Chance, contingency, and necessity in the replicated experimental evolution of ancestral proteins

73.     Cochran, V.; Pu, J.; Metzger, B.; Thornton, J.; Dickinson, B.C. submitted, (2020). bioRxiv

Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors

72.     Osipiuk, J.; Azizi, S.-A.; Dvorkin, S.; Endres, M.; Jedrzejczak, R.; Jones, K.; Kathayat, R.S.; Lisnyak, V.G.; Maki, S.; Kang, S.; Kim, Y.; Nicolaescu, V.; Taylor, C.A.; Tesar, C.; Zhang, Y,; Zhou, Z.; Randall, G.; Michalska, K.; Snyder, S.A.*; Dickinson, B.C.*; Joachimiak, A.* Accepted Nat. Commun., (2020). *co-corresponding authors. bioRxiv 

Drug repurposing screen identifies masitinib as 3CLpro inhibitor that blocks SARS-CoV-2 in vitro 

71.     Drayman, N.; Jones, K.; Azizi, S.-A.; Froggatt, H.M.; Tan, K.; Maltseva, N.I.; Chen, S.; Nicolaescu, V.; Dvorkin, S.; Furlong, K.; Kathayat, R.S.; Firpo, M.R.; Mastrodomenico, V.; Bruce, E.A.; Schmidt, M.M.; Jedrzejczak, R.; Munoz-Alia, M.A.; Schuster, B.; Nair, V.; Botten, J.W.; Crooke, C.B.; Baker, S.C.; Mpunce, B.C.; Heaton, N.S.; Dickinson, B.C.; Jaochimiak, A.; Randall, G.; Tay, S.  submitted, (2020). BioRxiv

Bisindolylmaleimide IX as a novel anti-SARS-CoV-2 therapeutic candidate with a validated mechanism of action 

70.     Gupta, Y.; Maciorowski, D.; Zak, S.; Jones, K.A.; Kathayat, R.S.; Azizi, S.-A.; Mathur, R.;  Pearce, C.M.; Husein, H.; Herbert, A.; Bharti, A.; Rathi, B.; Durvasula, R.; Becker, D.P.; Dickinson, B.C.; Dye, J.M. Kempaiah, P. submitted (2020). preprint

Small molecule-inducible RNA-targeting systems for temporal control of RNA regulation

69.     Rauch, S.; Jones, K.; and Dickinson, B.C. Accepted, ACS Central Science (2020). ChemRxiv

Split T7 RNA Polymerase Biosensors to Study Multiprotein Interaction Dynamics

68.     Dewey, J.A. and Dickinson, B.C. Methods Enzymol., 641, 413-432 (2020).

Endothelial palmitoylation cycling coordinates vessel remodeling in peripheral artery disease 

67.     Wei, X.; Adak, S.; Zayed, M.; Yin, L.; Feng, C.; Speck, S.L.; Kathayat, R.S.; Zhang, Q.; Dickinson, B.C.; Semenkovich, C.F. Circ. Res., 127, 249-265 (2020). link

ABHD10 is an S-depalmitoylase affecting redox homeostasis through peroxiredoxin-5 

66.     Cao, Y.; Qiu, T.; Kathayat, R.; Azizi, S.-A.; Thorne, A.K.; Ahn, D.; Fukata, Y.; Fukata, M.; Rice, P.; and Dickinson, B.C. Nat. Chem Biol., 15, 1232-1240 (2019).​​

Graphical Abstract - 4 (1).001.jpeg
A phage-assisted continuous selection approach for deep mutational scanning of protein-protein interactions 

65.     Zinkus-Boltz, J.; DeValk, C.; Dickinson, B.C. ACS Chem. Biol., 14, 2757-2767 (2019). ChemRxiv 

TOC.v1 (1).jpg
Recent advances in developing and applying biosensors for synthetic biology 

64.     Jones; K.; , S.-A.; Zinkus-Boltz, J.; Dickinson, B.C. Nano Futures, 3, 042002 (2019).

Fig3 Split T7 copy.jpg
Activity-Based Sensing of S-Depalmitoylases: Chemical Technologies and Biological Discovery

