi F, Peng W, Feng W, Yang Y, Chen J, Zhu YY, Zhang LH, Du Q. Sci Rep 7 40638 (2017)
  59. A Single-Chain Photoswitchable CRISPR-Cas9 Architecture for Light-Inducible Gene Editing and Transcription. Zhou XX, Zou X, Chung HK, Gao Y, Liu Y, Qi LS, Lin MZ. ACS Chem Biol 13 443-448 (2018)
  60. Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease. Lim Y, Bak SY, Sung K, Jeong E, Lee SH, Kim JS, Bae S, Kim SK. Nat Commun 7 13350 (2016)
  61. Guide-bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Knott GJ, East-Seletsky A, Cofsky JC, Holton JM, Charles E, O'Connell MR, Doudna JA. Nat Struct Mol Biol 24 825-833 (2017)
  62. Precise and efficient scarless genome editing in stem cells using CORRECT. Kwart D, Paquet D, Teo S, Tessier-Lavigne M. Nat Protoc 12 329-354 (2017)
  63. Gaussian accelerated molecular dynamics (GaMD): principles and applications. Wang J, Arantes PR, Bhattarai A, Hsu RV, Pawnikar S, Huang YM, Palermo G, Miao Y. Wiley Interdiscip Rev Comput Mol Sci 11 e1521 (2021)
  64. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Q Rev Biophys 51 e91 (2018)
  65. Diverse Mechanisms of CRISPR-Cas9 Inhibition by Type IIC Anti-CRISPR Proteins. Zhu Y, Gao A, Zhan Q, Wang Y, Feng H, Liu S, Gao G, Serganov A, Gao P. Mol Cell 74 296-309.e7 (2019)
  66. Rapid generation of CRISPR/dCas9-regulated, orthogonally repressible hybrid T7-lac promoters for modular, tuneable control of metabolic pathway fluxes in Escherichia coli. Cress BF, Jones JA, Kim DC, Leitz QD, Englaender JA, Collins SM, Linhardt RJ, Koffas MA. Nucleic Acids Res 44 4472-4485 (2016)
  67. Structures of Neisseria meningitidis Cas9 Complexes in Catalytically Poised and Anti-CRISPR-Inhibited States. Sun W, Yang J, Cheng Z, Amrani N, Liu C, Wang K, Ibraheim R, Edraki A, Huang X, Wang M, Wang J, Liu L, Sheng G, Yang Y, Lou J, Sontheimer EJ, Wang Y. Mol Cell 76 938-952.e5 (2019)
  68. Systematic Review Which Factors Affect the Occurrence of Off-Target Effects Caused by the Use of CRISPR/Cas: A Systematic Review in Plants. Modrzejewski D, Hartung F, Lehnert H, Sprink T, Kohl C, Keilwagen J, Wilhelm R. Front Plant Sci 11 574959 (2020)
  69. DNase H Activity of Neisseria meningitidis Cas9. Zhang Y, Rajan R, Seifert HS, Mondragón A, Sontheimer EJ. Mol Cell 60 242-255 (2015)
  70. RNA-Independent DNA Cleavage Activities of Cas9 and Cas12a. Sundaresan R, Parameshwaran HP, Yogesha SD, Keilbarth MW, Rajan R. Cell Rep 21 3728-3739 (2017)
  71. Temperature-Responsive Competitive Inhibition of CRISPR-Cas9. Jiang F, Liu JJ, Osuna BA, Xu M, Berry JD, Rauch BJ, Nogales E, Bondy-Denomy J, Doudna JA. Mol Cell 73 601-610.e5 (2019)
  72. Staphylococcus aureus Cas9 is a multiple-turnover enzyme. Yourik P, Fuchs RT, Mabuchi M, Curcuru JL, Robb GB. RNA 25 35-44 (2019)
  73. Cas9 interrogates DNA in discrete steps modulated by mismatches and supercoiling. Ivanov IE, Wright AV, Cofsky JC, Aris KDP, Doudna JA, Bryant Z. Proc Natl Acad Sci U S A 117 5853-5860 (2020)
