Publications 2026Janik Clement, Tim Lkhagvajargal, Brad L Hoare, Tiffany Myint, Daniel R Fox, Chunxiao Wang, Gavin J Knott, Ross AD Bathgate, and Rhys Grinter (2026). A complete RXFP1-relaxin interaction model unlocks the design of potent mini-protein modulators. bioRxiv.Fabian Munder, Matthew D Johnson, Imogen Samuels, Laura McCaughey, Oleksii Zdorevskyi, Chunxiao Wang, Ashleigh Kropp, Lauren Zavan, Erin P Price, Derek S Sarovich, Swati Varshney, Christopher A McDevitt, Hari Venugopal, Vivek Sharma, Matthew T Doyle, Francesca Short, Debnath Ghosal, James PR Connolly, Gavin J Knott, and Rhys Grinter (2026). L-type pyocins inhibit the BAM complex to kill without cell entry. Nature Communications.Jie-Ning Chuang, Jacob Purcell, Loki Sangalli, Joseph Rosenbluh, Gavin J Knott, Simon Corrie, and Gil Garnier (2026). Dissecting the disconnect between circuit activation and dominant adaptive evolution in cytoplasmic phage-assisted continuous evolution (PACE) of an EGFR nanobody. Frontiers in Bioengineering and Biotechnology. 14.Jacob Purcell, Ling Liu, Roland W Calvert, Brooke K Hayes, Cheng Huang, Chen Davidovich, Gavin J Knott, and Joseph Rosenbluh (2026). DUSP11 is an RNA triphosphatase that limits PspCas13b activity by destabilizing gRNA abundance in mammalian cells. Nucleic Acids Research. 54 (8) gkag412.Sungmin Son, Amy Lyden, Carlos F Ng, Andres Dextre, Jeffrey Shu, Stephanie I Stephens, Parinaz Fozouni, Gavin J Knott, Dylan CJ Smock, Tina Y Liu, Daniela Boehm, Camille Simoneau, G Renuka Kumar, Jennifer A Doudna, Melanie Ott, and Daniel A Fletcher (2026). Programmable kinetic barcoding for multiplexed RNA detection with Cas13a. Nature Biomedical Engineering. 1-12.Cyntia Taveneau, Her Xiang Chai, Jovita D’Silva, Rebecca S Bamert, Honglin Chen, Brooke K Hayes, Roland W Calvert, Jacob Purcell, Daniel J Curwen, Fabian Munder, Lisandra L Martin, Jeremy J Barr, Joseph Rosenbluh, Mohamed Fareh, Rhys Grinter, and Gavin J Knott (2026). De novo design of potent CRISPR–Cas13 inhibitors. Nature Chemical Biology. 22, 1342–1350.2025Roland W Calvert, Brooke K Hayes, Her Xiang Chai, Yongyi Peng, Cheng Huang, Hariprasad Venugopal, Cyntia Taveneau, Jovita D’Silva, Joseph Rosenbluh, Chen Davidovich, Chris Greening, Rebecca S Bamert, and Gavin J Knott (2025). Structures of tRNA-bound CRISPR-Cas13 reveal universal HEPN RNase mechanisms. bioRxiv.Jillian F Banfield, Luis E Valentin-Alvarado, Ling-Dong Shi, Colin Michael Robinson, Rebecca S Bamert, Fasseli Coulibaly, Zachary K Barth, Frank O Aylward, Marie C Schoelmerich, Shufei Lei, Rohan Sachdeva, and Gavin J Knott (2025). Convergent evolution of viral-like Borg archaeal extrachromosomal elements and giant eukaryotic viruses. Nature Communications. 16 (10641).Daniel R Fox, Cyntia Taveneau, Janik Clement, Rhys Grinter, and Gavin J Knott (2025). Code to complex: AI-driven de novo binder design. Structure. 33 (10) 1631-1642.Roland W Calvert, and Gavin J Knott (2025). And… cut!–how conformational regulation of CRISPR-Cas effectors directs nuclease activity. Biochemical Journal. 482 (19) 1431-1448.Daniel R Fox, Kazem Asadollahi, Imogen Samuels, Bradley A Spicer, Ashleigh Kropp, Christopher J Lupton, Kevin Lim, Chunxiao Wang, Hari Venugopal, Marija Dramicanin, Gavin J Knott, and Rhys Grinter (2025). Inhibiting heme piracy by pathogenic Escherichia coli using de novo-designed proteins. Nature Communications. 16 (1) 6066.Katharina G Wandera, Jeremy Dubrulle, Russell Greene, Meric Ozturk, Gavin Knott, Dipali G Sashital, and Peter C Fineran (2025). CRISPR2025 New Zealand: Innovation and Collaboration. The CRISPR Journal. 8 (3) 166-173.Luis E Valentin-Alvarado, and Gavin J Knott (2025). From Code to Comprehension: AI Captures the Language of Life. The CRISPR Journal. 8, (1) 2-4.Heidar J Koning, Jia Y Lai, Andrew C Marshall, Elke Stroeher, Gavin Monahan, Anuradha Pullakhandam, Gavin J Knott, Timothy M Ryan, Archa H Fox, Andrew Whitten, Mihwa Lee, and Charles S Bond (2025). Nucleic Acids Research. 53 (2) gkae1198.Hariprasad Venugopal, Jesse Mobbs, Cyntia Taveneau, Daniel R Fox, Ziva Vuckovic, Sahil Gulati, Gavin Knott, Rhys Grinter, David Thal, Stephen Mick, Cory Czarnik, and Georg Ramm (2025) High-resolution cryo-EM using a common LaB6 120-keV electron microscope equipped with a sub–200-keV direct electron detector. Science Advances. 11 (1) eadr0438.Her Xiang Chai, Rebecca S Bamert, and Gavin J Knott (2025). Methods for Cas13a expression and purification for use in CRISPR diagnostics. Methods in Enzymology. 712, 225-244.2024Tricia L Lo, Qi Wang, Joshua Nickson, Bryce JW van Denderen, Deanna Deveson Lucas, Her Xiang Chai, Gavin J Knott, Harshini Weerasinghe, and Ana Traven (2024). The C-terminal protein interaction domain of the chromatin reader Yaf9 is critical for pathogenesis of Candida albicans. Msphere. 9 (3) e00696-23.2023Benjamin 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. 52 (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) Caenorhabditiselegans 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.