Dangerfield, T.L.; Zhou, J.; Eickbush, T.; Johnson, K.A. Single-turnover kinetic analysis of non-LTR retrotransposition defines the mechanism and rate constants governing each step. bioRxiv 2024. (Submitted)
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
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.
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.
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.
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.
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).
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
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
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
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
Johnson, K.A.; Dangerfield. T.L. (2021) Mechanisms of inhibition of viral RNA replication by nucleotide analogs. The Enzymes 49 39-62
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
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
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
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
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
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.
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
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.
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.
The Dangerfield Lab 