Publications

Recent Publications

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; 14(10):1229. 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.

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.