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Peter A Beal

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InstitutionUniversity of California Davis
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Fisher AJ, Beal P. Structural basis for eukaryotic mRNA modification. Curr Opin Struct Biol. 2018 Jun 15; 53:59-68. PMID: 29913347.
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    2. Wang Y, Park S, Beal P. Selective Recognition of RNA Substrates by ADAR Deaminase Domains. Biochemistry. 2018 03 13; 57(10):1640-1651. PMID: 29457714.
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    3. Suter SR, Ball-Jones A, Mumbleau MM, Valenzuela R, Ibarra-Soza J, Owens H, Fisher AJ, Beal P. Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. Org Biomol Chem. 2017 Dec 06; 15(47):10029-10036. PMID: 29164215.
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    4. 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. Nat Methods. 2018 Jan; 15(1):53-56. PMID: 29176591.
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    5. Hu T, Suter SR, Mumbleau MM, Beal P. TLR8 activation and inhibition by guanosine analogs in RNA: Importance of functional groups and chain length. Bioorg Med Chem. 2018 01 01; 26(1):77-83. PMID: 29174509.
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    6. Wang Y, Zheng Y, Beal P. Adenosine Deaminases That Act on RNA (ADARs). Enzymes. 2017; 41:215-268. PMID: 28601223.
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    7. Zheng Y, Lorenzo C, Beal P. DNA editing in DNA/RNA hybrids by adenosine deaminases that act on RNA. Nucleic Acids Res. 2017 Apr 07; 45(6):3369-3377. PMID: 28132026.
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    8. Onizuka K, Hazemi ME, Thomas JM, Monteleone LR, Yamada K, Imoto S, Beal P, Nagatsugi F. Synthesis of native-like crosslinked duplex RNA and study of its properties. Bioorg Med Chem. 2017 04 01; 25(7):2191-2199. PMID: 28268052.
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    9. Thomas JM, Beal P. How do ADARs bind RNA? New protein-RNA structures illuminate substrate recognition by the RNA editing ADARs. Bioessays. 2017 04; 39(4). PMID: 28217931.
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    10. Fisher AJ, Beal P. Effects of Aicardi-Goutières syndrome mutations predicted from ADAR-RNA structures. RNA Biol. 2017 02; 14(2):164-170. PMID: 27937139.
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    11. Valenzuela RA, Onizuka K, Ball-Jones AA, Hu T, Suter SR, Beal P. Guide Strand 3'-End Modifications Regulate siRNA Specificity. Chembiochem. 2016 Dec 14; 17(24):2340-2345. PMID: 27731539.
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    12. Wang Y, Beal P. Probing RNA recognition by human ADAR2 using a high-throughput mutagenesis method. Nucleic Acids Res. 2016 Nov 16; 44(20):9872-9880. PMID: 27614075.
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    13. Suter SR, Sheu-Gruttadauria J, Schirle NT, Valenzuela R, Ball-Jones AA, Onizuka K, MacRae IJ, Beal P. Structure-Guided Control of siRNA Off-Target Effects. J Am Chem Soc. 2016 07 20; 138(28):8667-9. PMID: 27387838.
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    14. Matthews MM, Thomas JM, Zheng Y, Tran K, Phelps KJ, Scott AI, Havel J, Fisher AJ, Beal P. Structures of human ADAR2 bound to dsRNA reveal base-flipping mechanism and basis for site selectivity. Nat Struct Mol Biol. 2016 05; 23(5):426-33. PMID: 27065196; PMCID: PMC4918759 [Available on 10/11/16].
    15. Zheng Y, Beal P. Synthesis and evaluation of an alkyne-modified ATP analog for enzymatic incorporation into RNA. Bioorg Med Chem Lett. 2016 Apr 01; 26(7):1799-802. PMID: 26927424; PMCID: PMC4785081 [Available on 04/01/17].
    16. Wang Y, Havel J, Beal P. A Phenotypic Screen for Functional Mutants of Human Adenosine Deaminase Acting on RNA 1. ACS Chem Biol. 2015 Nov 20; 10(11):2512-9. PMID: 26372505; PMCID: PMC4900682 [Available on 11/20/16].
    17. Mizrahi RA, Shin D, Sinkeldam RW, Phelps KJ, Fin A, Tantillo DJ, Tor Y, Beal P. A Fluorescent Adenosine Analogue as a Substrate for an A-to-I RNA Editing Enzyme. Angew Chem Int Ed Engl. 2015 Jul 20; 54(30):8713-6. PMID: 26095193; PMCID: PMC4532316.