  74. Heavily and fully modified RNAs guide efficient SpyCas9-mediated genome editing. Mir A, Alterman JF, Hassler MR, Debacker AJ, Hudgens E, Echeverria D, Brodsky MH, Khvorova A, Watts JK, Sontheimer EJ. Nat Commun 9 2641 (2018)
  75. MicroRNA-focused CRISPR-Cas9 library screen reveals fitness-associated miRNAs. Kurata JS, Lin RJ. RNA 24 966-981 (2018)
  76. Programmable DNA looping using engineered bivalent dCas9 complexes. Hao N, Shearwin KE, Dodd IB. Nat Commun 8 1628 (2017)
  77. Simultaneous reprogramming and gene editing of human fibroblasts. Howden SE, Thomson JA, Little MH. Nat Protoc 13 875-898 (2018)
  78. The initiation, propagation and dynamics of CRISPR-SpyCas9 R-loop complex. Zeng Y, Cui Y, Zhang Y, Zhang Y, Liang M, Chen H, Lan J, Song G, Lou J. Nucleic Acids Res 46 350-361 (2018)
  79. Mechanism of duplex DNA destabilization by RNA-guided Cas9 nuclease during target interrogation. Mekler V, Minakhin L, Severinov K. Proc Natl Acad Sci U S A 114 5443-5448 (2017)
  80. Conditional Single Vector CRISPR/SaCas9 Viruses for Efficient Mutagenesis in the Adult Mouse Nervous System. Hunker AC, Soden ME, Krayushkina D, Heymann G, Awatramani R, Zweifel LS. Cell Rep 30 4303-4316.e6 (2020)
  81. Programmed Self-Assembly of an Active P22-Cas9 Nanocarrier System. Qazi S, Miettinen HM, Wilkinson RA, McCoy K, Douglas T, Wiedenheft B. Mol Pharm 13 1191-1196 (2016)
  82. Two HEPN domains dictate CRISPR RNA maturation and target cleavage in Cas13d. Zhang B, Ye Y, Ye W, Perčulija V, Jiang H, Chen Y, Li Y, Chen J, Lin J, Wang S, Chen Q, Han YS, Ouyang S. Nat Commun 10 2544 (2019)
  83. In Vitro CRISPR/Cas9 System for Efficient Targeted DNA Editing. Liu Y, Tao W, Wen S, Li Z, Yang A, Deng Z, Sun Y. mBio 6 e01714-15 (2015)
  84. De novo computational RNA modeling into cryo-EM maps of large ribonucleoprotein complexes. Kappel K, Liu S, Larsen KP, Skiniotis G, Puglisi EV, Puglisi JD, Zhou ZH, Zhao R, Das R. Nat Methods 15 947-954 (2018)
  85. Inhibition of CRISPR-Cas9 ribonucleoprotein complex assembly by anti-CRISPR AcrIIC2. Thavalingam A, Cheng Z, Garcia B, Huang X, Shah M, Sun W, Wang M, Harrington L, Hwang S, Hidalgo-Reyes Y, Sontheimer EJ, Doudna J, Davidson AR, Moraes TF, Wang Y, Maxwell KL. Nat Commun 10 2806 (2019)
  86. SaCas9 Requires 5'-NNGRRT-3' PAM for Sufficient Cleavage and Possesses Higher Cleavage Activity than SpCas9 or FnCpf1 in Human Cells. Xie H, Tang L, He X, Liu X, Zhou C, Liu J, Ge X, Li J, Liu C, Zhao J, Qu J, Song Z, Gu F. Biotechnol J 13 e1700561 (2018)
  87. Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency. Gisler S, Gonçalves JP, Akhtar W, de Jong J, Pindyurin AV, Wessels LFA, van Lohuizen M. Nat Commun 10 1598 (2019)
  88. Bridge helix arginines play a critical role in Cas9 sensitivity to mismatches. Bratovič M, Fonfara I, Chylinski K, Gálvez EJC, Sullivan TJ, Boerno S, Timmermann B, Boettcher M, Charpentier E. Nat Chem Biol 16 587-595 (2020)
  89. Programming sites of meiotic crossovers using Spo11 fusion proteins. Sarno R, Vicq Y, Uematsu N, Luka M, Lapierre C, Carroll D, Bastianelli G, Serero A, Nicolas A. Nucleic Acids Res 45 e164 (2017)
