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

cb-2014-00270x_0009

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.