    18. Tran K, Arkin MR, Beal P. Tethering in RNA: an RNA-binding fragment discovery tool. Molecules. 2015 Mar 04; 20(3):4148-61. PMID: 25749683; PMCID: PMC4760646.
    19. Kuhn CD, Wilusz JE, Zheng Y, Beal P, Joshua-Tor L. On-enzyme refolding permits small RNA and tRNA surveillance by the CCA-adding enzyme. Cell. 2015 Feb 12; 160(4):644-658. PMID: 25640237.
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    20. Phelps KJ, Tran K, Eifler T, Erickson AI, Fisher AJ, Beal P. Recognition of duplex RNA by the deaminase domain of the RNA editing enzyme ADAR2. Nucleic Acids Res. 2015 Jan; 43(2):1123-32. PMID: 25564529; PMCID: PMC4333395.
    21. Valenzuela RA, Suter SR, Ball-Jones AA, Ibarra-Soza JM, Zheng Y, Beal P. Base modification strategies to modulate immune stimulation by an siRNA. Chembiochem. 2015 Jan 19; 16(2):262-7. PMID: 25487859; PMCID: PMC4337945.
    22. Phelps KJ, Ibarra-Soza JM, Tran K, Fisher AJ, Beal P. Click modification of RNA at adenosine: structure and reactivity of 7-ethynyl- and 7-triazolyl-8-aza-7-deazaadenosine in RNA. ACS Chem Biol. 2014 Aug 15; 9(8):1780-7. PMID: 24896732; PMCID: PMC4136661.
    23. Onizuka K, Harrison JG, Ball-Jones AA, Ibarra-Soza JM, Zheng Y, Ly D, Lam W, Mac S, Tantillo DJ, Beal P. Short interfering RNA guide strand modifiers from computational screening. J Am Chem Soc. 2013 Nov 13; 135(45):17069-77. PMID: 24152142; PMCID: PMC3884816.
    24. Eifler T, Pokharel S, Beal P. RNA-Seq analysis identifies a novel set of editing substrates for human ADAR2 present in Saccharomyces cerevisiae. Biochemistry. 2013 Nov 12; 52(45):7857-69. PMID: 24124932; PMCID: PMC3856204.
    25. Harrison JG, Zheng YB, Beal P, Tantillo DJ. Computational approaches to predicting the impact of novel bases on RNA structure and stability. ACS Chem Biol. 2013 Nov 15; 8(11):2354-9. PMID: 24063428; PMCID: PMC3856235.
    26. Mizrahi RA, Schirle NT, Beal P. Potent and selective inhibition of A-to-I RNA editing with 2'-O-methyl/locked nucleic acid-containing antisense oligoribonucleotides. ACS Chem Biol. 2013 Apr 19; 8(4):832-9. PMID: 23394403; PMCID: PMC3631459.
    27. Eifler T, Chan D, Beal P. A screening protocol for identification of functional mutants of RNA editing adenosine deaminases. Curr Protoc Chem Biol. 2012 Dec 01; 4(4):357-69. PMID: 23788559; PMCID: PMC3690185.
    28. Ghanty U, Fostvedt E, Valenzuela R, Beal P, Burrows CJ. Promiscuous 8-alkoxyadenosines in the guide strand of an siRNA: modulation of silencing efficacy and off-pathway protein binding. J Am Chem Soc. 2012 Oct 24; 134(42):17643-52. PMID: 23030736; PMCID: PMC3491887.
    29. Mizrahi RA, Phelps KJ, Ching AY, Beal P. Nucleoside analog studies indicate mechanistic differences between RNA-editing adenosine deaminases. Nucleic Acids Res. 2012 Oct; 40(19):9825-35. PMID: 22885375; PMCID: PMC3479202.
    30. Ibarra-Soza JM, Morris AA, Jayalath P, Peacock H, Conrad WE, Donald MB, Kurth MJ, Beal P. 7-Substituted 8-aza-7-deazaadenosines for modification of the siRNA major groove. Org Biomol Chem. 2012 Aug 28; 10(32):6491-7. PMID: 22766576; PMCID: PMC3417767.
    31. Onizuka K, Yeo J, David SS, Beal P. NEIL1 binding to DNA containing 2'-fluorothymidine glycol stereoisomers and the effect of editing. Chembiochem. 2012 Jun 18; 13(9):1338-48. PMID: 22639086; PMCID: PMC3454477.
    32. Goodman RA, Macbeth MR, Beal P. ADAR proteins: structure and catalytic mechanism. Curr Top Microbiol Immunol. 2012; 353:1-33. PMID: 21769729.
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    33. Phelps K, Morris A, Beal P. Novel modifications in RNA. ACS Chem Biol. 2012 Jan 20; 7(1):100-9. PMID: 22148740; PMCID: PMC3270579.