63.     Azizi, S.-A.; Kathayat, R.S.; Dickinson, B.C. Acc. Chem. Res., 53, 3029-3038 (2019).

Development of a split esterase for protein-protein interaction dependent small molecule activation 

62.     Jones, K.A.; Kentala, K.; Beck, M.W.; An, W.; Lippert, A. Lippert, J.; Dickinson, B.C. ACS Cent. Sci., 5, 1768-1776 (2019). ChemRxiv

Expanding the chemical scope of RNA base editors

60.     Rauch, S. and Dickinson, B.C. Biochemistry, 58, 3555-3556 (2019).

Palmitoylation is required for TNF-R1 signaling

59.     Zingler, P.; Särchen, V.; Glatter, T.; Caning, L.; Saggau, C.; Kathayat, R.S.; Dickinson, B.C.; Adam, D.; Schneider-Brachert, W.; Schütze, S.; Fritsch, J. Cell Commun. Signal., 17:90 (2019). 

GA Dickinson.jpg
Evolution of C‐terminal modification tolerance in full‐length and split T7 RNA Polymerase biosensors

57.     Pu, J.; Disare, M.; Dickinson, B.C. ChemBioChem, 20, 1547-1553 (2019). Part of the "ChemBioTalents" edition.

Targeted m6A reader proteins to study the epitranscriptome

56.     Rauch, S. and Dickinson, B.C. Methods Enzymol., 621, 1-16 (2019).

Measuring S-depalmitoylation activity in vitro and in live cells using fluorescent probes

55.     Kathayat, R.S.; Dickinson, B.C. Protein Lipidation: Methods and ProtocolsMethods Mol. Biol., 99-109 (2019). 

Targeted m6A reader proteins to study epitranscriptomic regulation of single RNAs

54.     Rauch, S.; He, C.; Dickinson, B.C. J. Am. Chem. Soc., 140, 11974–11981 (2018). Vectors on Addgene.

Repurposing a viral protein and drugs that target it for synthetic biology 

53.     Dickinson, B.C. Nat. Methods, 15, 489-490 (2018). 

Wnt5a signaling induced phosphorylation increases APT1 activity and promotes melanoma metastatic behavior

52.     Sagedhi, R.S.; Kulej, K.; Kathayat, R.S.; Garcia, B.A.; Dickinson, B.C., Brady D.C.; Witze, E.S. eLife 7:e34362 (2018). 

Active and dynamic mitochondrial S-depalmitoylation revealed by targeted fluorescent probes  

51.     Kathayat, R.S.; Cao, Y.; Elvira, P.; Sandoz, P.A.; Zaballa, M.-E.; Springer, M.Z.; Drake, L.E.; MacLeod, K.F.; van der Goot, F.G.; Dickinson, B.C. 

Nat. Commun., 9, 334 (2018). 

Programmable RNA binding proteins for imaging and therapeutics

50. Rauch, S. and Dickinson, B.C. Biochemistry, 57, 363-364 (2018). 

A fluorescent probe with improved water solubility permits the analysis of protein S-depalmitoylation activity in live cells

49. Qiu, T.; Kathayat, R.S.; Cao, Y.; Beck, M.W.; Dickinson, B.C. Biochemistry, 57, 221-225 (2018). Part of the "Future of Biochemistry" special issue.

Multidimensional control of Cas9 by evolved RNA polymerase-based biosensors

48. Pu, J.; Kentala, K.; Dickinson, B.C. ACS Chem. Biol., 13, 431-437 (2018). Vectors on Addgene.


Michael addition-based probes for ratiometric fluorescence imaging of protein S-depalmitoylases in live cells and tissues

47. Beck, M.W.; Kathayat, R.S.; Cham, C.M.; Chang, E.B.; Dickinson, B.C. Chem. Sci., 8, 7588-7592 (2017). 

RNA polymerase tags to monitor multidimensional protein-protein interactions reveal pharmacological engagement of Bcl-2 proteins

