Publications

2023

ME Sherlock, CJ Langeberg, JS Kieft. Diversity and modularity of tyrosine-accepting tRNA-like structures. 2023 Jul 10; BioRxiv, doi: 10.1101/2023.07.08.548219.

JS Kieft, C Langeberg. A generalizable scaffold-based approach for structure determination of RNAs by cryo-EM. Nucleic Acids Research. 2023 Oct; gkad784.

2022

Bonilla SL, Kieft JS. The promise of cryo-EM to explore RNA structural dynamics. J Mol Biol. 2022 Sep 30;434(18):167802. doi: 10.1016/j.jmb.2022.167802. Epub 2022 Aug 29.

Bonilla SL, Vicens Q, Kieft JS. Cryo-EM reveals an entangled kinetic trap in the folding of a catalytic RNA. Sci Adv. 2022 Aug 26;8(34):eabq4144. doi: 10.1126/sciadv.abq4144. Epub 2022 Aug 26.

Vicens, Q. & Kieft, J.S. Thought on how to think (and talk) about RNA structure. PNAS, 2022 April;119(17)e2112677119.

2021

Bonilla, S.L., Sherlock, M.E., MacFadden, A., & Kieft, J.S. A viral RNA hijacks host machinery using dynamic conformational changes of a tRNA-like structure. Science. 2021 Nov;374(6570):955-960.

Balas MM, Hartwick EW, Barrington C, Roberts JT, Wu SK, Bettcher R, Griffin AM, Kieft JS, Johnson AM. Establishing RNA-RNA interactions remodels lncRNA structure and promotes PRC2 activity. Sci Adv. 2021 Apr;7(16).

Nichols PJ, Bevers S, Henen M, Kieft JS, Vicens Q, Vögeli B. Recognition of non-CpG repeats in Alu and ribosomal RNAs by the Z-RNA binding domain of ADAR1 induces A-Z junctions. Nat Commun. 2021 Feb 4;12(1):793.

Sherlock ME, Hartwick EW, MacFadden A, Kieft JS. Structural diversity and phylogenetic distribution of valyl tRNA-like structures in viruses. RNA. 2021 Jan;27(1):27-39.

Jones RA, Steckelberg AL, Vicens Q, Szucs MJ, Akiyama BM, Kieft JS. Different tertiary interactions create the same important 3D features in a distinct flavivirus xrRNA. RNA. 2021 Jan;27(1):54-65.

2020

Steckelberg AL, Vicens Q, Costantino DA, Nix JC, Kieft JS. The crystal structure of a Polerovirus exoribonuclease-resistant RNA shows how diverse sequences are integrated into a conserved fold. RNA. 2020 Dec;26(12):1767-1776.

Sparks H, Monogue B, Akiyama B, Kieft J, Beckham JD. Disruption of Zika Virus xrRNA1-Dependent sfRNA1 Production Results in Tissue-Specific Attenuated Viral Replication. Viruses. 2020 Oct 18;12(10).

Szucs MJ, Nichols PJ, Jones RA, Vicens Q, Kieft JS. A New Subclass of Exoribonuclease-Resistant RNA Found in Multiple Genera of Flaviviridae. mBio. 2020 Sep 29;11(5).

Thulson E, Hartwick EW, Cooper-Sansone A, Williams MAC, Soliman ME, Robinson LK, Kieft JS, Mouzakis KD. An RNA pseudoknot stimulates HTLV-1 pro-pol programmed -1 ribosomal frameshifting. RNA. 2020 Apr;26(4):512-528.

2019

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. Computational design of three-dimensional RNA structure and function. Nat Nanotechnol. 2019 Sep;14(9):866-873.

Eisenmesser EZ, Gottschlich A, Redzic JS, Paukovich N, Nix JC, Azam T, Zhang L, Zhao R, Kieft JS, The E, Meng X, Dinarello CA. Interleukin-37 monomer is the active form for reducing innate immunity. Proc Natl Acad Sci U S A. 2019 Mar 19;116(12):5514-5522.