    34. Peacock H, Kannan A, Beal P, Burrows CJ. Chemical modification of siRNA bases to probe and enhance RNA interference. J Org Chem. 2011 Sep 16; 76(18):7295-300. PMID: 21834582; PMCID: PMC3170502.
    35. Peacock H, Fucini RV, Jayalath P, Ibarra-Soza JM, Haringsma HJ, Flanagan WM, Willingham A, Beal P. Nucleobase and ribose modifications control immunostimulation by a microRNA-122-mimetic RNA. J Am Chem Soc. 2011 Jun 22; 133(24):9200-3. PMID: 21612237; PMCID: PMC3116021.
    36. Peacock H, Bachu R, Beal P. Covalent stabilization of a small molecule-RNA complex. Bioorg Med Chem Lett. 2011 Sep 01; 21(17):5002-5. PMID: 21601451; PMCID: PMC3156283.
    37. Kannan A, Fostvedt E, Beal P, Burrows CJ. 8-Oxoguanosine switches modulate the activity of alkylated siRNAs by controlling steric effects in the major versus minor grooves. J Am Chem Soc. 2011 Apr 27; 133(16):6343-51. PMID: 21452817; PMCID: PMC3086133.
    38. Yeo J, Goodman RA, Schirle NT, David SS, Beal P. RNA editing changes the lesion specificity for the DNA repair enzyme NEIL1. Proc Natl Acad Sci U S A. 2010 Nov 30; 107(48):20715-9. PMID: 21068368; PMCID: PMC2996456.
    39. Peacock H, Fostvedt E, Beal P. Minor-groove-modulating adenosine replacements control protein binding and RNAi activity in siRNAs. ACS Chem Biol. 2010 Dec 17; 5(12):1115-24. PMID: 20863128; PMCID: PMC3003776.
    40. Schirle NT, Goodman RA, Krishnamurthy M, Beal P. Selective inhibition of ADAR2-catalyzed editing of the serotonin 2c receptor pre-mRNA by a helix-threading peptide. Org Biomol Chem. 2010 Nov 07; 8(21):4898-904. PMID: 20820662.
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    41. Peacock H, Maydanovych O, Beal P. N(2)-Modified 2-aminopurine ribonucleosides as minor-groove-modulating adenosine replacements in duplex RNA. Org Lett. 2010 Mar 05; 12(5):1044-7. PMID: 20108910; PMCID: PMC2830388.
    42. Wang SC, Beal P, Tantillo DJ. Covalent hydration energies for purine analogs by quantum chemical methods. J Comput Chem. 2010 Mar; 31(4):721-5. PMID: 19569207.
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    43. Pokharel S, Jayalath P, Maydanovych O, Goodman RA, Wang SC, Tantillo DJ, Beal P. Matching active site and substrate structures for an RNA editing reaction. J Am Chem Soc. 2009 Aug 26; 131(33):11882-91. PMID: 19642681.
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    44. Jayalath P, Pokharel S, Véliz E, Beal P. Synthesis and evaluation of an RNA editing substrate bearing 2'-deoxy-2'-mercaptoadenosine. Nucleosides Nucleotides Nucleic Acids. 2009 Feb; 28(2):78-88. PMID: 19219738; PMCID: PMC2747504.
    45. Krishnamurthy M, Schirle NT, Beal P. Screening helix-threading peptides for RNA binding using a thiazole orange displacement assay. Bioorg Med Chem. 2008 Oct 01; 16(19):8914-21. PMID: 18789700; PMCID: PMC2585546.
    46. Beal P, Maydanovych O, Pokharel S. The chemistry and biology of RNA editing by adenosine deaminases. Nucleic Acids Symp Ser (Oxf). 2007; (51):83-4. PMID: 18029597.
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    47. Maydanovych O, Easterwood LM, Cui T, Véliz EA, Pokharel S, Beal P. Probing adenosine-to-inosine editing reactions using RNA-containing nucleoside analogs. Methods Enzymol. 2007; 424:369-86. PMID: 17662850.
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    48. Krishnamurthy M, Simon K, Orendt AM, Beal P. Macrocyclic helix-threading peptides for targeting RNA. Angew Chem Int Ed Engl. 2007; 46(37):7044-7. PMID: 17691090.
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    49. Pokharel S, Beal P. High-throughput screening for functional adenosine to inosine RNA editing systems. ACS Chem Biol. 2006 Dec 15; 1(12):761-5. PMID: 17240974.
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    50. Puthenveetil S, Whitby L, Ren J, Kelnar K, Krebs JF, Beal P. Controlling activation of the RNA-dependent protein kinase by siRNAs using site-specific chemical modification. Nucleic Acids Res. 2006; 34(17):4900-11. PMID: 16982647; PMCID: PMC1635244.