46. Pu, J.; Dewey, J.A.; Hadji, A.; LaBelle, J.L.; Dickinson, B.C. J. Am. Chem. Soc., 139, 11964–11972 (2017). 


Evolution of a split RNA polymerase as a versatile biosensor platform

45. Pu, J.; Zinkus, J.; Dickinson, B.C. Nat. Chem. Biol. 13, 432-438 (2017). Vectors on Addgene.

A fluorescent probe for cysteine depalmitoylation reveals dynamic APT signaling

44. Kathayat, R.S.; Elvira, P.D.; Dickinson, B.C. Nat. Chem. Biol. 13, 150-152 (2017).

A panel of protease-responsive RNA polymerases respond to biochemical signals by production of defined RNA outputs in live cells

43. Pu J.; Chronis I.; Ahn, D.; Dickinson, B.C. J. Am. Chem. Soc. 137, 15996-15999 (2015). 

41. Huet, O.; Pickering, R.J.; Tikellis, C.; Latouche, C.; Long, F.; Kingwell, B.; Dickinson, B.C.; Chang, C.J.; Masters, S.; Mackay, F.; Cooper, M.E.; de Haan, J.B. “Protective Effect of Inflammasome Activation by Hydrogen Peroxide in a Mouse Model of Septic Shock.” Crit. Care Med. 45, e184-e194 (2017).

40. Rodella, U.;, Scorzeto, M.; Duregotti, E.; Negro, S.; Dickinson, B.C.; Chang, C.J.; Yuki, N.; Rigoni, M.; Montecucco, C. “An animal model of Miller Fisher syndrome: Mitochondrial hydrogen peroxide is produced by the autoimmune attack of nerve terminals and activates Schwann cells.” Neurobiol. Dis. 96, 95-104 (2016).

39. Tong, Q.; Zhu, Y.; Galaske, J.W.; Kosmacek, E.A.; Chatterjee, A.; Dickinson, B.C.; Oberley-Deegan, R.E.; “MnTE-2-PyP modulates thiol oxidation in a hydrogen peroxide-mediated manner in a human prostate cancer cell.” Free Radic. Biol. Med. 101, 32-43 (2016).

38. Cox, A.G.; Kim, A.J.; Saunders, D.; Tsomides, A.; Hwang, K.L.; Evason, K.J.; Heidel, J.R.; Brown, K.K.; Yuan, M.; Lien, E.; Lee, B.C.; Nissim, S.; Dickinson, B.C.; Chhangawala, S.; Chang, C.J.; Gladyshev, V.N.; Asara, J.; Houvras, Y.; Goessling, W.  “Selenoprotein H suppresses ROS and cooperates with p53 during development and tumorigenesis.” Proc. Natl. Acad. Sci. USA. 113, E5562-E5571 (2016).

37. Tomalin, L.E.; Day, A.M.; Underwood, Z.E.; Smith, G.R.; Pezze, P.D.; Rallis, C.; Patel, W.; Dickinson, B.C.; Bähler, J.; Brewer, T.F.; Chang, C.J.; Shanley, D.P.; Veal, E.A. “Increasing extracellular H2O2 produces a bi-phasic response in intracellular H2O2,with peroxiredoxin hyperoxidation only triggered once the cellular H2O2-buffering capacity is overwhelmed.” Free Rad. Biol. Med. 95, 333-348 (2016).

36. Andresen, E.; Kroenlein, S.; Stärk, H.-J.; Riegger, U.; Borovec, J.; Mattusch, J.; Heinz, A,; Schmelzer, C.; Matoušková, S.; Dickinson, B.C.; Küpper, H. "Cadmium toxicity investigated on physiological and biophysical level under environmentally relevant conditions using the aquatic model plant Ceratophyllum demersum L.” New Phytologist. 210, 1244-1258 (2016).


35. Duregotti, E.; Negro, S.; Scorzeto, M.; Zornetta, I.; Dickinson, B.C.; Chang, C.J.; Montecuccoa, C.; Rigoni, M. “Mitochondrial alarmins released by degenerating motor axon terminals activate perisynaptic Schwann cells.” Proc. Natl. Acad. Sci. USA. 112, E497-E505 (2015).


