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Differentiating Positional Isomers of Nucleoside Modifications by Higher-Energy Collisional Dissociation Mass Spectrometry (HCD MS).

Jora M, Burns AP, Ross RL, Lobue PA, Zhao R, Palumbo CM, Beal PA, Addepalli B, Limbach PA.

J Am Soc Mass Spectrom. 2018 Aug;29(8):1745-1756. doi: 10.1007/s13361-018-1999-6. Epub 2018 Jun 12.


Structural basis for eukaryotic mRNA modification.

Fisher AJ, Beal PA.

Curr Opin Struct Biol. 2018 Jun 15;53:59-68. doi: 10.1016/ [Epub ahead of print] Review.


Selective Recognition of RNA Substrates by ADAR Deaminase Domains.

Wang Y, Park S, Beal PA.

Biochemistry. 2018 Mar 13;57(10):1640-1651. doi: 10.1021/acs.biochem.7b01100. Epub 2018 Feb 21.


Identifying metabolites by integrating metabolome databases with mass spectrometry cheminformatics.

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.

Nat Methods. 2018 Jan;15(1):53-56. doi: 10.1038/nmeth.4512. Epub 2017 Nov 27.


TLR8 activation and inhibition by guanosine analogs in RNA: Importance of functional groups and chain length.

Hu T, Suter SR, Mumbleau MM, Beal PA.

Bioorg Med Chem. 2018 Jan 1;26(1):77-83. doi: 10.1016/j.bmc.2017.11.020. Epub 2017 Nov 11.


Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications.

Suter SR, Ball-Jones A, Mumbleau MM, Valenzuela R, Ibarra-Soza J, Owens H, Fisher AJ, Beal PA.

Org Biomol Chem. 2017 Dec 6;15(47):10029-10036. doi: 10.1039/c7ob02654d.


Adenosine Deaminases That Act on RNA (ADARs).

Wang Y, Zheng Y, Beal PA.

Enzymes. 2017;41:215-268. doi: 10.1016/bs.enz.2017.03.006. Epub 2017 Apr 14.


Synthesis of native-like crosslinked duplex RNA and study of its properties.

Onizuka K, Hazemi ME, Thomas JM, Monteleone LR, Yamada K, Imoto S, Beal PA, Nagatsugi F.

Bioorg Med Chem. 2017 Apr 1;25(7):2191-2199. doi: 10.1016/j.bmc.2017.02.034. Epub 2017 Feb 21.


How do ADARs bind RNA? New protein-RNA structures illuminate substrate recognition by the RNA editing ADARs.

Thomas JM, Beal PA.

Bioessays. 2017 Apr;39(4). doi: 10.1002/bies.201600187. Epub 2017 Feb 20. Review.


DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA.

Zheng Y, Lorenzo C, Beal PA.

Nucleic Acids Res. 2017 Apr 7;45(6):3369-3377. doi: 10.1093/nar/gkx050.


Effects of Aicardi-Goutières syndrome mutations predicted from ADAR-RNA structures.

Fisher AJ, Beal PA.

RNA Biol. 2017 Feb;14(2):164-170. doi: 10.1080/15476286.2016.1267097. Epub 2016 Dec 12. Review.


Guide Strand 3'-End Modifications Regulate siRNA Specificity.

Valenzuela RA, Onizuka K, Ball-Jones AA, Hu T, Suter SR, Beal PA.

Chembiochem. 2016 Dec 14;17(24):2340-2345. doi: 10.1002/cbic.201600453. Epub 2016 Nov 7.


Probing RNA recognition by human ADAR2 using a high-throughput mutagenesis method.

Wang Y, Beal PA.

Nucleic Acids Res. 2016 Nov 16;44(20):9872-9880. Epub 2016 Sep 9.


Structure-Guided Control of siRNA Off-Target Effects.

Suter SR, Sheu-Gruttadauria J, Schirle NT, Valenzuela R, Ball-Jones AA, Onizuka K, MacRae IJ, Beal PA.

J Am Chem Soc. 2016 Jul 20;138(28):8667-9. doi: 10.1021/jacs.6b06137. Epub 2016 Jul 12.


Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity.

Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal PA.

Nat Struct Mol Biol. 2016 May;23(5):426-33. doi: 10.1038/nsmb.3203. Epub 2016 Apr 11.


Synthesis and evaluation of an alkyne-modified ATP analog for enzymatic incorporation into RNA.

Zheng Y, Beal PA.

Bioorg Med Chem Lett. 2016 Apr 1;26(7):1799-802. doi: 10.1016/j.bmcl.2016.02.038. Epub 2016 Feb 18.


A Phenotypic Screen for Functional Mutants of Human Adenosine Deaminase Acting on RNA 1.

Wang Y, Havel J, Beal PA.

ACS Chem Biol. 2015 Nov 20;10(11):2512-9. doi: 10.1021/acschembio.5b00711. Epub 2015 Sep 22.


A Fluorescent Adenosine Analogue as a Substrate for an A-to-I RNA Editing Enzyme.