  90. Atomic-scale insights into allosteric inhibition and evolutional rescue mechanism of Streptococcus thermophilus Cas9 by the anti-CRISPR protein AcrIIA6. Li X, Wang C, Peng T, Chai Z, Ni D, Liu Y, Zhang J, Chen T, Lu S. Comput Struct Biotechnol J 19 6108-6124 (2021)
  91. Molecular Dynamics Reveals a DNA-Induced Dynamic Switch Triggering Activation of CRISPR-Cas12a. Saha A, Arantes PR, Hsu RV, Narkhede YB, Jinek M, Palermo G. J Chem Inf Model 60 6427-6437 (2020)
  92. Real-time observation of flexible domain movements in CRISPR-Cas9. Osuka S, Isomura K, Kajimoto S, Komori T, Nishimasu H, Shima T, Nureki O, Uemura S. EMBO J 37 e96941 (2018)
  93. Unified energetics analysis unravels SpCas9 cleavage activity for optimal gRNA design. Zhang D, Hurst T, Duan D, Chen SJ. Proc Natl Acad Sci U S A 116 8693-8698 (2019)
  94. A screening method to identify efficient sgRNAs in Arabidopsis, used in conjunction with cell-specific lignin reduction. Liang Y, Eudes A, Yogiswara S, Jing B, Benites VT, Yamanaka R, Cheng-Yue C, Baidoo EE, Mortimer JC, Scheller HV, Loqué D. Biotechnol Biofuels 12 130 (2019)
  95. Extensive CRISPR RNA modification reveals chemical compatibility and structure-activity relationships for Cas9 biochemical activity. O'Reilly D, Kartje ZJ, Ageely EA, Malek-Adamian E, Habibian M, Schofield A, Barkau CL, Rohilla KJ, DeRossett LB, Weigle AT, Damha MJ, Gagnon KT. Nucleic Acids Res 47 546-558 (2019)
  96. Structural basis for two metal-ion catalysis of DNA cleavage by Cas12i2. Huang X, Sun W, Cheng Z, Chen M, Li X, Wang J, Sheng G, Gong W, Wang Y. Nat Commun 11 5241 (2020)
  97. Letter Structural basis of stringent PAM recognition by CRISPR-C2c1 in complex with sgRNA. Wu D, Guan X, Zhu Y, Ren K, Huang Z. Cell Res 27 705-708 (2017)
  98. Engineering designer beta cells with a CRISPR-Cas9 conjugation platform. Lim D, Sreekanth V, Cox KJ, Law BK, Wagner BK, Karp JM, Choudhary A. Nat Commun 11 4043 (2020)
  99. Solution structure and dynamics of anti-CRISPR AcrIIA4, the Cas9 inhibitor. Kim I, Jeong M, Ka D, Han M, Kim NK, Bae E, Suh JY. Sci Rep 8 3883 (2018)
  100. StaPLs: versatile genetically encoded modules for engineering drug-inducible proteins. Jacobs CL, Badiee RK, Lin MZ. Nat Methods 15 523-526 (2018)
  101. Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9. Hirano S, Abudayyeh OO, Gootenberg JS, Horii T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O. Nat Commun 10 1968 (2019)
  102. CRISPR-Cas9 bends and twists DNA to read its sequence. Cofsky JC, Soczek KM, Knott GJ, Nogales E, Doudna JA. Nat Struct Mol Biol 29 395-402 (2022)
  103. Structural and functional insights into the bona fide catalytic state of Streptococcus pyogenes Cas9 HNH nuclease domain. Zuo Z, Zolekar A, Babu K, Lin VJ, Hayatshahi HS, Rajan R, Wang YC, Liu J. Elife 8 e46500 (2019)
  104. Bridge Helix of Cas9 Modulates Target DNA Cleavage and Mismatch Tolerance. Babu K, Amrani N, Jiang W, Yogesha SD, Nguyen R, Qin PZ, Rajan R. Biochemistry 58 1905-1917 (2019)
  105. Nucleosomes Selectively Inhibit Cas9 Off-target Activity at a Site Located at the Nucleosome Edge. Hinz JM, Laughery MF, Wyrick JJ. J Biol Chem 291 24851-24856 (2016)
