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Small-Molecule Antagonists of the RIG-I Innate Immune Receptor.

Rawling DC, Jagdmann GE Jr, Potapova O, Pyle AM.

ACS Chem Biol. 2020 Feb 21;15(2):311-317. doi: 10.1021/acschembio.9b00810. Epub 2020 Jan 27.


RIG-I Recognition of RNA Targets: The Influence of Terminal Base Pair Sequence and Overhangs on Affinity and Signaling.

Ren X, Linehan MM, Iwasaki A, Pyle AM.

Cell Rep. 2019 Dec 17;29(12):3807-3815.e3. doi: 10.1016/j.celrep.2019.11.052.


RNA binding activates RIG-I by releasing an autorepressed signaling domain.

Dickey TH, Song B, Pyle AM.

Sci Adv. 2019 Oct 2;5(10):eaax3641. doi: 10.1126/sciadv.aax3641. eCollection 2019 Oct.


Intratumoral delivery of RIG-I agonist SLR14 induces robust antitumor responses.

Jiang X, Muthusamy V, Fedorova O, Kong Y, Kim DJ, Bosenberg M, Pyle AM, Iwasaki A.

J Exp Med. 2019 Dec 2;216(12):2854-2868. doi: 10.1084/jem.20190801. Epub 2019 Oct 10.


Discovery of N-Substituted 3-Amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic Acids as Highly Potent Third-Generation Inhibitors of Human Arginase I and II.

Van Zandt MC, Jagdmann GE, Whitehouse DL, Ji M, Savoy J, Potapova O, Cousido-Siah A, Mitschler A, Howard EI, Pyle AM, Podjarny AD.

J Med Chem. 2019 Sep 12;62(17):8164-8177. doi: 10.1021/acs.jmedchem.9b00931. Epub 2019 Aug 23.


Sensitive detection of structural features and rearrangements in long, structured RNA molecules.

Adams RL, Huston NC, Tavares RCA, Pyle AM.

Methods Enzymol. 2019;623:249-289. doi: 10.1016/bs.mie.2019.04.002. Epub 2019 Apr 22.


Phylogenetic Analysis with Improved Parameters Reveals Conservation in lncRNA Structures.

Tavares RCA, Pyle AM, Somarowthu S.

J Mol Biol. 2019 Apr 5;431(8):1592-1603. doi: 10.1016/j.jmb.2019.03.012. Epub 2019 Mar 16.


RIG-I Selectively Discriminates against 5'-Monophosphate RNA.

Ren X, Linehan MM, Iwasaki A, Pyle AM.

Cell Rep. 2019 Feb 19;26(8):2019-2027.e4. doi: 10.1016/j.celrep.2019.01.107.


Small molecules that target group II introns are potent antifungal agents.

Fedorova O, Jagdmann GE Jr, Adams RL, Yuan L, Van Zandt MC, Pyle AM.

Nat Chem Biol. 2018 Dec;14(12):1073-1078. doi: 10.1038/s41589-018-0142-0. Epub 2018 Oct 15.


Therapeutically Active RIG-I Agonist Induces Immunogenic Tumor Cell Killing in Breast Cancers.

Elion DL, Jacobson ME, Hicks DJ, Rahman B, Sanchez V, Gonzales-Ericsson PI, Fedorova O, Pyle AM, Wilson JT, Cook RS.

Cancer Res. 2018 Nov 1;78(21):6183-6195. doi: 10.1158/0008-5472.CAN-18-0730. Epub 2018 Sep 17.


Regional Differences in Airway Epithelial Cells Reveal Tradeoff between Defense against Oxidative Stress and Defense against Rhinovirus.

Mihaylova VT, Kong Y, Fedorova O, Sharma L, Dela Cruz CS, Pyle AM, Iwasaki A, Foxman EF.

Cell Rep. 2018 Sep 11;24(11):3000-3007.e3. doi: 10.1016/j.celrep.2018.08.033.


microRNA-122 amplifies hepatitis C virus translation by shaping the structure of the internal ribosomal entry site.

Schult P, Roth H, Adams RL, Mas C, Imbert L, Orlik C, Ruggieri A, Pyle AM, Lohmann V.

Nat Commun. 2018 Jul 4;9(1):2613. doi: 10.1038/s41467-018-05053-3.


A minimal RNA ligand for potent RIG-I activation in living mice.

Linehan MM, Dickey TH, Molinari ES, Fitzgerald ME, Potapova O, Iwasaki A, Pyle AM.

Sci Adv. 2018 Feb 21;4(2):e1701854. doi: 10.1126/sciadv.1701854. eCollection 2018 Feb.


Environmentally Triggerable Retinoic Acid-Inducible Gene I Agonists Using Synthetic Polymer Overhangs.

Palmer CR, Jacobson ME, Fedorova O, Pyle AM, Wilson JT.

Bioconjug Chem. 2018 Mar 21;29(3):742-747. doi: 10.1021/acs.bioconjchem.7b00697. Epub 2018 Jan 19.