Mizrahi RA, Shin D, Sinkeldam RW, Phelps KJ, Fin A, Tantillo DJ, Tor Y, Beal PA.

Angew Chem Int Ed Engl. 2015 Jul 20;54(30):8713-6. doi: 10.1002/anie.201502070. Epub 2015 Jun 10.


Tethering in RNA: an RNA-binding fragment discovery tool.

Tran K, Arkin MR, Beal PA.

Molecules. 2015 Mar 4;20(3):4148-61. doi: 10.3390/molecules20034148.


Influence of the addition of natural antioxidant from mate leaves (Ilex paraguariensis St. Hill) on the chemical, microbiological and sensory characteristics of different formulations of Prato cheese.

Faion AM, Beal P, Ril FT, Cichoski AJ, Cansian RL, Valduga AT, de Oliveira D, Valduga E.

J Food Sci Technol. 2015 Mar;52(3):1516-24. doi: 10.1007/s13197-013-1045-4. Epub 2013 Aug 16.


On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme.

Kuhn CD, Wilusz JE, Zheng Y, Beal PA, Joshua-Tor L.

Cell. 2015 Feb 12;160(4):644-658. doi: 10.1016/j.cell.2015.01.005. Epub 2015 Jan 29.


Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2.

Phelps KJ, Tran K, Eifler T, Erickson AI, Fisher AJ, Beal PA.

Nucleic Acids Res. 2015 Jan;43(2):1123-32. doi: 10.1093/nar/gku1345. Epub 2015 Jan 6.


Base modification strategies to modulate immune stimulation by an siRNA.

Valenzuela RA, Suter SR, Ball-Jones AA, Ibarra-Soza JM, Zheng Y, Beal PA.

Chembiochem. 2015 Jan 19;16(2):262-7. doi: 10.1002/cbic.201402551. Epub 2014 Dec 8.


Click modification of RNA at adenosine: structure and reactivity of 7-ethynyl- and 7-triazolyl-8-aza-7-deazaadenosine in RNA.

Phelps KJ, Ibarra-Soza JM, Tran K, Fisher AJ, Beal PA.

ACS Chem Biol. 2014 Aug 15;9(8):1780-7. doi: 10.1021/cb500270x. Epub 2014 Jun 16.


Short interfering RNA guide strand modifiers from computational screening.

Onizuka K, Harrison JG, Ball-Jones AA, Ibarra-Soza JM, Zheng Y, Ly D, Lam W, Mac S, Tantillo DJ, Beal PA.

J Am Chem Soc. 2013 Nov 13;135(45):17069-77. doi: 10.1021/ja4079754. Epub 2013 Nov 5.


RNA-Seq analysis identifies a novel set of editing substrates for human ADAR2 present in Saccharomyces cerevisiae.

Eifler T, Pokharel S, Beal PA.

Biochemistry. 2013 Nov 12;52(45):7857-69. doi: 10.1021/bi4006539. Epub 2013 Oct 31.


Computational approaches to predicting the impact of novel bases on RNA structure and stability.

Harrison JG, Zheng YB, Beal PA, Tantillo DJ.

ACS Chem Biol. 2013 Nov 15;8(11):2354-9. doi: 10.1021/cb4006062. Epub 2013 Oct 8. Review.


A screening protocol for identification of functional mutants of RNA editing adenosine deaminases.

Eifler T, Chan D, Beal PA.

Curr Protoc Chem Biol. 2012 Dec 1;4(4):357-69. doi: 10.1002/9780470559277.ch120139.


Potent and selective inhibition of A-to-I RNA editing with 2'-O-methyl/locked nucleic acid-containing antisense oligoribonucleotides.

Mizrahi RA, Schirle NT, Beal PA.

ACS Chem Biol. 2013 Apr 19;8(4):832-9. doi: 10.1021/cb300692k. Epub 2013 Feb 21.


Promiscuous 8-alkoxyadenosines in the guide strand of an siRNA: modulation of silencing efficacy and off-pathway protein binding.

Ghanty U, Fostvedt E, Valenzuela R, Beal PA, Burrows CJ.

J Am Chem Soc. 2012 Oct 24;134(42):17643-52. doi: 10.1021/ja307102g. Epub 2012 Oct 11.


Nucleoside analog studies indicate mechanistic differences between RNA-editing adenosine deaminases.

Mizrahi RA, Phelps KJ, Ching AY, Beal PA.

Nucleic Acids Res. 2012 Oct;40(19):9825-35. doi: 10.1093/nar/gks752. Epub 2012 Aug 11.


7-Substituted 8-aza-7-deazaadenosines for modification of the siRNA major groove.

Ibarra-Soza JM, Morris AA, Jayalath P, Peacock H, Conrad WE, Donald MB, Kurth MJ, Beal PA.

Org Biomol Chem. 2012 Aug 28;10(32):6491-7. doi: 10.1039/c2ob25647a. Epub 2012 Jul 5.


NEIL1 binding to DNA containing 2'-fluorothymidine glycol stereoisomers and the effect of editing.

