Publications

  1. Dangerfield, T. L., Marko, I., & Johnson, K. A. (2026). Slow PPi release enhances fidelity of the SARS-CoV-2 RNA-dependent RNA polymerase. Journal of Biological Chemistry, 302(6), Article 111457. https://doi.org/10.1016/j.jbc.2026.111457
  2. Wright, J. T., Yendluri, S., Thomas, N. C., Butterfield, C. N., Dangerfield, T. L., & Taylor, D. W. (2026). Structural and kinetic insights into a metagenomics-derived Cas12a with high specificity. bioRxiv. https://doi.org/10.64898/2026.05.13.724879
  3. Konttinen, O., Dangerfield, T., Vargas, J., Johnson, K. A., & Reich, N. (2026). Protein loops are major contributors to DNA strand separation and high-fidelity substrate recognition for DNA methyltransferase CcrM. Journal of Biological Chemistry, 302(5), Article 111398. https://doi.org/10.1016/j.jbc.2026.111398 
  4. Tyler L Dangerfield, Jun Zhou, Joseph Neumeyer, Thomas Eickbush, Kenneth A Johnson, Single-turnover kinetic analysis of non-long terminal repeat retrotransposition defines the pathway and rate constants leading to second-strand synthesis, Nucleic Acids Research, Volume 54, Issue 6, 13 April 2026, gkag223, https://doi.org/10.1093/nar/gkag223
  5. Guan, K., Ocampo, R.F., Matheus Carnevali, P.B. et al. Comparative characterization of Cas12f orthologs reveals mechanistic features underlying enhanced genome editing efficiency. Nat Struct Mol Biol 33, 756–767 (2026). https://doi.org/10.1038/s41594-026-01788-6
  6. Goyal, S., Nguyen, V., Lyons, S. N., Dangerfield, T. L., Yang, W., Fields, C., Chan, H.-R., Mahendravarman, Y., Cantu, L., Rubin, N., Deloney, K., Johnson, K. A., & Cambronne, X. A. (2026). Transient signaling of free ADP-ribose monitored with an intracellular biosensor. bioRxiv. https://doi.org/10.64898/2026.02.06.704453
  7. Ocampo, R.F.; Bravo, J.P.K.; Dangerfield, T.L.; Noceda, I.; Jirde, S.; Alexander, L.M.; Das, A.; Nielsen, S.; Johnson, K.A.; Brown, C.T.; Butterfield, C.N.; Goltsman, D.S.A.; Taylor, D.W. (2025) DNA targeting by compact Cas9d and its resurrected ancestor. Nat Commun 16, 457. https://doi.org/10.1101/2024.04.08.588528
  8. Hibshman, G.N.; Bravo, J.P.K.; Hooper, M.M.; Dangerfield, T.L.; Zhang, H.; Finkelstein, I.J.; Johnson, K.A.;  Taylor, D.W. (2024) Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9. Nat Commun 15, 3663. 10.1038/s41467-024-47830-3
  9. D’Oelsnitz, S. ; Diaz, D.J. ; Kim, W.; Acosta, D.J.; Dangerfield, T.L.; Schechter, M.W.; Minus, M.B.; Howard, J.R.; Do, H; Loy, J.M.; Alper, H.S.; Zhang, Y.J.; Ellington, A.D. (2024) Biosensor and machine learning-aided engineering of an amaryllidaceae enzyme. Nat Commun 15, 2084. 10.1038/s41467-024-46356-y
  10. Schwartz, E. A.; Bravo, J. P. K.; Macias, L. A.; McCafferty, C. L.; Dangerfield, T. L.; Walker, J. N.; Brodbelt, J. S.; Fineran, P. C.; Fagerlund, R. D.; Taylor, D. W. (2024)  RNA targeting and cleavage by the type III-Dv CRISPR effector complex. Nat Commun 15, 3324. 10.1038/s41467-024-47506-y
  11. Dangerfield, T.L.; Johnson, K.A. (2023) Design and interpretation of experiments to establish enzyme pathway and define the role of conformational changes in enzyme specificity. Methods Enzymol. 685 461-492. 10.1016/bs.mie.2023.03.01
  12. Dangerfield, T.L.; Johnson, K. A. (2023) Kinetics of DNA strand transfer between polymerase and proofreading exonuclease active sites regulates error correction during high-fidelity replication. Journal of Biological Chemistry 299 (1). 10.1016/j.jbc.2022.102744
  13. Dangerfield, T.L.; Paik, I.; Bhadra, S.; Johnson, K.A.; Ellington, A.D. (2023) Kinetics of elementary steps in loop-mediated isothermal amplification (LAMP) show that strand invasion during initiation is rate-limiting, Nucleic Acids Research, Volume 51, Issue 1, Pages 488–499. 10.1093/nar/gkac1221