An ultraprocessive, accurate reverse transcriptase encoded by a metazoan group II intron.

Zhao C, Liu F, Pyle AM.

RNA. 2018 Feb;24(2):183-195. doi: 10.1261/rna.063479.117. Epub 2017 Nov 6.


NS3 from Hepatitis C Virus Strain JFH-1 Is an Unusually Robust Helicase That Is Primed To Bind and Unwind Viral RNA.

Zhou T, Ren X, Adams RL, Pyle AM.

J Virol. 2017 Dec 14;92(1). pii: e01253-17. doi: 10.1128/JVI.01253-17. Print 2018 Jan 1.


The SMAD3 transcription factor binds complex RNA structures with high affinity.

Dickey TH, Pyle AM.

Nucleic Acids Res. 2017 Nov 16;45(20):11980-11988. doi: 10.1093/nar/gkx846.


Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling.

Ren X, Gelinas AD, von Carlowitz I, Janjic N, Pyle AM.

Nat Commun. 2017 Oct 9;8(1):810. doi: 10.1038/s41467-017-00864-2.


The group II intron maturase: a reverse transcriptase and splicing factor go hand in hand.

Zhao C, Pyle AM.

Curr Opin Struct Biol. 2017 Dec;47:30-39. doi: 10.1016/ Epub 2017 May 18. Review.


Functional RNA structures throughout the Hepatitis C Virus genome.

Adams RL, Pirakitikulr N, Pyle AM.

Curr Opin Virol. 2017 Jun;24:79-86. doi: 10.1016/j.coviro.2017.04.007. Epub 2017 May 13. Review.


Structural Insights into the Mechanism of Group II Intron Splicing.

Zhao C, Pyle AM.

Trends Biochem Sci. 2017 Jun;42(6):470-482. doi: 10.1016/j.tibs.2017.03.007. Epub 2017 Apr 21. Review.


Selective RNA targeting and regulated signaling by RIG-I is controlled by coordination of RNA and ATP binding.

Fitzgerald ME, Rawling DC, Potapova O, Ren X, Kohlway A, Pyle AM.

Nucleic Acids Res. 2017 Feb 17;45(3):1442-1454. doi: 10.1093/nar/gkw816.


Opportunities and Challenges in RNA Structural Modeling and Design.

Schlick T, Pyle AM.

Biophys J. 2017 Jul 25;113(2):225-234. doi: 10.1016/j.bpj.2016.12.037. Epub 2017 Feb 2.


Visualizing the secondary and tertiary architectural domains of lncRNA RepA.

Liu F, Somarowthu S, Pyle AM.

Nat Chem Biol. 2017 Mar;13(3):282-289. doi: 10.1038/nchembio.2272. Epub 2017 Jan 9.


Group II Intron Self-Splicing.

Pyle AM.

Annu Rev Biophys. 2016 Jul 5;45:183-205. doi: 10.1146/annurev-biophys-062215-011149. Review.


Transcriptome analysis of human cumulus cells reveals hypoxia as the main determinant of follicular senescence.

Molinari E, Bar H, Pyle AM, Patrizio P.

Mol Hum Reprod. 2016 Aug;22(8):866-76. doi: 10.1093/molehr/gaw038. Epub 2016 Jun 6.


Crystal structures of a group II intron maturase reveal a missing link in spliceosome evolution.

Zhao C, Pyle AM.

Nat Struct Mol Biol. 2016 Jun;23(6):558-65. doi: 10.1038/nsmb.3224. Epub 2016 May 2.


Editorial overview: Nucleic acids and their protein complexes.

Lilley DM, Pyle AM.

Curr Opin Struct Biol. 2016 Feb;36:vii-viii. doi: 10.1016/ Epub 2016 Mar 2. No abstract available.


The Coding Region of the HCV Genome Contains a Network of Regulatory RNA Structures.

Pirakitikulr N, Kohlway A, Lindenbach BD, Pyle AM.

Mol Cell. 2016 Apr 7;62(1):111-20. doi: 10.1016/j.molcel.2016.01.024. Epub 2016 Feb 25.


Challenges in RNA Structural Modeling and Design.

Pyle AM, Schlick T.

J Mol Biol. 2016 Feb 27;428(5 Pt A):733-735. doi: 10.1016/j.jmb.2016.02.012. Epub 2016 Feb 12. No abstract available.


Crystal structure of group II intron domain 1 reveals a template for RNA assembly.

Zhao C, Rajashankar KR, Marcia M, Pyle AM.

Nat Chem Biol. 2015 Dec;11(12):967-72. doi: 10.1038/nchembio.1949. Epub 2015 Oct 26.


Establishing the role of ATP for the function of the RIG-I innate immune sensor.

Rawling DC, Fitzgerald ME, Pyle AM.

Elife. 2015 Sep 15;4. pii: e09391. doi: 10.7554/eLife.09391.