34. *Fu, X.; *Tang, Y.; *Dickinson, B.C.; Chang, C.J.; Chang, Z. “An oxidative fluctuation hypothesis of aging generated by imaging H2O2 levels in live C. elegans with altered lifespans." Biochem. Biophys. Res. Commun., 458, 896-900 (2015).

*denotes equal contribution


33. Lippert, A.R.; Dickinson, B.C.; New, E.J. "Imaging Mitchondrial Hydrogen Peroxide in Living Cells." Methods Mol. Biol., 1264, 231-243 (2015).


32. Dickinson, B.C.; Packer, M.S.; Badran, A.H.; Liu, D.R.  “A system for the continuous directed evolution of proteases rapidly reveals drug-resistance mutations.” Nat. Commun., 5, 5352 (2014).


31. Yang, M. Haase, A.D.; Huang, F.-K.; Coulis, G.; Rivera, K.D.; Dickinson, B.C.; Chang, C.J.; Pappin, D.; Neubert, T.A.; Hannon, G.J.; Boivin, B.; Tonks, N.K. “Dephosphorylation of Tyrosine 393 in Argonaute 2 by Protein Tyrosine Phosphatase 1B Regulates Gene Silencing in Oncogenic RAS-Induced Senescence.” Mol. Cell, 55, 782-790 (2014).


30. Sanders, L.H.; McCoy, J.; Hu, X.; Mastroberardino, P.G.; Dickinson, B.C.; Chang, C.J.; Chu, C.T.; Van Houten, B.; Greenamyre, J.T. “Mitochondrial DNA damage: A molecular marker of vulnerable nigral neurons in Parkinson’s disease.” Neurobiol. Dis., 70, 214-223 (2014). 


29. Basu, S.; Rajakaruna, S.; Dickinson, B.C.; Chang, C.J.; Menko A. “Endogenous hydrogen peroxide (H2O2) production in the epithelium of the developing embryonic lens.” Mol. Vis., 20, 458-467 (2014). 


28. Banerjee, B.; Ghatak, P.D.; Soy, S.; Khanna, S.; Sequin, E.K.; Bellman, K.; Dickinson, B.C.; Suri, P.; Subramaniam, V.V.; Chang, C.J.; Sen, C.K. “Improvement of human keratinocyte migration by a redox active bioelectric dressing." PLOS One, 9, e89239 (2014). 


27. Guo, H.; Aleyasin, H.; Dickinson, B.C.; Haskew-Layton, R.E.; Ratan, R.R. "Recent advances in hydrogen peroxide imaging for biological applications." Cell Biosci., 4, 64 (2014).


26. Dickinson, B.C.; Leconte, A.M.; Allen, B.; Esvelt, K.M.; Liu, D.R.L. "Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution.“ Proc. Natl. Acad. Sci. USA. 110, 9007-9012 (2013). 


25. *Leconte, A.M.; *Dickinson, B.C.; Yang, D.D.; Chen, I.A.; Allen, B.; Liu, D.R.L. "A population-based experimental model for protein evolution: Effects of mutation rate and selection stringency on evolutionary outcomes.“ Biochemistry, 52, 1490-1499 (2013). 

*denotes equal contribution


24. Dickinson, B.C.; Lin, V.S.; Chang. C.J. "Preparation and use of MitoPY1 imaging hydrogen peroxide in mitochondria of live cells.“ Nat. Prot., 8, 1249-1259 (2013). 


23. Boivin, B.; Chaudhary, F.; Dickinson, B.C.; Haque, A.; Pero, S.C.; Chang, C.J.; Tonks, N.K. "Receptor protein tyrosine phosphatase α regulates focal adhesion kinase phosphorylation and contributes to ErbB2 oncoprotein-mediated mammary epithelial cell motility.“ J. Biol. Chem., 288, 36926-36935 (2013). 