Jaafar ZA, Kieft JS. Viral RNA structure-based strategies to manipulate translation. Nat Rev Microbiol. 2019 Jan;17(2):110-123.

2018

Steckelberg AL, Vicens Q, Kieft JS. Exoribonuclease-Resistant RNAs Exist within both Coding and Noncoding Subgenomic RNAs. mBio. 2018 Dec 18;9(6).

Vicens Q, Kieft JS, Rissland OS. Revisiting the Closed-Loop Model and the Nature of mRNA 5'-3' Communication. Mol Cell. 2018 Dec 6;72(5):805-812.

Hartwick EW, Costantino DA, MacFadden A, Nix JC, Tian S, Das R, Kieft JS. Ribosome-induced RNA conformational changes in a viral 3'-UTR sense and regulate translation levels. Nat Commun. 2018 Nov 29;9(1):5074.

Steckelberg AL, Akiyama BM, Costantino DA, Sit TL, Nix JC, Kieft JS. A folded viral noncoding RNA blocks host cell exoribonucleases through a conformationally dynamic RNA structure. Proc Natl Acad Sci U S A. 2018 Jun 19;115(25):6404-6409.

MacFadden A, O'Donoghue Z, Silva PAGC, Chapman EG, Olsthoorn RC, Sterken MG, Pijlman GP, Bredenbeek PJ, Kieft JS. Mechanism and structural diversity of exoribonuclease-resistant RNA structures in flaviviral RNAs. Nat Commun. 2018 Jan 9;9(1):119.

2016

Jaafar ZA, Oguro A, Nakamura Y, Kieft JS. Translation initiation by the hepatitis C virus IRES requires eIF1A and ribosomal complex remodeling. Elife. 2016 Dec 23;5.

Akiyama BM, Laurence HM, Massey AR, Costantino DA, Xie X, Yang Y, Shi PY, Nix JC, Beckham JD, Kieft JS. Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease. Science. 2016 Dec 2;354(6316):1148-1152.

Hussain T, Llácer JL, Wimberly BT, Kieft JS, Ramakrishnan V. Large-Scale Movements of IF3 and tRNA during Bacterial Translation Initiation. Cell. 2016 Sep 22;167(1):133-144.e13.

Filbin ME, Kieft JS. Linking Α to Ω: diverse and dynamic RNA-based mechanisms to regulate gene expression by 5'-to-3' communication. F1000Res. 2016;5.

Hao Y, Kieft JS. Three-way junction conformation dictates self-association of phage packaging RNAs. RNA Biol. 2016 Jul 2;13(7):635-45.

Akiyama BM, Eiler D, Kieft JS. Structured RNAs that evade or confound exonucleases: function follows form. Curr Opin Struct Biol. 2016 Feb;36:40-7.

Batey RT, Kieft JS. Soaking Hexammine Cations into RNA Crystals to Obtain Derivatives for Phasing Diffraction Data. Methods Mol Biol. 2016;1320:219-32.

2015

Ruehle MD, Zhang H, Sheridan RM, Mitra S, Chen Y, Gonzalez RL, Cooperman BS, Kieft JS. A dynamic RNA loop in an IRES affects multiple steps of elongation factor-mediated translation initiation. Elife. 2015 Nov 2;4.

Ruehle MD, Kieft JS. Molecular prejudice: RNA discrimination against purines allows response to a cellular alarm. Nat Struct Mol Biol. 2015 Oct;22(10):754-6.

Kieft JS, Rabe JL, Chapman EG. New hypotheses derived from the structure of a flaviviral Xrn1-resistant RNA: Conservation, folding, and host adaptation. RNA Biol. 2015;12(11):1169-77.

Kieft JS. Experiences gathered and lessons learned from 20 years of RNA structure. RNA. 2015 Apr;21(4):661-3.

Colussi TM, Costantino DA, Zhu J, Donohue JP, Korostelev AA, Jaafar ZA, Plank TD, Noller HF, Kieft JS. Initiation of translation in bacteria by a structured eukaryotic IRES RNA. Nature. 2015 Mar 5;519(7541):110-3.