Onizuka K, Yeo J, David SS, Beal PA.

Chembiochem. 2012 Jun 18;13(9):1338-48. doi: 10.1002/cbic.201200139. Epub 2012 May 25.


Novel modifications in RNA.

Phelps K, Morris A, Beal PA.

ACS Chem Biol. 2012 Jan 20;7(1):100-9. doi: 10.1021/cb200422t. Epub 2011 Dec 23. Review.


Chemical modification of siRNA bases to probe and enhance RNA interference.

Peacock H, Kannan A, Beal PA, Burrows CJ.

J Org Chem. 2011 Sep 16;76(18):7295-300. doi: 10.1021/jo2012225. Epub 2011 Aug 17. Review.


ADAR proteins: structure and catalytic mechanism.

Goodman RA, Macbeth MR, Beal PA.

Curr Top Microbiol Immunol. 2012;353:1-33. doi: 10.1007/82_2011_144. Review.


Nucleobase and ribose modifications control immunostimulation by a microRNA-122-mimetic RNA.

Peacock H, Fucini RV, Jayalath P, Ibarra-Soza JM, Haringsma HJ, Flanagan WM, Willingham A, Beal PA.

J Am Chem Soc. 2011 Jun 22;133(24):9200-3. doi: 10.1021/ja202492e. Epub 2011 Jun 1.


Covalent stabilization of a small molecule-RNA complex.

Peacock H, Bachu R, Beal PA.

Bioorg Med Chem Lett. 2011 Sep 1;21(17):5002-5. doi: 10.1016/j.bmcl.2011.04.136. Epub 2011 May 5.


Oxidative stability of fermented Italian-type sausages using mate leaves (Ilex paraguariensis St. Hil) extract as natural antioxidant.

Beal P, Faion AM, Cichoski AJ, Cansian RL, Valduga AT, de Oliveira D, Valduga E.

Int J Food Sci Nutr. 2011 Nov;62(7):703-10. doi: 10.3109/09637486.2011.579089. Epub 2011 May 19.


8-Oxoguanosine switches modulate the activity of alkylated siRNAs by controlling steric effects in the major versus minor grooves.

Kannan A, Fostvedt E, Beal PA, Burrows CJ.

J Am Chem Soc. 2011 Apr 27;133(16):6343-51. doi: 10.1021/ja2003878. Epub 2011 Mar 31.


RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1.

Yeo J, Goodman RA, Schirle NT, David SS, Beal PA.

Proc Natl Acad Sci U S A. 2010 Nov 30;107(48):20715-9. doi: 10.1073/pnas.1009231107. Epub 2010 Nov 10.


Minor-groove-modulating adenosine replacements control protein binding and RNAi activity in siRNAs.

Peacock H, Fostvedt E, Beal PA.

ACS Chem Biol. 2010 Dec 17;5(12):1115-24. doi: 10.1021/cb100245u. Epub 2010 Oct 7.


Selective inhibition of ADAR2-catalyzed editing of the serotonin 2c receptor pre-mRNA by a helix-threading peptide.

Schirle NT, Goodman RA, Krishnamurthy M, Beal PA.

Org Biomol Chem. 2010 Nov 7;8(21):4898-904. doi: 10.1039/c0ob00309c. Epub 2010 Aug 31.


N(2)-Modified 2-aminopurine ribonucleosides as minor-groove-modulating adenosine replacements in duplex RNA.

Peacock H, Maydanovych O, Beal PA.

Org Lett. 2010 Mar 5;12(5):1044-7. doi: 10.1021/ol100019r.


Human resources: Why bullying has no benefits.

Beal P.

Health Serv J. 2009 Oct 22;119(6179):26. No abstract available.


Matching active site and substrate structures for an RNA editing reaction.

Pokharel S, Jayalath P, Maydanovych O, Goodman RA, Wang SC, Tantillo DJ, Beal PA.

J Am Chem Soc. 2009 Aug 26;131(33):11882-91. doi: 10.1021/ja9034076.


Covalent hydration energies for purine analogs by quantum chemical methods.

Wang SC, Beal PA, Tantillo DJ.

J Comput Chem. 2010 Mar;31(4):721-5. doi: 10.1002/jcc.21364.


Synthesis and evaluation of an RNA editing substrate bearing 2'-deoxy-2'-mercaptoadenosine.

Jayalath P, Pokharel S, Véliz E, Beal PA.

Nucleosides Nucleotides Nucleic Acids. 2009 Feb;28(2):78-88. doi: 10.1080/15257770902736459.


Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay.

Krishnamurthy M, Schirle NT, Beal PA.

Bioorg Med Chem. 2008 Oct 1;16(19):8914-21. doi: 10.1016/j.bmc.2008.08.066. Epub 2008 Aug 29.


The chemistry and biology of RNA editing by adenosine deaminases.

Beal PA, Maydanovych O, Pokharel S.

Nucleic Acids Symp Ser (Oxf). 2007;(51):83-4.


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