  106. Primed CRISPR DNA uptake in Pyrococcus furiosus. Garrett S, Shiimori M, Watts EA, Clark L, Graveley BR, Terns MP. Nucleic Acids Res 48 6120-6135 (2020)
  107. R-loop formation and conformational activation mechanisms of Cas9. Pacesa M, Loeff L, Querques I, Muckenfuss LM, Sawicka M, Jinek M. Nature 609 191-196 (2022)
  108. Structural insights into a high fidelity variant of SpCas9. Guo M, Ren K, Zhu Y, Tang Z, Wang Y, Zhang B, Huang Z. Cell Res 29 183-192 (2019)
  109. Tissue- and time-directed electroporation of CAS9 protein-gRNA complexes in vivo yields efficient multigene knockout for studying gene function in regeneration. Fei JF, Knapp D, Schuez M, Murawala P, Zou Y, Pal Singh S, Drechsel D, Tanaka EM. NPJ Regen Med 1 16002 (2016)
  110. Elasticity of the transition state for oligonucleotide hybridization. Whitley KD, Comstock MJ, Chemla YR. Nucleic Acids Res 45 547-555 (2017)
  111. Guide-free Cas9 from pathogenic Campylobacter jejuni bacteria causes severe damage to DNA. Saha C, Mohanraju P, Stubbs A, Dugar G, Hoogstrate Y, Kremers GJ, van Cappellen WA, Horst-Kreft D, Laffeber C, Lebbink JHG, Bruens S, Gaskin D, Beerens D, Klunder M, Joosten R, Demmers JAA, van Gent D, Mouton JW, van der Spek PJ, van der Oost J, van Baarlen P, Louwen R. Sci Adv 6 eaaz4849 (2020)
  112. Structural basis for Cas9 off-target activity. Pacesa M, Lin CH, Cléry A, Saha A, Arantes PR, Bargsten K, Irby MJ, Allain FH, Palermo G, Cameron P, Donohoue PD, Jinek M. Cell 185 4067-4081.e21 (2022)
  113. Comprehensive deletion landscape of CRISPR-Cas9 identifies minimal RNA-guided DNA-binding modules. Shams A, Higgins SA, Fellmann C, Laughlin TG, Oakes BL, Lew R, Kim S, Lukarska M, Arnold M, Staahl BT, Doudna JA, Savage DF. Nat Commun 12 5664 (2021)
  114. Condensation of pericentrin proteins in human cells illuminates phase separation in centrosome assembly. Jiang X, Ho DBT, Mahe K, Mia J, Sepulveda G, Antkowiak M, Jiang L, Yamada S, Jao LE. J Cell Sci 134 jcs258897 (2021)
  115. Structure of the mini-RNA-guided endonuclease CRISPR-Cas12j3. Carabias A, Fuglsang A, Temperini P, Pape T, Sofos N, Stella S, Erlendsson S, Montoya G. Nat Commun 12 4476 (2021)
  116. CRISPR-Cas9 Mediated DNA Unwinding Detected Using Site-Directed Spin Labeling. Tangprasertchai NS, Di Felice R, Zhang X, Slaymaker IM, Vazquez Reyes C, Jiang W, Rohs R, Qin PZ. ACS Chem Biol 12 1489-1493 (2017)
  117. Real-time observation of Cas9 postcatalytic domain motions. Wang Y, Mallon J, Wang H, Singh D, Hyun Jo M, Hua B, Bailey S, Ha T. Proc Natl Acad Sci U S A 118 e2010650118 (2021)
  118. Molecular organization of the type II-A CRISPR adaptation module and its interaction with Cas9 via Csn2. Ka D, Jang DM, Han BW, Bae E. Nucleic Acids Res 46 9805-9815 (2018)
  119. A CRISPR/Cas9 eraser strategy for contamination-free PCR end-point detection. Lin W, Tian T, Jiang Y, Xiong E, Zhu D, Zhou X. Biotechnol Bioeng 118 2053-2066 (2021)
  120. CRISPR-Cas9 system-driven site-specific selection pressure on Herpes simplex virus genomes. Li Z, Bi Y, Xiao H, Sun L, Ren Y, Li Y, Chen C, Cun W. Virus Res 244 286-295 (2018)
