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Computational design of three-dimensional RNA structure and function.

Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R.

Nat Nanotechnol. 2019 Sep;14(9):866-873. doi: 10.1038/s41565-019-0517-8. Epub 2019 Aug 19.


Interleukin-37 monomer is the active form for reducing innate immunity.

Eisenmesser EZ, Gottschlich A, Redzic JS, Paukovich N, Nix JC, Azam T, Zhang L, Zhao R, Kieft JS, The E, Meng X, Dinarello CA.

Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5514-5522. doi: 10.1073/pnas.1819672116. Epub 2019 Feb 28.


Exoribonuclease-Resistant RNAs Exist within both Coding and Noncoding Subgenomic RNAs.

Steckelberg AL, Vicens Q, Kieft JS.

MBio. 2018 Dec 18;9(6). pii: e02461-18. doi: 10.1128/mBio.02461-18.


Revisiting the Closed-Loop Model and the Nature of mRNA 5'-3' Communication.

Vicens Q, Kieft JS, Rissland OS.

Mol Cell. 2018 Dec 6;72(5):805-812. doi: 10.1016/j.molcel.2018.10.047. Review.


Viral RNA structure-based strategies to manipulate translation.

Jaafar ZA, Kieft JS.

Nat Rev Microbiol. 2019 Jan;17(2):110-123. doi: 10.1038/s41579-018-0117-x. Review.


Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels.

Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS.

Nat Commun. 2018 Nov 29;9(1):5074. doi: 10.1038/s41467-018-07542-x.


A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure.

Steckelberg AL, Akiyama BM, Costantino DA, Sit TL, Nix JC, Kieft JS.

Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6404-6409. doi: 10.1073/pnas.1802429115. Epub 2018 Jun 4.


Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs.

MacFadden A, O'Donoghue Z, Silva PAGC, Chapman EG, Olsthoorn RC, Sterken MG, Pijlman GP, Bredenbeek PJ, Kieft JS.

Nat Commun. 2018 Jan 9;9(1):119. doi: 10.1038/s41467-017-02604-y.


Translation initiation by the hepatitis C virus IRES requires eIF1A and ribosomal complex remodeling.

Jaafar ZA, Oguro A, Nakamura Y, Kieft JS.

Elife. 2016 Dec 23;5. pii: e21198. doi: 10.7554/eLife.21198.


Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease.

Akiyama BM, Laurence HM, Massey AR, Costantino DA, Xie X, Yang Y, Shi PY, Nix JC, Beckham JD, Kieft JS.

Science. 2016 Dec 2;354(6316):1148-1152. Epub 2016 Nov 10.


Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation.

Hussain T, Llácer JL, Wimberly BT, Kieft JS, Ramakrishnan V.

Cell. 2016 Sep 22;167(1):133-144.e13. doi: 10.1016/j.cell.2016.08.074.


Linking Α to Ω: diverse and dynamic RNA-based mechanisms to regulate gene expression by 5'-to-3' communication.

Filbin ME, Kieft JS.

F1000Res. 2016 Aug 19;5. pii: F1000 Faculty Rev-2037. doi: 10.12688/f1000research.7913.1. eCollection 2016. Review.


Three-way junction conformation dictates self-association of phage packaging RNAs.

Hao Y, Kieft JS.

RNA Biol. 2016 Jul 2;13(7):635-45. doi: 10.1080/15476286.2016.1190075. Epub 2016 May 24.


Structured RNAs that evade or confound exonucleases: function follows form.

Akiyama BM, Eiler D, Kieft JS.

Curr Opin Struct Biol. 2016 Feb;36:40-7. doi: 10.1016/ Epub 2016 Jan 12. Review.


A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation.

Ruehle MD, Zhang H, Sheridan RM, Mitra S, Chen Y, Gonzalez RL, Cooperman BS, Kieft JS.

Elife. 2015 Nov 2;4. pii: e08146. doi: 10.7554/eLife.08146.


Molecular prejudice: RNA discrimination against purines allows response to a cellular alarm.

Ruehle MD, Kieft JS.

Nat Struct Mol Biol. 2015 Oct;22(10):754-6. doi: 10.1038/nsmb.3095. No abstract available.


New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation.

Kieft JS, Rabe JL, Chapman EG.

