Publications

Recent Publications

Wilcox XE, Zhang H, Mah JL, Cazet JF, Mozumder S, Venkatesh S, Juliano CE, Beal PA, Fisher AJ. Phylogenetic and structural analysis of Hydra ADAR. Arch Biochem Biophys. 2025 DOI: 10.1016/j.abb.2025.110353

Salvador PJ, Dugan NM, Ouye R, Beal PA. En masse evaluation of RNA guides (EMERGe) for ADARs. Methods Enzymol. 2025 DOI: 10.1016/bs.mie.2024.11.030

Campbell KB, Cheng J, Mendoza HG, Karki A, Beal PA, Fisher AJ. Structural analysis of human ADAR2-RNA complexes by X-ray crystallography. Methods Enzymol. 2025 . DOI: 10.1016/bs.mie.2024.11.023

Manjunath A, Cheng J, Campbell KB, Jacobsen CS, Mendoza HG, Bierbaum L, Jauregui-Matos V, Doherty EE, Fisher AJ, Beal PA. Nucleoside Analogs in ADAR Guide Strands Enable Editing at 5′-GA Sites. Biomolecules. 2024 DOI: 10.3390/biom14101229 

Jauregui-Matos, V.; Jacobs, O.; Ouye, R.; Mozumder, S.; Salvador, P. J.; Fink, K. D.; Beal, P. A. Site-Specific Regulation of RNA Editing with Ribose-Modified Nucleoside Analogs in ADAR Guide Strands. Nucleic Acids Res. 2024, DOI: 10.1093/nar/gkae461.

Fisher AJ, Beal PA. Structural perspectives on adenosine to inosine RNA editing by ADARs. Mol Ther Nucleic Acids. 2024 DOI: 10.1016/j.omtn.2024.102284

Wong B. L, Mendoza H. G, Jacobsen C. S, Beal P. A. RNA sequences that direct selective ADAR editing from a SELEX library bearing 8-azanebularine. Bioorg Med Chem 2024; DOI: 10.1016/j.bmc.2024.117700

Mendoza H. G, Beal P.A. Structural and functional effects of inosine modification in mRNA. RNA 2024; DOI:10.1261/rna.079977.124

Karki, A.; Campbell, K. B.; Mozumder, S.; Fisher, A. J.; Beal, P. A. Impact of Disease-Associated Mutations on the Deaminase Activity of ADAR1. Biochemistry 2024, DOI: 10.1021/acs.biochem.3c00405

Jacobsen, C.S.; Salvador, P.; Yung, J.F.; Kragness, S.; Mendoza, H.G.; Mandel, G.; Beal, P.A. Library Screening Reveals Sequence Motifs That Enable ADAR2 Editing at Recalcitrant Sites. ACS Chemical Biology 2023. DOI: 10.1021/acschembio.3c00107

Mendoza, H.G.; Matos, V.J.; Park, S.; Pham, K.M.; Beal, P.A. Selective inhibition of ADAR1 Using 8-Azanebularine-Modified RNA Duplexes. Biochemistry 2023. DOI: 10.1021/acs.biochem.2c00686

Pham, K.M. and P.A. Beal. “Structure-Guided Optimization of siRNA and Anti-miRNA Properties.” In: Sugimoto, N. (eds) Handbook of Chemical Modifications of Nucleic Acids. Springer, Singapore 2023. DOI:10.1007/978-981-16-1313-5_41-1

Brinkman, H.F.; Matos, V.J.; Mendoza, H.G.; Doherty, E.E.; Beal, P.A. Nucleoside analogs in ADAR guide strands targeting 5′-UA sites. RSC. Chem. Biol. 2022. DOI: https://doi.org/10.1039/D2CB00165A

Doherty, E.E.; Karki, A; Wilcox, X.E.; Mendoza, H.G.; Manjunath, A.; Matos, V.J.; Fisher, A.J.; Beal, P.A. ADAR activation by inducing a syn conformation at guanosine adjacent to editing site. Nucleic Acids Research 2022. DOI: https://doi.org/10.1093/nar/gkac897