  121. Probing the structural dynamics of the CRISPR-Cas9 RNA-guided DNA-cleavage system by coarse-grained modeling. Zheng W. Proteins 85 342-353 (2017)
  122. Visualizing looping of two endogenous genomic loci using synthetic zinc-finger proteins with anti-FLAG and anti-HA frankenbodies in living cells. Liu Y, Zhao N, Kanemaki MT, Yamamoto Y, Sadamura Y, Ito Y, Tokunaga M, Stasevich TJ, Kimura H. Genes Cells 26 905-926 (2021)
  123. A CRISPR-Cas9-integrase complex generates precise DNA fragments for genome integration. Jakhanwal S, Cress BF, Maguin P, Lobba MJ, Marraffini LA, Doudna JA. Nucleic Acids Res 49 3546-3556 (2021)
  124. Molecular basis for the PAM expansion and fidelity enhancement of an evolved Cas9 nuclease. Chen W, Zhang H, Zhang Y, Wang Y, Gan J, Ji Q. PLoS Biol 17 e3000496 (2019)
  125. Recent advances in structural studies of the CRISPR-Cas-mediated genome editing tools. Zhu Y, Huang Z. Natl Sci Rev 6 438-451 (2019)
  126. Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1. Zhang B, Luo D, Li Y, Perčulija V, Chen J, Lin J, Ye Y, Ouyang S. Nat Commun 12 3476 (2021)
  127. In silico Analysis Suggests Common Appearance of scaRNAs in Type II Systems and Their Association With Bacterial Virulence. Guzina J, Chen WH, Stankovic T, Djordjevic M, Zdobnov E, Djordjevic M. Front Genet 9 474 (2018)
  128. CRISPR-Cas9 Targeting of the eIF4E1 Gene Extends the Potato Virus Y Resistance Spectrum of the Solanum tuberosum L. cv. Desirée. Lucioli A, Tavazza R, Baima S, Fatyol K, Burgyan J, Tavazza M. Front Microbiol 13 873930 (2022)
  129. Defective heart chamber growth and myofibrillogenesis after knockout of adprhl1 gene function by targeted disruption of the ancestral catalytic active site. Smith SJ, Smith SJ, Towers N, Demetriou K, Mohun TJ. PLoS One 15 e0235433 (2020)
  130. Nucleotide-amino acid π-stacking interactions initiate photo cross-linking in RNA-protein complexes. Knörlein A, Sarnowski CP, de Vries T, Stoltz M, Götze M, Aebersold R, Allain FH, Leitner A, Hall J. Nat Commun 13 2719 (2022)
  131. Structural basis of Staphylococcus aureus Cas9 inhibition by AcrIIA14. Liu H, Zhu Y, Lu Z, Huang Z. Nucleic Acids Res 49 6587-6595 (2021)
  132. A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity. Eslami-Mossallam B, Klein M, Smagt CVD, Sanden KVD, Jones SK, Hawkins JA, Finkelstein IJ, Depken M. Nat Commun 13 1367 (2022)
  133. Active-Site Models of Streptococcus pyogenes Cas9 in DNA Cleavage State. Tang H, Yuan H, Du W, Li G, Xue D, Huang Q. Front Mol Biosci 8 653262 (2021)
  134. Engineering of the genome editing protein Cas9 to slide along DNA. Banerjee T, Takahashi H, Subekti DRG, Kamagata K. Sci Rep 11 14165 (2021)
  135. Inhibition mechanisms of CRISPR-Cas9 by AcrIIA17 and AcrIIA18. Wang X, Li X, Ma Y, He J, Liu X, Yu G, Yin H, Zhang H. Nucleic Acids Res 50 512-521 (2022)
  136. Kinetic characterization of Cas9 enzymes. Liu MS, Gong S, Yu HH, Taylor DW, Johnson KA. Methods Enzymol 616 289-311 (2019)
