Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA

Ren, Xiaoming; Gelinas, Amy D.; Linehan, Melissa; Iwasaki, Akiko; Wang, Wenshuai; Janjic, Nebojsa; Pyle, Anna Marie

doi:10.1016/j.jmb.2021.167227

Evolving A RIG-I Antagonist: A Modified DNA Aptamer Mimics Viral RNA

Journal Article · 01 October 2021 · J. Mol. Biol.

DOI:https://doi.org/10.1016/j.jmb.2021.167227· OSTI ID:1844718

Ren, Xiaoming; Gelinas, Amy D.; Linehan, Melissa; Iwasaki, Akiko; Wang, Wenshuai; Janjic, Nebojsa; Pyle, Anna Marie

Research Organization:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: DOE - Office Of Science; National Institutes of Health (NIH)

OSTI ID:: 1844718

Journal Information:: J. Mol. Biol., Vol. 433, Issue (21)

Country of Publication:: United States

Language:: ENGLISH

References (39)

The RNA helicase RIG-I has an essential function in double-stranded RNA-induced innate antiviral responses Yoneyama, Mitsutoshi; Kikuchi, Mika; Natsukawa, Takashi Nature Immunology, Vol. 5, Issue 7 https://doi.org/10.1038/ni1087	journal	June 2004
RIG-I-Mediated Antiviral Responses to Single-Stranded RNA Bearing 5'-Phosphates Pichlmair, A.; Schulz, O.; Tan, C. P. Science, Vol. 314, Issue 5801 https://doi.org/10.1126/science.1132998	journal	November 2006
Master sensors of pathogenic RNA – RIG-I like receptors Schlee, Martin Immunobiology, Vol. 218, Issue 11 https://doi.org/10.1016/j.imbio.2013.06.007	journal	November 2013
Novel interferonopathies associated with mutations in RIG-I like receptors Buers, Insa; Nitschke, Yvonne; Rutsch, Frank Cytokine & Growth Factor Reviews, Vol. 29 https://doi.org/10.1016/j.cytogfr.2016.03.005	journal	June 2016
RIG-I-Like Receptors and Type I Interferonopathies Kato, Hiroki; Oh, Seong-Wook; Fujita, Takashi Journal of Interferon & Cytokine Research, Vol. 37, Issue 5 https://doi.org/10.1089/jir.2016.0095	journal	May 2017
Aptamer-Based Multiplexed Proteomic Technology for Biomarker Discovery Gold, Larry; Ayers, Deborah; Bertino, Jennifer PLoS ONE, Vol. 5, Issue 12 https://doi.org/10.1371/journal.pone.0015004	journal	December 2010
5'-Triphosphate RNA Is the Ligand for RIG-I Hornung, V.; Ellegast, J.; Kim, S. Science, Vol. 314, Issue 5801 https://doi.org/10.1126/science.1132505	journal	November 2006
Recognition of 5′ Triphosphate by RIG-I Helicase Requires Short Blunt Double-Stranded RNA as Contained in Panhandle of Negative-Strand Virus Schlee, Martin; Roth, Andreas; Hornung, Veit Immunity, Vol. 31, Issue 1 https://doi.org/10.1016/j.immuni.2009.05.008	journal	July 2009
RIG-I Detects Viral Genomic RNA during Negative-Strand RNA Virus Infection Rehwinkel, Jan; Tan, Choon Ping; Goubau, Delphine Cell, Vol. 140, Issue 3 https://doi.org/10.1016/j.cell.2010.01.020	journal	February 2010
RIG-I in RNA virus recognition Kell, Alison M.; Gale, Michael Virology, Vol. 479-480 https://doi.org/10.1016/j.virol.2015.02.017	journal	May 2015
Unique motifs and hydrophobic interactions shape the binding of modified DNA ligands to protein targets Davies, D. R.; Gelinas, A. D.; Zhang, C. Proceedings of the National Academy of Sciences, Vol. 109, Issue 49 https://doi.org/10.1073/pnas.1213933109	journal	November 2012
Generation of high-affinity DNA aptamers using an expanded genetic alphabet Kimoto, Michiko; Yamashige, Rie; Matsunaga, Ken-ichiro Nature Biotechnology, Vol. 31, Issue 5 https://doi.org/10.1038/nbt.2556	journal	April 2013
Chemically Modified DNA Aptamers Bind Interleukin-6 with High Affinity and Inhibit Signaling by Blocking Its Interaction with Interleukin-6 Receptor Gupta, Shashi; Hirota, Masao; Waugh, Sheela M. Journal of Biological Chemistry, Vol. 289, Issue 12 https://doi.org/10.1074/jbc.M113.532580	journal	January 2014
The C-Terminal Regulatory Domain Is the RNA 5′-Triphosphate Sensor of RIG-I Cui, Sheng; Eisenächer, Katharina; Kirchhofer, Axel Molecular Cell, Vol. 29, Issue 2 https://doi.org/10.1016/j.molcel.2007.10.032	journal	February 2008
The Structural Basis of 5′ Triphosphate Double-Stranded RNA Recognition by RIG-I C-Terminal Domain Lu, Cheng; Xu, Hengyu; Ranjith-Kumar, C. T. Structure, Vol. 18, Issue 8 https://doi.org/10.1016/j.str.2010.05.007	journal	August 2010
Visualizing the Determinants of Viral RNA Recognition by Innate Immune Sensor RIG-I Luo, Dahai; Kohlway, Andrew; Vela, Adriana Structure, Vol. 20, Issue 11 https://doi.org/10.1016/j.str.2012.08.029	journal	November 2012
Parts, assembly and operation of the RIG-I family of motors Rawling, David C.; Pyle, Anna Marie Current Opinion in Structural Biology, Vol. 25 https://doi.org/10.1016/j.sbi.2013.11.011	journal	April 2014
The Thermodynamic Basis for Viral RNA Detection by the RIG-I Innate Immune Sensor Vela, Adriana; Fedorova, Olga; Ding, Steve C. Journal of Biological Chemistry, Vol. 287, Issue 51 https://doi.org/10.1074/jbc.M112.385146	journal	December 2012