22. Andresen, E.; Opitz, J.; Thomas, G.; Stärk, H.-J.; Dienemann, H.; Jenemann, K.; Dickinson, B.C.; Küpper, H. "Effects of Cd & Ni toxicity to Ceratophyllum demersum under environmentally relevant conditions in soft & hard water including a German lake." Aquat. Toxicol., 142-143, 387-402 (2013). 


21. Guo, H.; Aleyasin H.; Howard, S.S.; Dickinson, B.C.; Lin, V.S.; Haskew-Layton, R.E.; Xu, C.; Chen, Y.; Ratan, R.R. “Two-photon fluorescence imaging of intracellular hydrogen peroxide with chemoselective fluorescent probes.” J. Biomed. Opt., 18, 106002 (2013). 


20. Lin, V.S.; Dickinson, B.C.; Chang, C.J. “Boronate-based fluorescent probes: Imaging hydrogen peroxide in living systems.“ Meth. Enzymol., 526, 19-43 (2013). 


19. Thomas, G.; Stärk, H.-J.; Wellenreuther, G.; Dickinson, B.C.; Küpper, H. “Effects of nanomolar copper on water plants - Comparison of biochemical and biophysical mechanisms of deficiency and sublethal toxicity under environmentally relevant conditions.” Aquat. Toxicol., 140-141, 27-36 (2013). 


18. Gray, J.E.; Starmer, J.; Lin, V.S.; Dickinson, B.C.; Magnuson, T. “Mitochondrial hydrogen peroxide and defective cholesterol efflux prevent in vitro fertilization by cryopreserved inbred mouse sperm.” Biol. Reprod., 89, 17, 1-12 (2013). 


17. Harris, J.M.; Esain, V.; Frechette, G.M.; Harris, L.J.; Cox, A.G.; Cortes, M.; Garnaas, M.K.; Carroll, K.J.; Cutting, C.C.; Khan, T.; Elks, P.M.; Renshaw, S.A.; Dickinson, B.C.; Chang, C.J.; Murphy, M.P.; Paw, B.H.; Vander Heiden, M.G.; Goessling, W.; North, T.E. "Glucose metabolism impacts the spatiotemporal onset and magnitude of HSC induction in vivo." Blood, 121, 2483-2493 (2013). 


16. Sakai, J.; Li, J.; Subramanian, K.K.; Mondal, S.; Bajrami, B.; Hattori, H.; Jia, Y.; Dickinson, B.C.; Zhong, J.; Ye, K.; Chang, C.J.; Ho, Y-S.; Zhou, J.; Luo, H.R. "Reactive oxygen species-induced actin glutathionylation controls actin dynamics in neutrophils." Immunity, 37, 1037-1049 (2012). 


15. Woolley, J.F.; Naughton, R.; Stanicka, J.; Gough, D.R.; Bhatt, L.; Dickinson, B.C.; Chang, C.J.; Cotter, T.G. "H2O2 production downstream of FLT3 is mediated by p22phox in the Endoplasmic Reticulum and is required for STAT5 Signalling." PLOS One, 7, e34050 (2012). 


14. Bhatt, L.; Dickinson, B.C.; Gough, D.R.; O’Leary, D.P.; Cotter, T.G. "Imaging localised hydrogen peroxide production in living systems." Curr. Chem. Biol., 6, 113-122 (2012). 


13. Hu, C.; Mori, T.; Lu. Y.; Guo, Q.; Sun, Y.; Yoneki, Y.; Ohsaki, Y.; Nakamichi, T.; Oba, T.; Sato, E.; Ogawa, S.; Dickinson, B.C.; Chang, C.J.; Miyata, T.; Sato, H.; Ito. S. "Role of specific T-type calcium channel blocker R(-) Efonidipine in the regulation of renal medullary circulation." J. Hypertens., 30, 1620-1631 (2012). 