  137. Structure of the OMEGA nickase IsrB in complex with ωRNA and target DNA. Hirano S, Kappel K, Altae-Tran H, Faure G, Wilkinson ME, Kannan S, Demircioglu FE, Yan R, Shiozaki M, Yu Z, Makarova KS, Koonin EV, Macrae RK, Zhang F. Nature 610 575-581 (2022)
  138. Amide Internucleoside Linkages Are Well Tolerated in Protospacer Adjacent Motif-Distal Region of CRISPR RNAs. Kotikam V, Gajula PK, Coyle L, Rozners E. ACS Chem Biol 17 509-512 (2022)
  139. CRISPR-Cas molecular beacons as tool for studies of assembly of CRISPR-Cas effector complexes and their interactions with DNA. Mekler V, Kuznedelov K, Minakhin L, Murugan K, Sashital DG, Severinov K. Methods Enzymol 616 337-363 (2019)
  140. Directed evolution studies of a thermophilic Type II-C Cas9. Hand TH, Das A, Li H. Methods Enzymol 616 265-288 (2019)
  141. Exploiting dCas9 fusion proteins for dynamic assembly of synthetic metabolons. Berckman EA, Chen W. Chem Commun (Camb) 55 8219-8222 (2019)
  142. Gene editing with CRISPR-Cas12a guides possessing ribose-modified pseudoknot handles. Ageely EA, Chilamkurthy R, Jana S, Abdullahu L, O'Reilly D, Jensik PJ, Damha MJ, Gagnon KT. Nat Commun 12 6591 (2021)
  143. Guide RNAs containing universal bases enable Cas9/Cas12a recognition of polymorphic sequences. Krysler AR, Cromwell CR, Tu T, Jovel J, Hubbard BP. Nat Commun 13 1617 (2022)
  144. Versatile 3' Functionalization of CRISPR Single Guide RNA. Palumbo CM, Gutierrez-Bujari JM, O'Geen H, Segal DJ, Beal PA. Chembiochem 21 1633-1640 (2020)
  145. Systematic Review A Decade of Progress in Gene Targeted Therapeutic Strategies in Duchenne Muscular Dystrophy: A Systematic Review. Chung Liang L, Sulaiman N, Yazid MD. Front Bioeng Biotechnol 10 833833 (2022)
  146. A Mutated Nme1Cas9 Is a Functional Alternative RNase to Both LwaCas13a and RfxCas13d in the Yeast S. cerevisiae. Zhang Y, Ge H, Marchisio MA. Front Bioeng Biotechnol 10 922949 (2022)
  147. Electronic Circular Dichroism of the Cas9 Protein and gRNA:Cas9 Ribonucleoprotein Complex. Halat M, Klimek-Chodacka M, Orleanska J, Baranska M, Baranski R. Int J Mol Sci 22 2937 (2021)
  148. Probing the Dynamics of Streptococcus pyogenes Cas9 Endonuclease Bound to the sgRNA Complex Using Hydrogen-Deuterium Exchange Mass Spectrometry. Zhdanova PV, Chernonosov AA, Prokhorova DV, Stepanov GA, Kanazhevskaya LY, Koval VV. Int J Mol Sci 23 1129 (2022)
  149. Single- and duplex TaqMan-quantitative PCR for determining the copy numbers of integrated selection markers during site-specific mutagenesis in Toxoplasma gondii by CRISPR-Cas9. Hänggeli KPA, Hemphill A, Müller N, Schimanski B, Olias P, Müller J, Boubaker G. PLoS One 17 e0271011 (2022)
  150. Single-chromosome dynamics reveals locus-dependent dynamics and chromosome territory orientation. Chung YC, Bisht M, Thuma J, Tu LC. J Cell Sci 136 jcs260137 (2023)
  151. Structure of the IscB-ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9. Kato K, Okazaki S, Kannan S, Altae-Tran H, Esra Demircioglu F, Isayama Y, Ishikawa J, Fukuda M, Macrae RK, Nishizawa T, Makarova KS, Koonin EV, Zhang F, Nishimasu H. Nat Commun 13 6719 (2022)