Doherty, E.E.; Wilcox, X.E.; van Sint Fiet, L.; Kemmel, C.; Turunen, J.J.; Klein, B.; Tantillo, D.J.; Fisher, A.J.; Beal, P.A. Rational Design of RNA Editing Guide Strands: Cytidine Analogs at the Orphan Position. J. Am. Chem. Soc. 2021. DOI: https://pubs.acs.org/doi/10.1021/jacs.0c13319

Malik, T.N.; Doherty, E.E.; Gaded, V.M.; Hill, T.M.; Beal, P.A.; Emeson, R.B. Regulation of RNA editing by intracellular acidification. Nucleic Acids Research 2020. DOI:https://doi.org/10.1093/nar/gkab157

Pham, K.M.; Suter, S.R.; Lu, S.S.; Beal, P.A. Ester modification at the 3′ end of anti-microRNA oligonucleotides increases potency of microRNA inhibition. Bioorganic & Medicinal Chemistry 2020. DOI:10.1016/j.bmc.2020.115894

Park, S.; Doherty, E.E.; Xie, Y.; Padyana, A.K.; Fang, F.; Zhang, Y.; Karki, A.; Lebrilla, C.B.; Siegel, J.B.; Beal, P.A. High-throughput mutagenesis reveals unique structural features of human ADAR1. Nat Commun 2020, 11 (5130). DOI: https://doi.org/10.1038/s41467-020-18862-2

Lapinaite, A.; Knott, G.J.; Palumbo, C.M.; Lin-Shiao, E.; Richter, M.F.; Zhao, K.T.; Beal, P.A.; Liu, D.R., Doudna, J.A. DNA capture by a CRISPR-Cas9–guided adenine base editor. Science 2020. DOI: 10.1126/science.abb1390 

Thuy-Boun, A.S.; Thomas, J.M.; Grajo, H.L.; Palumbo, C.M.; Park, S.H.; Nguyen, L.T.; Fisher, A.J.; Beal, P.A. Asymmetric dimerization of adenosine deaminase acting on RNA facilitates substrate recognition. Nucleic Acids Research 2020. DOI: https://doi.org/10.1093/nar/gkaa532

Knutson, S.D.; Korn, M.M.; Johnson, R.P.; Monteleone, L.R.; Dailey, D.M.; Swenson, C.S.; Beal, P.A. and Heemstra, J.M. Chemical Profiling of A‐to‐I RNA Editing Using a Click‐Compatible Phenylacrylamide. Chem. Eur. J. 2020. DOI:10.1002/chem.202001667

Palumbo, C. M.; Gutierrez-Bujari, J. M.; O’Geen, H.; Segal, D. J.; Beal, P. A. Versatile 3′ Functionalization of CRISPR Single Guide RNA. ChemBioChem 2020 , 21, 1633. DOI: https://doi.org/10.1002/cbic.201900736

Wang, Y.; Chung, D.; Monteleone, L.R.; Li J.; Chiang, Y.; Toney, M.D.; Beal, P.A., RNA binding candidates for human ADAR3 from substrates of a gain of function mutant expressed in neuronal cells. Nucleic Acids Research 2019, 47 (20), 10801-10814.  DOI: 10.1093/nar/gkz815

Park, S.; Beal, P.A., Off-Target Editing by CRISPR-Guided DNA Base Editors. Biochemistry 2019, 58 (36), 3727-3734. DOI: 10.1021/acs.biochem.9b00573

Palumbo, C.M.; Beal, P.A. Nucleoside analogs in the study of the epitranscriptome. Methods 2019,  Vol. 156, 46-52. DOI: 10.1016/j.ymeth.2018.10.014.