RNA Biol. 2015;12(11):1169-77. doi: 10.1080/15476286.2015.1094599. Epub 2015 Sep 23. Review.


Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data.

Batey RT, Kieft JS.

Methods Mol Biol. 2016;1320:219-32. doi: 10.1007/978-1-4939-2763-0_14.


Experiences gathered and lessons learned from 20 years of RNA structure.

Kieft JS.

RNA. 2015 Apr;21(4):661-3. doi: 10.1261/rna.050831.115. No abstract available.


Initiation of translation in bacteria by a structured eukaryotic IRES RNA.

Colussi TM, Costantino DA, Zhu J, Donohue JP, Korostelev AA, Jaafar ZA, Plank TD, Noller HF, Kieft JS.

Nature. 2015 Mar 5;519(7541):110-3. doi: 10.1038/nature14219. Epub 2015 Feb 4.


Diverse self-association properties within a family of phage packaging RNAs.

Hao Y, Kieft JS.

RNA. 2014 Nov;20(11):1759-74. doi: 10.1261/rna.045948.114. Epub 2014 Sep 22.


Structural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity.

Clayton GM, Wang Y, Crawford F, Novikov A, Wimberly BT, Kieft JS, Falta MT, Bowerman NA, Marrack P, Fontenot AP, Dai S, Kappler JW.

Cell. 2014 Jul 3;158(1):132-42. doi: 10.1016/j.cell.2014.04.048.


The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA.

Colussi TM, Costantino DA, Hammond JA, Ruehle GM, Nix JC, Kieft JS.

Nature. 2014 Jul 17;511(7509):366-9. doi: 10.1038/nature13378. Epub 2014 Jun 8.


The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production.

Chapman EG, Costantino DA, Rabe JL, Moon SL, Wilusz J, Nix JC, Kieft JS.

Science. 2014 Apr 18;344(6181):307-10. doi: 10.1126/science.1250897.


RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA.

Chapman EG, Moon SL, Wilusz J, Kieft JS.

Elife. 2014 Apr 1;3:e01892. doi: 10.7554/eLife.01892.


Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure.

Plank TD, Whitehurst JT, Cencic R, Pelletier J, Kieft JS.

Translation (Austin). 2014 Jan 29;2(1):e27694. doi: 10.4161/trla.27694. eCollection 2014.


Cell type specificity and structural determinants of IRES activity from the 5' leaders of different HIV-1 transcripts.

Plank TD, Whitehurst JT, Kieft JS.

Nucleic Acids Res. 2013 Jul;41(13):6698-714. doi: 10.1093/nar/gkt358. Epub 2013 May 9.


Translation initiation factor eIF3b expression in human cancer and its role in tumor growth and lung colonization.

Wang H, Ru Y, Sanchez-Carbayo M, Wang X, Kieft JS, Theodorescu D.

Clin Cancer Res. 2013 Jun 1;19(11):2850-60. doi: 10.1158/1078-0432.CCR-12-3084. Epub 2013 Apr 10.


HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation.

Filbin ME, Vollmar BS, Shi D, Gonen T, Kieft JS.

Nat Struct Mol Biol. 2013 Feb;20(2):150-8. doi: 10.1038/nsmb.2465. Epub 2012 Dec 23.


The structures of nonprotein-coding RNAs that drive internal ribosome entry site function.

Plank TD, Kieft JS.

Wiley Interdiscip Rev RNA. 2012 Mar-Apr;3(2):195-212. doi: 10.1002/wrna.1105. Epub 2012 Jan 3. Review.


Structural architecture of an RNA that competitively inhibits RNase L.

Keel AY, Jha BK, Kieft JS.

RNA. 2012 Jan;18(1):88-99. doi: 10.1261/rna.030007.111. Epub 2011 Nov 23.


The retinal specific CD147 Ig0 domain: from molecular structure to biological activity.

Redzic JS, Armstrong GS, Isern NG, Jones DN, Kieft JS, Eisenmesser EZ.

J Mol Biol. 2011 Aug 5;411(1):68-82. doi: 10.1016/j.jmb.2011.04.060. Epub 2011 May 19.


HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove.

Filbin ME, Kieft JS.

RNA. 2011 Jul;17(7):1258-73. doi: 10.1261/rna.2594011. Epub 2011 May 23.


Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors.

Vallejos M, Deforges J, Plank TD, Letelier A, Ramdohr P, Abraham CG, Valiente-Echeverría F, Kieft JS, Sargueil B, López-Lastra M.

Nucleic Acids Res. 2011 Aug;39(14):6186-200. doi: 10.1093/nar/gkr189. Epub 2011 Apr 10.


Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome.

Zhu J, Korostelev A, Costantino DA, Donohue JP, Noller HF, Kieft JS.

Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1839-44. doi: 10.1073/pnas.1018582108. Epub 2011 Jan 18.


Identification and characterization of anion binding sites in RNA.

Kieft JS, Chase E, Costantino DA, Golden BL.

RNA. 2010 Jun;16(6):1118-23. doi: 10.1261/rna.2072710. Epub 2010 Apr 21.


Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA.

Hammond JA, Rambo RP, Kieft JS.

J Mol Biol. 2010 Jun 11;399(3):450-63. doi: 10.1016/j.jmb.2010.04.016. Epub 2010 Apr 14.


A synonymous variant in scavenger receptor, class B, type I gene is associated with lower SR-BI protein expression and function.

Constantineau J, Greason E, West M, Filbin M, Kieft JS, Carletti MZ, Christenson LK, Rodriguez A.

Atherosclerosis. 2010 May;210(1):177-82. doi: 10.1016/j.atherosclerosis.2009.11.029. Epub 2009 Nov 26.


Mechanistic role of structurally dynamic regions in Dicistroviridae IGR IRESs.

Pfingsten JS, Castile AE, Kieft JS.

J Mol Biol. 2010 Jan 8;395(1):205-17. doi: 10.1016/j.jmb.2009.10.047. Epub 2009 Oct 28.


Toward a structural understanding of IRES RNA function.

Filbin ME, Kieft JS.

Curr Opin Struct Biol. 2009 Jun;19(3):267-76. doi: 10.1016/ Epub 2009 Apr 9. Review.


An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets.

Lee SJ, Hyun S, Kieft JS, Yu J.

J Am Chem Soc. 2009 Feb 18;131(6):2224-30. doi: 10.1021/ja807609m.


Comparison and functional implications of the 3D architectures of viral tRNA-like structures.

Hammond JA, Rambo RP, Filbin ME, Kieft JS.

RNA. 2009 Feb;15(2):294-307. doi: 10.1261/rna.1360709.


Large-scale native preparation of in vitro transcribed RNA.

Keel AY, Easton LE, Lukavsky PJ, Kieft JS.

Methods Enzymol. 2009;469:3-25. doi: 10.1016/S0076-6879(09)69001-7. Epub 2009 Nov 17.


The 5' leader of the mRNA encoding the mouse neurotrophin receptor TrkB contains two internal ribosomal entry sites that are differentially regulated.

Timmerman SL, Pfingsten JS, Kieft JS, Krushel LA.

PLoS One. 2007 Sep 19;3(9):e3242. doi: 10.1371/journal.pone.0003242.


Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures.

Kieft JS.

Virus Res. 2009 Feb;139(2):148-56. doi: 10.1016/j.virusres.2008.07.007. Epub 2008 Aug 15. Review.


RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes.

Pfingsten JS, Kieft JS.

RNA. 2008 Jul;14(7):1255-63. doi: 10.1261/rna.987808. Epub 2008 May 30. Review.


Viral IRES RNA structures and ribosome interactions.

Kieft JS.

Trends Biochem Sci. 2008 Jun;33(6):274-83. doi: 10.1016/j.tibs.2008.04.007. Epub 2008 May 28. Review.


tRNA-mRNA mimicry drives translation initiation from a viral IRES.

Costantino DA, Pfingsten JS, Rambo RP, Kieft JS.

Nat Struct Mol Biol. 2008 Jan;15(1):57-64. Epub 2007 Dec 23.


Structural methods for studying IRES function.

Kieft JS, Costantino DA, Filbin ME, Hammond J, Pfingsten JS.

Methods Enzymol. 2007;430:333-71.


A general strategy to solve the phase problem in RNA crystallography.

Keel AY, Rambo RP, Batey RT, Kieft JS.

Structure. 2007 Jul;15(7):761-72.

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