  152. RNxQuest: An Extension to the xQuest Pipeline Enabling Analysis of Protein-RNA Cross-Linking/Mass Spectrometry Data. Sarnowski CP, Götze M, Leitner A. J Proteome Res 22 3368-3382 (2023)
  153. CRISPRtracrRNA: robust approach for CRISPR tracrRNA detection. Mitrofanov A, Ziemann M, Alkhnbashi OS, Hess WR, Backofen R. Bioinformatics 38 ii42-ii48 (2022)
  154. Computationally designed hyperactive Cas9 enzymes. Vos PD, Rossetti G, Mantegna JL, Siira SJ, Gandadireja AP, Bruce M, Raven SA, Khersonsky O, Fleishman SJ, Filipovska A, Rackham O. Nat Commun 13 3023 (2022)
  155. Coordinated Actions of Cas9 HNH and RuvC Nuclease Domains Are Regulated by the Bridge Helix and the Target DNA Sequence. Babu K, Kathiresan V, Kumari P, Newsom S, Parameshwaran HP, Chen X, Liu J, Qin PZ, Rajan R. Biochemistry 60 3783-3800 (2021)
  156. Hepatitis C virus NS5A inhibitor daclatasvir allosterically impairs NS4B-involved protein-protein interactions within the viral replicase and disrupts the replicase quaternary structure in a replicase assembly surrogate system. Zhang Y, Zou J, Zhao X, Yuan Z, Yi Z. J Gen Virol 100 69-83 (2019)
  157. In vitro CRISPR-Cas9-mediated efficient Ad5 vector modification. Tang L, Gong M, Zhang P. Biochem Biophys Res Commun 474 395-399 (2016)
  158. Polarity of the CRISPR roadblock to transcription. Hall PM, Inman JT, Fulbright RM, Le TT, Brewer JJ, Lambert G, Darst SA, Wang MD. Nat Struct Mol Biol 29 1217-1227 (2022)
  159. Position-dependent sequence motif preferences of SpCas9 are largely determined by scaffold-complementary spacer motifs. Huszár K, Welker Z, Györgypál Z, Tóth E, Ligeti Z, Kulcsár PI, Dancsó J, Tálas A, Krausz SL, Varga É, Welker E. Nucleic Acids Res 51 5847-5863 (2023)
  160. Pre-organized Guide RNA in the Cas9 Complex Is Ready for the Selection of Target Double-Stranded DNA. Kamiya Y, Asanuma H. Chembiochem 16 2273-2275 (2015)
  161. Split complementation of base editors to minimize off-target edits. Xiong X, Liu K, Li Z, Xia FN, Ruan XM, He X, Li JF. Nat Plants 9 1832-1847 (2023)
  162. Structural biology. Cas9, poised for DNA cleavage. Chen H, Bailey S. Science 351 811-812 (2016)
  163. Structural insights into target DNA recognition and cleavage by the CRISPR-Cas12c1 system. Zhang B, Lin J, Perčulija V, Li Y, Lu Q, Chen J, Ouyang S. Nucleic Acids Res 50 11820-11833 (2022)
  164. The Electronic Structure of Genome Editors from the First Principles. Nierzwicki Ł, Ahsan M, Palermo G. Electron Struct 5 014003 (2023)
  165. 1H, 13C, 15 N backbone resonance assignment of the recognition lobe subdomain 3 (Rec3) from Streptococcus pyogenes CRISPR-Cas9. Skeens E, East KW, Lisi GP. Biomol NMR Assign 15 25-28 (2021)
  166. AcrIIC4 inhibits type II-C Cas9 by preventing R-loop formation. Sun W, Cheng Z, Wang J, Yang J, Li X, Wang J, Chen M, Yang X, Sheng G, Lou J, Wang Y. Proc Natl Acad Sci U S A 120 e2303675120 (2023)