Monteleone L.R.; Matthews, M.M.; Palumbo, C.M.; Thomas, J.M.; Zheng Y.; Chiang, Y.; Fisher, A.J.; Beal, P.A. A Bump-Hole Approach for Directed RNA Editing. Cell Chemical Biology 2019, 26 (2), 269-277. DOI: 10.1016/j.chembiol.2018.10.025

Jora, M.; Burns, A. P.; Ross, R. L.; Lobue, P. A.; Zhao, R.; Palumbo, C. M.; Beal, P. A.; Addepalli, B.; Limbach, P. A., Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS). Journal of The American Society for Mass Spectrometry 2018, 29 (8), 1745-1756.
DOI:10.1007/s13361-018-1999-6

Fisher, A. J.; Beal, P. A., Structural basis for eukaryotic mRNA modification. Current Opinion in Structural Biology 2018, 53, 59-68.
DOI:10.1016/j.sbi.2018.05.003

Wang, Y.; Park, S.; Beal, P. A., Selective Recognition of RNA Substrates by ADAR Deaminase Domains. Biochemistry 2018, 57 (10), 1640-1651
DOI:10.1021/acs.biochem.7b01100

Lai, Z.; Tsugawa, H.; Wohlgemuth, G.; Mehta, S.; Mueller, M.; Zheng, Y.; Ogiwara, A.; Meissen, J.; Showalter, M.; Takeuchi, K.; Kind, T.; Beal, P.; Arita, M.; Fiehn, O., Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics. Nature Methods 2017, 15, 53.
DOI:10.1038/nmeth.4512

Wang, Y.; Zheng, Y.; Beal, P. A., Chapter Seven – Adenosine Deaminases That Act on RNA (ADARs). In The Enzymes, Chanfreau, G. F., Ed. Academic Press: 2017; Vol. 41, pp 215-268.
DOI:10.1016/bs.enz.2017.03.006

Onizuka, K.; Hazemi, M. E.; Thomas, J. M.; Monteleone, L. R.; Yamada, K.; Imoto, S.; Beal, P. A.; Nagatsugi, F., Synthesis of native-like crosslinked duplex RNA and study of its properties. Bioorganic & Medicinal Chemistry 2017, 25 (7), 2191-2199
DOI:10.1016/j.bmc.2017.02.034

Hu, T.; Suter, S. R.; Mumbleau, M. M.; Beal, P. A., TLR8 activation and inhibition by guanosine analogs in RNA: Importance of functional groups and chain length. Bioorganic & Medicinal Chemistry 2017.
DOI:10.1016/j.bmc.2017.11.020

Suter, S. R.; Ball-Jones, A.; Mumbleau, M. M.; Valenzuela, R.; Ibarra-Soza, J.; Owens, H.; Fisher, A. J.; Beal, P. A., “Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications.” Organic & Biomolecular Chemistry 2017.
DOI:10.1039/C7OB02654D

Mizrahi, R.A.; Shin, Dongwon; Sinkeldam, R.W.; Phelps, K.J.; Fin, A.; Tantillo, D.J.; Tor, Y.; Beal, P.A.
“A Fluorescent Adenosine Analogue as a Substrate for an A-to-I Editing Enzyme” Angew.
Chem. Int. Ed., 2015, 54(30), 8713-8716. DOI:10.1002/anie.201502070

Wang, Y.; Havel, J.; Beal, P.A. “A Phenotypic Screen for Functional Mutants of Human
Adenosine Deaminase Acting on RNA 1” ACS Chem. Biol.,2015, DOI:10.1021/acschembio.5b00711

Kelly J. Phelps, Kiet Tran, Tristan Eifler, Anna L. Ericson, Andrew J. Fisher, and Peter A. Beal*,
“Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2”,
Nucl. Acids. Res., 2015,(43)(1), 1123-1132.

Kiet Tran, Michelle R. Arkin, and Peter A. Beal, “Tethering in RNA: An RNA-Binding Fragment
Discovery Tool”, Molecules, 2015,20, 4148-4161.