Publications 2023Benjamin A Adler, Marena I Trinidad, Daniel Bellieny-Rabelo, Elaine Zhang, Hannah M Karp, Petr Skopintsev, Brittney W Thornton, Rachel F Weissman, Peter H Yoon, LinXing Chen, Tomas Hessler, Amy R Eggers, David Colognori, Ron Boger, Erin E Doherty, Connor A Tsuchida, Ryan V Tran, Laura Hofman, Honglue Shi, Kevin M Wasko, Zehan Zhou, Chenglong Xia, Muntathar J Al-Shimary, Jaymin R Patel, Vienna C J X Thomas, Rithu Pattali, Matthew J Kan, Anna Vardapetyan, Alana Yang, Arushi Lahiri, Micaela F Maxwell, Andrew G Murdock, Glenn C Ramit, Hope R Henderson, Roland W Calvert, Rebecca S Bamert, Gavin J Knott, Audrone Lapinaite, Patrick Pausch, Joshua C Cofsky, Erik J Sontheimer, Blake Wiedenheft, Peter C Fineran, Stan J J Brouns, Dipali G Sashital, Brian C Thomas, Christopher T Brown, Daniela S A Goltsman, Rodolphe Barrangou, Virginius Siksnys, Jillian F Banfield, David F Savage, Jennifer A Doudna. (2023) CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes. Nucleic Acids Research. Volume 52, Issue D1, D590–D596.Knott, GJ., Lapinaite, A., and O’Connell, MR. (2023) Methods Special Issue: RNA-targeting technologies. Methods. 23, 10.1016/j.ymeth.2023.02.006. 2022Knott, GJ., Chong, YS., Passon, DM., Liang, X., Deplazes, E., Conte, MR., Marshall, AC., Lee, M., Fox, AH., and Bond, CS. (2022) Structural basis of dimerization and nucleic acid binding of human DBHS proteins NONO and PSPC1. Nucleic Acids Research. 50, 522-535.Lee, PW., Marshall, AC., Knott, GJ., Kobelke, S., Martelotto, L., Cho, E., McMillan, PJ., Lee, M., Bond, CS., and Fox, AH. (2022) Paraspeckle subnuclear bodies depend on dynamic heterodimerisation of DBHS RNA-binding proteins via their structured domains. Journal of Biological Chemistry. 298, 11, 102563.Cofsky, JC., Soczek, KM., Knott, GJ., Nogales, E., and Doudna, JA. (2022) CRISPR-Cas9 bends and twists DNA to read its sequence. Nature Structural and Molecular Biology. 29, 395-402.Cofsky, JC., Knott, GJ., Gee, CL., and Doudna, JA. (2022) Crystal structure of an RNA/DNA strand exchange junction. Plos one. 17, e0263547.Chandrasekaran et al., (2022) Rapid detection of SARS-CoV-2 RNA in saliva via Cas13a. Nature Biomedical Engineering. 6, 944-956. 2021Knott, GJ., and Lapinaite, A. (2021) CRISPR gets its origin story. The CRISPR Journal. 4, 631-633.Liu, TY., Knott, GJ., Smock, DCJ., Desmarais, JJ., Son, S., Bhuiya, A., Jakhanwal, S., Prywes, N., Agrawal, S., Díaz de León Derby, M., Switz, NA., Armstrong, M., Harris, AR., Charles, EJ., Thornton, BW., Fozouni, P., Shu, J., Stephens, SI., Kumar, GR., Zhao, C., Mok, A., Iavarone, AT., Escajeda, AM., McIntosh, R., Kim, S., Dugan, EJ., IGI Testing Consortium, Pollard, KS., Tan, MX., Ott, M., Fletcher, DA., Lareau, LF., Hsu, PD., Savage, DF., and Doudna, JA. (2021) Accelerated RNA detection using tandem CRISPR nucleases. Nature Chemical Biology. 