  167. Binding to the conserved and stably folded guide RNA pseudoknot induces Cas12a conformational changes during ribonucleoprotein assembly. Sudhakar S, Barkau CL, Chilamkurthy R, Barber HM, Pater AA, Moran SD, Damha MJ, Pradeepkumar PI, Gagnon KT. J Biol Chem 299 104700 (2023)
  168. Biochemical characterization of the two novel mgCas12a proteins from the human gut metagenome. Kim HS, Kim DW, Kim S, Choe S. Sci Rep 12 20857 (2022)
  169. Comparative structural and dynamics study of free and gRNA-bound FnCas9 and SpCas9 proteins. Panda G, Ray A. Comput Struct Biotechnol J 20 4172-4184 (2022)
  170. Conformational plasticity of SpyCas9 induced by AcrIIA4 and AcrIIA2: Insights from molecular dynamics simulation. Wen S, Zhao Y, Qi X, Cai M, Huang K, Liu H, Kong DX. Comput Struct Biotechnol J 23 537-548 (2024)
  171. Differential Divalent Metal Binding by SpyCas9's RuvC Active Site Contributes to Nonspecific DNA Cleavage. Newsom SN, Wang DS, Rostami S, Schuster I, Parameshwaran HP, Joseph YG, Qin PZ, Liu J, Rajan R. CRISPR J 6 527-542 (2023)
  172. Elongation roadblocks mediated by dCas9 across human genes modulate transcription and nascent RNA processing. Zukher I, Dujardin G, Sousa-Luís R, Proudfoot NJ. Nat Struct Mol Biol 30 1536-1548 (2023)
  173. Improving the on-target activity of high-fidelity Cas9 editors by combining rational design and random mutagenesis. Spasskaya DS, Davletshin AI, Bachurin SS, Tutyaeva VV, Garbuz DG, Karpov DS. Appl Microbiol Biotechnol 107 2385-2401 (2023)
  174. Knockout of Glycosyltransferases in Nicotiana benthamiana by Genome Editing to Improve Glycosylation of Plant-Produced Proteins. Jansing J, Bortesi L. Methods Mol Biol 2480 241-284 (2022)
  175. Molecular mechanisms of Streptococcus pyogenes Cas9: a single-molecule perspective. Zhang Q, Chen Z, Sun B. Biophys Rep 7 475-489 (2021)
  176. Nonspecific interactions between Cas12a and dsDNA located downstream of the PAM mediate target search and assist AsCas12a for DNA cleavage. Sun R, Zhao Y, Wang W, Liu JG, Chen C. Chem Sci 14 3839-3851 (2023)
  177. QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii. Shen B, Powell RH, Behnke MS. J Vis Exp (2017)
  178. Single Molecule FRET Analysis of CRISPR Cas9 Single Guide RNA Folding Dynamics. Okafor IC, Ha T. J Phys Chem B 127 45-51 (2023)
  179. Site-Specific Labeling Reveals Cas9 Induces Partial Unwinding Without RNA/DNA Pairing in Sequences Distal to the PAM. Li Y, Liu Y, Singh J, Tangprasertchai NS, Trivedi R, Fang Y, Qin PZ. CRISPR J 5 341-352 (2022)
  180. Sumoylation of Cas9 at lysine 848 regulates protein stability and DNA binding. Ergünay T, Ayhan Ö, Celen AB, Georgiadou P, Pekbilir E, Abaci YT, Yesildag D, Rettel M, Sobhiafshar U, Ogmen A, Emre NT, Sahin U. Life Sci Alliance 5 e202101078 (2022)
  181. Transposon-encoded nucleases use guide RNAs to promote their selfish spread. Meers C, Le HC, Pesari SR, Hoffmann FT, Walker MWG, Gezelle J, Tang S, Sternberg SH. Nature 622 863-871 (2023)
  182. Utilizing directed evolution to interrogate and optimize CRISPR/Cas guide RNA scaffolds. Bush K, Corsi GI, Yan AC, Haynes K, Layzer JM, Zhou JH, Llanga T, Gorodkin J, Sullenger BA. Cell Chem Biol 30 879-892.e5 (2023)