12. Ohsaki, Y.; O'Connor, P.; Mori, T.; Ryan, R.P.; Dickinson, B.C.; Chang, C.J.; Lu, Y.; Ito, S.; Cowley, A.W. "Increase of sodium delivery stimulates the mitochondrial respiratory chain H2O2 production in rat medullary thick ascending limb." Am. J. Physiol. Renal Physiol., 302, F95-F102 (2012). 


11. Dickinson, B.C.; Tang, Y.; Chang, Z.; Chang, C.J. "A nuclear-localized fluorescent hydrogen peroxide probe for monitoring sirtuin-mediated oxidative stress responses in vivo." Chem. Biol., 18, 943-948 (2011). 

10. Dickinson, B.C.; Chang, C.J. "Chemistry and biology of reactive oxygen species in signaling or stress responses." Nat. Chem. Biol., 7, 504-511 (2011). 


9. Dickinson, B.C.; Peltier, J.; Stone, D.; Schaffer, D.V.; Chang, C.J. “Nox2 redox signaling maintains essential cell population s in the brain.” Nat. Chem. Biol., 7, 106-112 (2011). 

Highlighted in: 

  • Chem. Eng. News, January 10, 2011, p. 32-33. “Peekaboo, H2O2.” 

  • Nat. Chem. Biol., 7, 71-72 (2011). News and Views: "Metabolite imaging: Knock, Nox-ROS there?" 


8. Lu, J.; Esposito, G.; Scuderi, C.; Steardo, L.; Delli-Bovi, L.C.; Hecht, J. L.; Dickinson, B.C.; Chang, C.J.; Mori, T.; Sheen, V. "S100B and APP promote a gliocentric shift and impaired neurogenesis in Down Syndrome neural progenitors." PLoS ONE, 6, e2212 6 (2011). 


7. *Miller, E.W.; *Dickinson, B.C.; Chang, C.J. “Aquaporin-3 mediates hydrogen peroxide uptake to regulate downstream intracellular signaling.” Proc. Natl. Acad. Sci. USA., 107, 15681-15686 (2010). 

*denotes equal contribution

Highlighted in:

  • ACS Chem. Biol., 5, 902 (2010). "Spotlight." 

  • Faculty of 1000, (2010) Evaluation rating 8, "Must read." ( 

  • Kidney International, 78, 946 (2010). "Journal Club." 


6. Dickinson, B.C.; Huynh, C.; Chang, C.J. “A palette of fluorescent probes with varying emission colors for imaging hydrogen peroxide signaling in living cells.” J. Am. Chem. Soc., 132, 5906–5915 (2010). 


5. Dickinson, B.C.; Srikun, D.; Chang, C.J. “Mitochondrial-targeted fluorescent probes for reactive oxygen species.” Curr. Opin. Chem. Biol., 14, 50–56 (2010). 


4. Sims, J. J.; Haririnia, A.; Dickinson, B.C.; Fushman, D.; Cohen, R.E. “Avid interactions underlie the Lys63-linked polyubiquitin binding specificities observed for UBA domains.” Nat. Struct. Mol. Biol., 16, 883–889 (2009). 


3. Dickinson, B.C.; Chang, C.J. "A targetable fluorescent probe for imaging hydrogen peroxide in the mitochondria of living cells." J. Am. Chem. Soc., 130, 9638–9639 (2008). 

Highlighted in:

  • Chem. Eng. News, July 28, 2008, p. 16. “Visualizing hydrogen peroxide: new fluorophore lights up hydrogen peroxide in live mitochondria.” 

  • Angew. Chem. Int. Ed., 48, 3022–3024 (2009). “Lighting up H2O2: the molecule that is a necessary evil in the cell.” 


2. Albers, A.E.; Dickinson, B.C.; Miller, E.W.; Chang, C.J. “A red-emitting naphthofluorescein-based fluorescent probe for selective detection of hydrogen peroxide in living cells.” Bioorg. Med. Chem. Lett., 18, 5948–5950 (2008). 


1. Dickinson, B.C.; Varadan, R.; Fushman, D. “Effects of cyclization on conformational dynamics and binding properties of Lys48-linked di-ubiquitin.” Protein Sci., 16, 369–378 (2007).