17, 982-988.Nalefski, EA., Patel, N., Leung, PJY., Islam, Z., Kooistra, RM., Parikh, I., Marion, E., Knott, GJ., Doudna, JA., Le Ny, AM., Madan, D. (2021) Kinetic analysis of Cas12a and Cas13a RNA-guided nucleases for development of improved CRISPR-based diagnostics. iScience. 24 (9).Amen, AA., Fellmann, C., Soczek, KM., Ren, SM., Lew, RJ., Knott, GJ., Park, JE., McKinney, AM., Mancini, A., Doudna, JA., and Costello, JF. (2021) Cancer-specific loss of TERT activation sensitizes glioblastoma to DNA damage. PNAS. 118 (13) e2008772118.Fozouni, P., Son, S., Díaz de León Derby, M., Knott, GJ., Gray, CN., D’Ambrosio, MV., Zhao, C., Switz, NA., Kumar., GR., Stephens, SI., Boehm, D., Tsou, CL., Shu, J., Bhuiya, A., Armstrong, M., Harris, AR., Chen, PY., Osterloh, JM., Meyer-Franke, A., Joehnk, B., Walcott, K., Sil, A., Langelier, C., Pollard, KS., Crawford, ED., Puschnik, AS., Phelps, M., Kistler, A., DeRisi, JL., Doudna, JA., Fletcher, DA., and Ott, M. (2021) Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy. Cell. 184, 323-333.Shivram, H., Cress, BF., Knott, GJ., and Doudna, JA. (2021) Controlling and enhancing CRISPR systems. Nature Chemical Biology. 17, 10-19. 2020Pausch, P., Al-Shayeb, B., Bisom-Rapp, E., Tsuchida, CA., Li, Z., Cress, BF., Knott, GJ., Jacobsen, SE., Banfield, JF., and Doudna, JA. (2020) CRISPR-CasΦ from huge phages is a hypercompact genome editor. Science. 369, 333-337. Lapinaite, A*., Knott, GJ*., Palumbo, CM., Lin-Shiao, E., Richter, MF., Zhao, KT., Beal, PA., Liu, DR and Doudna, JA. (2020) DNA capture by a CRISPR-Cas9 guided adenosine base editor. Science. 369, 566-571. (*Equal Contribution).Eitzinger S., Amina, A., Watters, KE., Iavarone, AT., Knott., GJ., Doudna, JA., and Minhas, FAA. (2020) Machine learning predicts new anti-CRISPR proteins. Nucleic Acids Research. 48, 4698-4708.Dai, J., Knott, GJ., Fu, W., Lin, TW., Furst, AL., Britt, D., and Francis MB. (2020) Protein-embedded metalloporphyrin arrays templated by circularly permuted tobacco mosaic virus coat proteins. ACS Nano. 15, 5, 8110-8119. 2019Knott, GJ., Cress, BF., Liu, JJ., Thornton, BW., Lew, RJ., Al-Shayeb, B., Rosenberg, DJ., Hammel, M., Adler, BA., Lobba, MJ., Xu, M., Arkin, AP., and Doudna, JA. (2019) Structural basis for AcrVA4 inhibition of specific CRISPR-Cas12a. eLife. 8:e49110.Knott, GJ., Thornton, BW., Lobba, MJ., Liu, JJ., Al-Shayeb, B., Watters, KE., and Doudna, JA. (2019) Broad spectrum enzymatic inhibiton of CRISPR-Cas12a. Nature Structural and Molecular Biology. 26, 315-321.Liu, JJ., Orlova, N., Oakes, BL., Ma, E., Spinner, HB., Baney, KLM., Chuck, J., Tan, D., Knott GJ., Harrington, LB., Al-Shayeb, B., Wagner, A., Brötzmann, J., Staahl, BT., Taylor, KL., Desmarais, J., Nogales, J., and Doudna, JA. (2018) CasX enzymes comprise a distinct family of RNA-guided genome editors. Nature. 566, 218-233. 2018Knott, GJ., & Dounda J.A. (2018) CRISPR-Cas guides the future of genetic engineering. Science. 