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
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
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
Yuxuan Zheng, Claire Lorenzo, Peter A. Beal; DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA. Nucleic Acids Res 2017 gkx050. doi: 10.1093/nar/gkx050
Wang, Y. and P. A. Beal (2016). “Probing RNA recognition by human ADAR2 using a high-throughput mutagenesis method.” Nucleic Acids Research. DOI: 10.1093/nar/gkw799
Matthews, M. M., Thomas, J., et al. (2016). “Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity.” Nat Struct Mol Biol advance online publication. DOI:10.1038/nsmb.3203
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. doi: 10.1093/nar/gku1345
Kuhn, Claus-D.; Wilusz, Jeremy E.; Zheng, Yuxuan; Beal, Peter A.; Joshua-Tor, Leemor, On-Enzyme Refolding Permits Small RNA and tRNA Surveillance by the CCA-Adding Enzyme, Cell, 2015,
160(4), 644-658. DOI: http://dx.doi.org/10.1016/j.cell.2015.01.005
Phelps, K. J., et al. (2014). “Click Modification of RNA at Adenosine: Structure and Reactivity of 7-Ethynyl- and 7-Triazolyl-8-aza-7-deazaadenosine in RNA.” ACS Chemical Biology 9(8): 1780-1787. DOI: 10.1021/cb500270x
Eifler, T., et al. (2013). “RNA-Seq Analysis Identifies a Novel Set of Editing Substrates for Human ADAR2 Present in Saccharomyces cerevisiae.” Biochemistry 52(45): 7857-7869. DOI:10.1021/bi4006539
Mizrahi, R. A., et al. (2013). “Potent and Selective Inhibition of A-to-I RNA Editing with 2′-O-Methyl/Locked Nucleic Acid-Containing Antisense Oligoribonucleotides.” ACS Chemical Biology 8(4): 832-839. DOI:10.1021/cb300692k
“Potent and Selective Inhibition of A to I RNA Editing with 2’-O-Methyl/Locked Nucleic Acid-containing Antisense Oligoribonucleotides” Rena A. Mizrahi, Nicole T. Schirle and Peter A. Beal ACS Chem.Biol. 2013, 8, 4, 832-839.
“NEIL1 Binding to DNA containing 2’-Fluorothymidine Glycol Stereoisomers and the Effect of Editing” Kazumitsu Onizuka, Jongchan Yeo, Sheila S. David and Peter A. Beal ChemBioChem 2012, 13, 9, 1338-1348.
“A Screening Protocol for Identification of Functional Mutants of RNA Editing Adenosine Deaminases” Tristan Eifler, Dalen Chan and Peter A. Beal Curr. Protoc. Chem. Biol. 2012 4, 357-369.
“RNA Editing Reactions of ADAR1 with Nucleoside Analog-containing Substrates” Rena A. Mizrahi, Kelly Phelps, Andrea Ching and Peter A. Beal Nucleic Acids Res. 2012, 40, 19, 9825-9835.
Mizrahi, R. A., et al. (2012). “Nucleoside analog studies indicate mechanistic differences between RNA-editing adenosine deaminases.” Nucleic Acids Research 40(19): 9825-9835. DOI:10.1093/nar/gks752
Goodman, R., et al. (2012). ADAR Proteins: Structure and Catalytic Mechanism. Adenosine Deaminases Acting on RNA (ADARs) and A-to-I Editing. C. E. Samuel, Springer Berlin Heidelberg. 353: 1-33. DOI:10.1007/82_2011_144
“Novel RNA modifications” Kelly Phelps, Alexi Morris and Peter A. Beal ACS Chem. Biol. 2012, 7, 100-109.
-Top 10 “Most Read” article in ACS Chem. Biol. in 2012.
“ADAR proteins: Structure and Catalytic Mechanism” Rena A. Goodman, Mark R. Macbeth and Peter A. Beal Curr. Top. Microbiol. Immunol. 2012, 353, 1-33.
“RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1” Jongchan Yeo, Rena A. Goodman, Nicole T. Schirle, Sheila S. David and Peter A. Beal Proc. Natl. Acad. Sci. USA 2010, 107, 48, 20715-20719.
-Highlighted in the Chemical & Engineering News Science & Technology Concentrates, Nov. 15 2010 issue. “RNA editing enhances DNA repair”
-Featured in local newspaper Davis Enterprise, November 11, 2010 issue “UCD researchers find way to fix damaged DNA”
“Selective inhibition of ADAR2-catalyzed editing of the serotonin 2c receptor pre-mRNA by a helix-threading peptide” Nicole T. Schirle, Rena A. Goodman, Malathy Krishnamurthy and Peter A. Beal Org. Biomol. Chem. 2010, 8, 21, 4898-4904.
“Covalent Hydration Energies for Purine Analogs by Quantum Chemical Methods” Selina C. Wang, Peter A. Beal and Dean J. Tantillo J. Comput. Chem. 2010, 31, 721-725.