Structural basis of RNA recognition and activation by innate immune receptor RIG-I Jiang, Fuguo; Ramanathan, Anand; Miller, Matthew T. Nature, Vol. 479, Issue 7373 https://doi.org/10.1038/nature10537	journal	September 2011
A structure-based model of RIG-I activation Kolakofsky, D.; Kowalinski, E.; Cusack, S. RNA, Vol. 18, Issue 12 https://doi.org/10.1261/rna.035949.112	journal	November 2012
Embracing proteins: structural themes in aptamer–protein complexes Gelinas, Amy D.; Davies, Douglas R.; Janjic, Nebojsa Current Opinion in Structural Biology, Vol. 36 https://doi.org/10.1016/j.sbi.2016.01.009	journal	February 2016
Nucleic Acid Ligands With Protein-like Side Chains: Modified Aptamers and Their Use as Diagnostic and Therapeutic Agents Rohloff, John C.; Gelinas, Amy D.; Jarvis, Thale C. Molecular Therapy - Nucleic Acids, Vol. 3 https://doi.org/10.1038/mtna.2014.49	journal	January 2014
Structural basis for IL-1α recognition by a modified DNA aptamer that specifically inhibits IL-1α signaling Ren, Xiaoming; Gelinas, Amy D.; von Carlowitz, Ira Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-00864-2	journal	October 2017
Structural and functional insights into 5′-ppp RNA pattern recognition by the innate immune receptor RIG-I Wang, Yanli; Ludwig, Janos; Schuberth, Christine Nature Structural & Molecular Biology, Vol. 17, Issue 7 https://doi.org/10.1038/nsmb.1863	journal	June 2010
Structural basis for m7G recognition and 2′-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I Devarkar, Swapnil C.; Wang, Chen; Miller, Matthew T. Proceedings of the National Academy of Sciences, Vol. 113, Issue 3 https://doi.org/10.1073/pnas.1515152113	journal	January 2016
Non-helical DNA Triplex Forms a Unique Aptamer Scaffold for High Affinity Recognition of Nerve Growth Factor Jarvis, Thale C.; Davies, Douglas R.; Hisaminato, Akihiko Structure, Vol. 23, Issue 7 https://doi.org/10.1016/j.str.2015.03.027	journal	July 2015
Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis Davlieva, Milya; Donarski, James; Wang, Jiachen Nucleic Acids Research, Vol. 42, Issue 16 https://doi.org/10.1093/nar/gku743	journal	August 2014
Crystal structure of NF- B (p50)2 complexed to a high-affinity RNA aptamer Huang, D. -B.; Vu, D.; Cassiday, L. A. Proceedings of the National Academy of Sciences, Vol. 100, Issue 16 https://doi.org/10.1073/pnas.1632011100	journal	July 2003
XDS Kabsch, Wolfgang Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2 https://doi.org/10.1107/S0907444909047337	journal	January 2010
Overview of the CCP 4 suite and current developments Winn, Martyn D.; Ballard, Charles C.; Cowtan, Kevin D. Acta Crystallographica Section D Biological Crystallography, Vol. 67, Issue 4 https://doi.org/10.1107/S0907444910045749	journal	March 2011
Phaser.MRage : automated molecular replacement Bunkóczi, Gábor; Echols, Nathaniel; McCoy, Airlie J. Acta Crystallographica Section D Biological Crystallography, Vol. 69, Issue 11 https://doi.org/10.1107/S0907444913022750	journal	October 2013
PHENIX: a comprehensive Python-based system for macromolecular structure solution Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221 https://doi.org/10.1107/S0907444909052925	journal	January 2010
RCrane : semi-automated RNA model building Keating, Kevin S.; Pyle, Anna Marie Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 8 https://doi.org/10.1107/S0907444912018549	journal	July 2012
Coot model-building tools for molecular graphics Emsley, Paul; Cowtan, Kevin Acta Crystallographica Section D Biological Crystallography, Vol. 60, Issue 12, p. 2126-2132 https://doi.org/10.1107/S0907444904019158	journal	November 2004
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Site-specific introduction of functional groups into phosphodiester oligodeoxynucleotides and their thermal stability and nuclease- resistance properties Nomura, Y. Nucleic Acids Research, Vol. 25, Issue 14 https://doi.org/10.1093/nar/25.14.2784	journal	July 1997
Synthesis, thermal stability and resistance to enzymatic hydrolysis of the oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2'-O-methyluridines Ito, T. Nucleic Acids Research, Vol. 31, Issue 10 https://doi.org/10.1093/nar/gkg374	journal	May 2003
Rapid chromatographic technique for preparative separations with moderate resolution Still, W. Clark; Kahn, Michael; Mitra, Abhijit The Journal of Organic Chemistry, Vol. 43, Issue 14 https://doi.org/10.1021/jo00408a041	journal	July 1978
Rapid and efficient synthesis of nucleoside 5'-0-(1-thiotriphosphates), 5'-triphosphates and 2',3'-cyclophosphorothioates using 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one Ludwig, Janos; Eckstein, Fritz The Journal of Organic Chemistry, Vol. 54, Issue 3 https://doi.org/10.1021/jo00264a024	journal	February 1989

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