361, 866-869.Tambe, A., East-Seletsky, A., Knott, GJ., Doudna, JA & O'Connell, MR. (2018) RNA binding and HEPN nuclease activation are decoupled in CRISPR-Cas13a. Cell Reports. 24, 1025-1036.Lahaye, X., Gentili, M., Silvin, A., Conrad, C., Picard, L., Jouve, M., Zueva, E., Maurin, M., Nadalin, F., Knott, GJ., Zhao, B., Du, F., Rio, M., Amiel, J., Fox, AH., Li, P., Etienne, L., Bond, CS., Colleaux, L., and Manel, N. (2018) NONO detects the nuclear HIV capsid to promote cGAS-mediated innate immune activation. Cell. 175, 2, 488-501. 2017Knott, GJ*., East-Seletsky, A*., Cofsky, JC., Holton, JM., Charles, E., O’Connell, MR., and Doudna, JA. (2017) Guide bound structures of an RNA-targeting A-cleaving CRISPR-Cas13a enzyme. Nature Structural and Molecular Biology. 24, 825-833. (*Equal Contribution).Harrington, LB., Doxzen, KW., Ma, E., Liu, JJ., Knott, GJ., Edraki, A., Garcia, B., Amrani, N., Chen, JS., Cofsky, JC., Kranzusch, PJ., Sontheimer, EJ., Davidson, AR., Maxwell, KL., and Doudna, JA. (2017) A broad-spectrum inhibitor of CRISPR-Cas9. Cell. Vol 170, 6, 1224-1233.East-Seletsky, A., O’Connell, MR., Burstein, D., Knott, GJ., and Doudna, JA. (2017) RNA targeting by functionally orthogonal Type VI-A CRISPR-Cas13 enzymes. Mol. Cell. 66, 373-383.Wright, AV., Liu, JJ., Knott, GJ., Doxzen, KW., Nogales, E., and Doudna, JA. (2017) Structures of the CRISPR genome integration complex. Science. 15, 1113-1118.James, AM., Jayasena, AS., Zhang, J., Berkowitz, O., Secco, D., Knott, GJ., Whelan, J., Bond, CS., and Mylne, JS. (2017) Evidence for ancient origins of Bowman-Brik inhibitors from Selaginella moellendorffii. The Plant Cell. 29, 461-473. 2016Knott, GJ., Panjikar, S., Thorn, A., Fox, AH., Conte, MR., and Bond, CS. (2016) A crystallographic study of human NONO (p54nrb): Overcoming pathological problems with purification, data collection and non-crystallographic symmetry. Acta. Cryst. D. 72, 761-769.Knott, GJ., Bond, CS., and Fox AH. (2016) The DBHS proteins SFPQ, NONO and PSPC1 – A multipurpose molecular scaffold. Nucleic Acids Research. 44, 3989-4004. 2015Knott, GJ., Lee, M., Passon, DM., Fox, AH., and Bond, CS. (2015) Caenorhabditis elegans NONO-1: Insights into DBHS protein structure, architecture and function. Protein Science. 24, 2033-2043.Hennig, S., Kong, G., Mannen, T., Sadowska, A., Kobelke, S., Blythe, A., Knott, GJ., Iyer, KS., Ho, D., Newcombe, EA., Hosoki, K., Goshima, N., Kawaguchi, T., Hatters, D., Trinkle-Mulcahy, L., Hirose, T., Bond, CS., and Fox, AH. (2015) Prion-like domains in RNA binding proteins are essential for building subnuclear paraspeckles. Journal of Cell Biology. 210, 529-539. 2014Middleton, CL., Parker, JL., Knott, GJ., White, MF., and Bond, CS. (2014) Crystal ‘unengineering’: reducing the crystallisability of Sulfolobus solfataricus Hjc. Aus. Journal of Chemistry. 67. 1818-1823.