2014

Hao Y, Kieft JS. Diverse self-association properties within a family of phage packaging RNAs. RNA. 2014 Nov;20(11):1759-74.

Colussi TM, Costantino DA, Hammond JA, Ruehle GM, Nix JC, Kieft JS. The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA. Nature. 2014 Jul 17;511(7509):366-9.

Clayton GM, Wang Y, Crawford F, Novikov A, Wimberly BT, Kieft JS, Falta MT, Bowerman NA, Marrack P, Fontenot AP, Dai S, Kappler JW. Structural basis of chronic beryllium disease: linking allergic hypersensitivity and autoimmunity. Cell. 2014 Jul 3;158(1):132-42.

Chapman EG, Costantino DA, Rabe JL, Moon SL, Wilusz J, Nix JC, Kieft JS. The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production. Science. 2014 Apr 18;344(6181):307-10.

Chapman EG, Moon SL, Wilusz J, Kieft JS. RNA structures that resist degradation by Xrn1 produce a pathogenic Dengue virus RNA. Elife. 2014 Apr 1;3:e01892.

Plank TD, Whitehurst JT, Cencic R, Pelletier J, Kieft JS. Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure. Translation (Austin). 2014;2(1):e27694.

2013

Plank TD, Whitehurst JT, Kieft JS. Cell type specificity and structural determinants of IRES activity from the 5' leaders of different HIV-1 transcripts. Nucleic Acids Res. 2013 Jul;41(13):6698-714.

Wang H, Ru Y, Sanchez-Carbayo M, Wang X, Kieft JS, Theodorescu D. Translation initiation factor eIF3b expression in human cancer and its role in tumor growth and lung colonization. Clin Cancer Res. 2013 Jun 1;19(11):2850-60.

Filbin ME, Vollmar BS, Shi D, Gonen T, Kieft JS. HCV IRES manipulates the ribosome to promote the switch from translation initiation to elongation. Nat Struct Mol Biol. 2013 Feb;20(2):150-8.

2012

Plank TD, Kieft JS. The structures of nonprotein-coding RNAs that drive internal ribosome entry site function. Wiley Interdiscip Rev RNA. 2012 Mar-Apr;3(2):195-212.

2011

Keel AY, Jha BK, Kieft JS. Structural architecture of an RNA that competitively inhibits RNase L. RNA. 2012 Jan;18(1):88-99.

Liu W, Jankowska-Anyszka M, Piecyk K, Dickson L, Wallace A, Niedzwiecka A, Stepinski J, Stolarski R, Darzynkiewicz E, Kieft J, Zhao R, Jones DN, Davis RE. Structural basis for nematode eIF4E binding an m(2,2,7)G-Cap and its implications for translation initiation. Nucleic Acids Res. 2011 Nov 1;39(20):8820-32.

Redzic JS, Armstrong GS, Isern NG, Jones DN, Kieft JS, Eisenmesser EZ. The retinal specific CD147 Ig0 domain: from molecular structure to biological activity. J Mol Biol. 2011 Aug 5;411(1):68-82.

Vallejos M, Deforges J, Plank TD, Letelier A, Ramdohr P, Abraham CG, Valiente-Echeverría F, Kieft JS, Sargueil B, López-Lastra M. Activity of the human immunodeficiency virus type 1 cell cycle-dependent internal ribosomal entry site is modulated by IRES trans-acting factors. Nucleic Acids Res. 2011 Aug;39(14):6186-200.

Filbin ME, Kieft JS. HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove. RNA. 2011 Jul;17(7):1258-73.

Zhu J, Korostelev A, Costantino DA, Donohue JP, Noller HF, Kieft JS. Crystal structures of complexes containing domains from two viral internal ribosome entry site (IRES) RNAs bound to the 70S ribosome. Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):1839-44.

2010

Feser J, Truong D, Das C, Carson JJ, Kieft J, Harkness T, Tyler JK. Elevated histone expression promotes life span extension. Mol Cell. 2010 Sep 10;39(5):724-35.