    51. Maydanovych O, Beal P. C6-substituted analogues of 8-azanebularine: probes of an RNA-editing enzyme active site. Org Lett. 2006 Aug 17; 8(17):3753-6. PMID: 16898809.
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    52. Maydanovych O, Beal P. Breaking the central dogma by RNA editing. Chem Rev. 2006 Aug; 106(8):3397-411. PMID: 16895334.
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    53. Krishnamurthy M, Gooch BD, Beal P. RNA binding and thiolytic stability of a quinoline-containing helix-threading peptide. Org Biomol Chem. 2006 Feb 21; 4(4):639-45. PMID: 16467938.
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    54. Gooch BD, Krishnamurthy M, Shadid M, Beal P. Binding of helix-threading peptides to E. coli 16S ribosomal RNA and inhibition of the S15-16S complex. Chembiochem. 2005 Dec; 6(12):2247-54. PMID: 16245373.
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    55. Beal P. Duplex RNA-binding enzymes: headliners from neurobiology, virology, and development. Chembiochem. 2005 Feb; 6(2):257-66. PMID: 15645515.
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    56. Haudenschild BL, Maydanovych O, Véliz EA, Macbeth MR, Bass BL, Beal P. A transition state analogue for an RNA-editing reaction. J Am Chem Soc. 2004 Sep 15; 126(36):11213-9. PMID: 15355102; PMCID: PMC1823040.
    57. Gooch BD, Beal P. Recognition of duplex RNA by helix-threading peptides. J Am Chem Soc. 2004 Sep 01; 126(34):10603-10. PMID: 15327318.
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    58. Stephens OM, Haudenschild BL, Beal P. The binding selectivity of ADAR2's dsRBMs contributes to RNA-editing selectivity. Chem Biol. 2004 Sep; 11(9):1239-50. PMID: 15380184.
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    59. Puthenveetil S, Véliz EA, Beal P. Site-specific modification of Epstein-Barr virus-encoded RNA 1 with N2-benzylguanosine limits the binding sites occupied by PKR. Chembiochem. 2004 Mar 05; 5(3):383-6. PMID: 14997533.
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    60. Krishnamurthy M, Gooch BD, Beal P. Peptide quinoline conjugates: a new class of RNA-binding molecules. Org Lett. 2004 Jan 08; 6(1):63-6. PMID: 14703351.
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    61. Véliz EA, Easterwood LM, Beal P. Substrate analogues for an RNA-editing adenosine deaminase: mechanistic investigation and inhibitor design. J Am Chem Soc. 2003 Sep 10; 125(36):10867-76. PMID: 12952466.
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    62. Carlson CB, Stephens OM, Beal P. Recognition of double-stranded RNA by proteins and small molecules. Biopolymers. 2003 Sep; 70(1):86-102. PMID: 12925995.
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    63. Jammi NV, Whitby LR, Beal P. Small molecule inhibitors of the RNA-dependent protein kinase. Biochem Biophys Res Commun. 2003 Aug 15; 308(1):50-7. PMID: 12890478.
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    64. Carlson CB, Vuyisich M, Gooch BD, Beal P. Preferred RNA binding sites for a threading intercalator revealed by in vitro evolution. Chem Biol. 2003 Jul; 10(7):663-72. PMID: 12890540.
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    65. Carlson CB, Spanggord RJ, Beal P. Selection of small-molecule mediators of the RNA regulation of PKR, the RNA-dependent protein kinase. Chembiochem. 2002 Sep 02; 3(9):859-65. PMID: 12210987.
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    66. Vuyisich M, Beal P. Controlling protein activity with ligand-regulated RNA aptamers. Chem Biol. 2002 Aug; 9(8):907-13. PMID: 12204690.
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    67. Carlson CB, Beal P. Point of attachment and sequence of immobilized peptide-acridine conjugates control affinity for nucleic acids. J Am Chem Soc. 2002 Jul 24; 124(29):8510-1. PMID: 12121075.
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    68. Vuyisich M, Spanggord RJ, Beal P. The binding site of the RNA-dependent protein kinase (PKR) on EBER1 RNA from Epstein-Barr virus. EMBO Rep. 2002 Jul; 3(7):622-7. PMID: 12101093; PMCID: PMC1084191.
    69. Spanggord RJ, Vuyisich M, Beal P. Identification of binding sites for both dsRBMs of PKR on kinase-activating and kinase-inhibiting RNA ligands. Biochemistry. 2002 Apr 09; 41(14):4511-20. PMID: 11926812.
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