  14. Dangerfield, T.L.; Johnson, K.A. (2022) Substrate Specificity and Kinetics of RNA Hydrolysis by SARS-CoV-2 NSP10/14 Exonuclease. ACS Bio & Med Chem AU. 10.1021/acsbiomedchemau.2c00046
  15. Dangerfield, T.L.; Kirmizialtin, S.; Johnson, K.A. (2021) Substrate specificity and proposed structure of the proofreading complex of T7 DNA polymerase. Journal of Biological Chemistry 298 101627. 10.1016/j.jbc.2022.101627
  16. Bravo, J.P.K.; Liu, M.S.; Hibshman, G.N.; Dangerfield, T.L.; Jung, K.; McCool, R.S.; Johnson, K.A.; Taylor, D.W. (2021) Structural basis for mismatch surveillance by CRISPR-Cas9. Nature 603 343-347. 10.1038/s41586-022-04470-1
  17. Dangerfield, T.L.; Johnson, K.A. (2021) Conformational dynamics during misincorporation and mismatch extension defined using a DNA polymerase with a fluorescent artificial amino acid, Journal of Biological Chemistry 298 101451. 10.1016/j.jbc.2021.101451
  18. Johnson, K.A.; Dangerfield. T.L. (2021) Mechanisms of inhibition of viral RNA replication by nucleotide analogs. The Enzymes 49 39-62. 10.1016/bs.enz.2021.07.001
  19. Bravo, J.P.K.; Dangerfield, T.L.; Taylor, D.W.; Johnson, K.A. (2021) Remdesivir is a delayed translocation inhibitor of SARS CoV-2 replication. Molecular Cell 81 1548-1552. 10.1016/j.molcel.2021.01.035
  20. Dangerfield, T.L.; Huang, N.Z.; Johnson, K.A. (2021) Expression and purification of tag-free SARS-CoV-2 RNA-dependent RNA polymerase in Escherichia coli. STAR Protocols 2 100357. 10.1016/j.xpro.2021.100357
  21. Fagan, S.; Mukherjee, P.; Jaremko, W.J.; Wilson, R.C.; Dangerfield, T.L.; Johnson, K.A.; Lahiri, I.; Pata, J.D. (2021) Pyrophosphate Release Acts as a Kinetic Checkpoint During High-Fidelity DNA Replication by the Staphylococcus aureus Replicative Polymerase PolC. Nucleic Acids Research 49 8324-8338. 10.1093/nar/gkab613
  22. Dangerfield, T.L.; Huang, N.Z.; Johnson, K.A. (2021) High Throughput Quantification of Short Nucleic Acid Samples by Capillary Electrophoresis with Automated Data Processing. Analytical Biochemistry 629 114239. 10.1016/j.ab.2021.114239
  23. Dangerfield, T.L.; Johnson, K.A. (2021) Conformational dynamics during high-fidelity DNA replication and translocation defined using a DNA polymerase with a fluorescent artificial amino acid. Journal of Biological Chemistry 296 100143. 10.1074/jbc.RA120.016617
  24. Dangerfield, T.L.; Huang, N.Z.; Johnson, K.A. (2020) Remdesivir Is Effective in Combating COVID-19 because It Is a Better Substrate than ATP for the Viral RNA-Dependent RNA Polymerase. iScience 23 101849. 10.1016/j.isci.2020.101849
  25. Dangerfield T.L.; Johnson, K.A. (2020) Optimized incorporation of an unnatural fluorescent amino acid affords measurement of conformational dynamics governing high-fidelity DNA replication. Journal of Biological Chemistry 295 17265 – 17280. 10.1074/jbc.RA120.015557
  26. Wang, H.; Huang, N.; Dangerfield, T.L.; Johnson, K.A.; Gao, J.; Elber, R. (2020) Exploring the Reaction Mechanism of HIV Reverse Transcriptase with a Nucleotide Substrate. The Journal of Physical Chemistry, 124 4270-4283. 10.1021/acs.jpcb.0c02632
  27. Aggerwal, K.; Kuka, T.; Banik, M.; Medellin, B.; Ngo, C.; Xie, D.; Fernandes, Y.; Dangerfield, T.L.; Ye, E.; Bouley, B.; Johnson, K.A.; Zhang, Y.; Eberhart, J.; Que, E. (2020) Visible Light Mediated Bidirectional Control over Carbonic Anhydrase Activity in Cells and in Vivo using Azobenzenesulfonamides. Journal of the American Chemical Society 142 14522-14531.https://doi.org/10.1021/jacs.0c05383