Hammond JA, Rambo RP, Kieft JS. Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA. J Mol Biol. 2010 Jun 11;399(3):450-63.

Kieft JS, Chase E, Costantino DA, Golden BL. Identification and characterization of anion binding sites in RNA. RNA. 2010 Jun;16(6):1118-23.

Constantineau J, Greason E, West M, Filbin M, Kieft JS, Carletti MZ, Christenson LK, Rodriguez A. A synonymous variant in scavenger receptor, class B, type I gene is associated with lower SR-BI protein expression and function. Atherosclerosis. 2010 May;210(1):177-82.

Pfingsten JS, Castile AE, Kieft JS. Mechanistic role of structurally dynamic regions in Dicistroviridae IGR IRESs. J Mol Biol. 2010 Jan 8;395(1):205-17.

2009

Keel AY, Easton LE, Lukavsky PJ, Kieft JS. Large-scale native preparation of in vitro transcribed RNA. Methods Enzymol. 2009;469:3-25.

Liu W, Zhao R, McFarland C, Kieft J, Niedzwiecka A, Jankowska-Anyszka M, Stepinski J, Darzynkiewicz E, Jones DN, Davis RE. Structural insights into parasite eIF4E binding specificity for m7G and m2,2,7G mRNA caps. J Biol Chem. 2009 Nov 6;284(45):31336-49.

Filbin ME, Kieft JS. Toward a structural understanding of IRES RNA function. Curr Opin Struct Biol. 2009 Jun;19(3):267-76.

Lee SJ, Hyun S, Kieft JS, Yu J. An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets. J Am Chem Soc. 2009 Feb 18;131(6):2224-30.

Kieft JS. Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures. Virus Res. 2009 Feb;139(2):148-56.

Hammond JA, Rambo RP, Filbin ME, Kieft JS. Comparison and functional implications of the 3D architectures of viral tRNA-like structures. RNA. 2009 Feb;15(2):294-307.

Kieft J, Martinez-Salas E. Preface: functionally critical RNA structures found in positive-sense RNA viruses. Virus Res. 2009 Feb;139(2):135-6.

2008

Pfingsten JS, Kieft JS. RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes. RNA. 2008 Jul;14(7):1255-63.

Kieft JS. Viral IRES RNA structures and ribosome interactions. Trends Biochem Sci. 2008 Jun;33(6):274-83.

Costantino DA, Pfingsten JS, Rambo RP, Kieft JS. tRNA-mRNA mimicry drives translation initiation from a viral IRES. Nat Struct Mol Biol. 2008 Jan;15(1):57-64.

2007

Timmerman SL, Pfingsten JS, Kieft JS, Krushel LA. The 5' leader of the mRNA encoding the mouse neurotrophin receptor TrkB contains two internal ribosomal entry sites that are differentially regulated. PLoS One. 2007 Sep 19;3(9):e3242.

Batey RT, Kieft JS. Improved native affinity purification of RNA. RNA. 2007 Aug;13(8):1384-9.

Pfingsten JS, Costantino DA, Kieft JS. Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes. J Mol Biol. 2007 Jul 27;370(5):856-69.

Keel AY, Rambo RP, Batey RT, Kieft JS. A general strategy to solve the phase problem in RNA crystallography. Structure. 2007 Jul;15(7):761-72.

Kieft JS, Costantino DA, Filbin ME, Hammond J, Pfingsten JS. Structural methods for studying IRES function. Methods Enzymol. 2007;430:333-71.

2006

Pfingsten JS, Costantino DA, Kieft JS. Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science. 2006 Dec 1;314(5804):1450-4.

2005

Kieft JS, Pfingsten JS. Weapons in the molecular arms race. Nat Struct Mol Biol. 2005 Nov;12(11):938-9.

Costantino D, Kieft JS. A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA. 2005 Mar;11(3):332-43.

2004

Kieft JS, Batey RT. A general method for rapid and nondenaturing purification of RNAs. RNA. 2004 Jun;10(6):988-95.