Native Purification and Analysis of Long RNAs.

Chillón I, Marcia M, Legiewicz M, Liu F, Somarowthu S, Pyle AM.

Methods Enzymol. 2015;558:3-37. doi: 10.1016/bs.mie.2015.01.008. Epub 2015 Feb 27.


HOTAIR forms an intricate and modular secondary structure.

Somarowthu S, Legiewicz M, Chillón I, Marcia M, Liu F, Pyle AM.

Mol Cell. 2015 Apr 16;58(2):353-61. doi: 10.1016/j.molcel.2015.03.006. Epub 2015 Apr 9.


Rediscovering RNA.

Pyle AM.

RNA. 2015 Apr;21(4):714-5. doi: 10.1261/rna.050807.115. No abstract available.


Temperature-dependent innate defense against the common cold virus limits viral replication at warm temperature in mouse airway cells.

Foxman EF, Storer JA, Fitzgerald ME, Wasik BR, Hou L, Zhao H, Turner PE, Pyle AM, Iwasaki A.

Proc Natl Acad Sci U S A. 2015 Jan 20;112(3):827-32. doi: 10.1073/pnas.1411030112. Epub 2015 Jan 5.


Looking at LncRNAs with the ribozyme toolkit.

Pyle AM.

Mol Cell. 2014 Oct 2;56(1):13-7. doi: 10.1016/j.molcel.2014.08.025. Review.


The RIG-I ATPase core has evolved a functional requirement for allosteric stabilization by the Pincer domain.

Rawling DC, Kohlway AS, Luo D, Ding SC, Pyle AM.

Nucleic Acids Res. 2014 Oct;42(18):11601-11. doi: 10.1093/nar/gku817. Epub 2014 Sep 12.


The linker region of NS3 plays a critical role in the replication and infectivity of hepatitis C virus.

Kohlway A, Pirakitikulr N, Ding SC, Yang F, Luo D, Lindenbach BD, Pyle AM.

J Virol. 2014 Sep;88(18):10970-4. doi: 10.1128/JVI.00745-14. Epub 2014 Jun 25.


An evolving arsenal: viral RNA detection by RIG-I-like receptors.

Fitzgerald ME, Rawling DC, Vela A, Pyle AM.

Curr Opin Microbiol. 2014 Aug;20:76-81. doi: 10.1016/j.mib.2014.05.004. Epub 2014 Jun 7. Review.


Parts, assembly and operation of the RIG-I family of motors.

Rawling DC, Pyle AM.

Curr Opin Struct Biol. 2014 Apr;25:25-33. doi: 10.1016/ Epub 2013 Dec 20. Review.


Principles of ion recognition in RNA: insights from the group II intron structures.

Marcia M, Pyle AM.

RNA. 2014 Apr;20(4):516-27. doi: 10.1261/rna.043414.113. Epub 2014 Feb 25.


Dicer-related helicase 3 forms an obligate dimer for recognizing 22G-RNA.

Fitzgerald ME, Vela A, Pyle AM.

Nucleic Acids Res. 2014 Apr;42(6):3919-30. doi: 10.1093/nar/gkt1383. Epub 2014 Jan 15.


Coordinating the party: assembly factors and ribogenesis.

Pyle AM.

Mol Cell. 2013 Nov 21;52(4):469-70. doi: 10.1016/j.molcel.2013.11.007.


Visualizing the ai5γ group IIB intron.

Somarowthu S, Legiewicz M, Keating KS, Pyle AM.

Nucleic Acids Res. 2014 Feb;42(3):1947-58. doi: 10.1093/nar/gkt1051. Epub 2013 Nov 6.


Solving nucleic acid structures by molecular replacement: examples from group II intron studies.

Marcia M, Humphris-Narayanan E, Keating KS, Somarowthu S, Rajashankar K, Pyle AM.

Acta Crystallogr D Biol Crystallogr. 2013 Nov;69(Pt 11):2174-85. doi: 10.1107/S0907444913013218. Epub 2013 Oct 12. Review.


Hepatitis C virus RNA replication and virus particle assembly require specific dimerization of the NS4A protein transmembrane domain.

Kohlway A, Pirakitikulr N, Barrera FN, Potapova O, Engelman DM, Pyle AM, Lindenbach BD.

J Virol. 2014 Jan;88(1):628-42. doi: 10.1128/JVI.02052-13. Epub 2013 Oct 30.


Noncoding RNAs: A story of networks and long-distance relationships.

Ostankovitch M, Pyle AM.

J Mol Biol. 2013 Oct 9;425(19):3577-81. doi: 10.1016/j.jmb.2013.07.032. Epub 2013 Jul 30. No abstract available.


Defining the functional determinants for RNA surveillance by RIG-I.

Kohlway A, Luo D, Rawling DC, Ding SC, Pyle AM.

EMBO Rep. 2013 Sep;14(9):772-9. doi: 10.1038/embor.2013.108. Epub 2013 Jul 30.

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