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University of Colorado Department of Biochemistry and Molecular Genetics

Biochemistry and Molecular Genetics
 

Publications


 2014

Plank, T-D.M., Whitehurst, J.T., Cencic, R., Pelletier, J. & Kieft, J.S. (2014) Internal translation initiation from HIV-1 transcripts is conferred by a common RNA structure Translation, 2, e27694; DOI: 10.4161/trla.27294
 
Chapman, E.G., Moon, S.L., Wilusz, J. & Kieft, J.S. (2014) RNA Structures that Resist Degradation by Xrn1 Produce a Pathogenic Dengue Virus RNA. eLife, April 1,  DOI: 10.7554/eLife.01892
 
Chapman, E.G., Costantino, D.A., Rabe, J.L., Moon, S.L., Wilusz, J., Nix, J., & Kieft, J.S. (2014) The structural basis of pathogenic subgenomic flavivirus RNA (sfRNA) production. Science, 344: 307-310.
 
Colussi, T.M., Costantino, D.A., Hammond, J.A., Ruehle, G.M., Nix, J., & Kieft, J.S. (2014) The structural basis of transfer RNA mimicry and conformational plasticity by a viral RNA. Nature, 511: 366-369.
 
Clayton, G. M., Wang, Y., Crawford, F., Novikov, A., Wimberly, B.T., Kieft, J.S., Falta, M.T., Bowerman, N.A., Marrack, P., Fontenot, A.P., Dai, S., & Kappler, J.W. (2014) Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity. Cell, 158, 132-142.
 
Batey, R.T. & Kieft, J.S. (2014) Soaking hexammine cations into RNA crystals to obtain derivatives for phasing diffraction data; In Nucleic Acid Crystallography, Human press series Methods in Molecular Biology, E. Ennifar, ed. in press.
 
Hao, Y., & Kieft, J.S. (2014) Diverse self-association properties within a family of phage packaging RNAs RNA, 20:1759-1774
11

 2013

​Filbin, M.E. Vollmar, B. S., Shi, D., Gonen, T., Kieft, J.S. (2013) HCV IRES manipulates the ribosome to promote the switch from translation to elongation. Nat Struct Mol Biol 20, 150-158.

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

Plank, T-D.M., Whitehurst, J.T., & Kieft, J.S. (2013) Cell type specificity and structural determinants of IRES activity from the 5’ leaders of different HIV-1 transcripts. Nucleic Acids Res. 41, 6698-6714.

10

 2012

Keel, A.Y., Jha, B.K., and Kieft, J.S. (2012) Structural architecture of an RNA that competitively inhibits RNase L. RNA 18: 88-99.
 
Plank, T-D., and Kieft, J.S., The structures of nonprotein-coding RNAs that driven internal ribosome entry site function. Wiley Interdiscip Rev RNA, 2012. 3: 195-212.
1

 2011

​Filbin, M.E. and J.S. Kieft, HCV IRES domain IIb affects the configuration of coding RNA in the 40S subunit's decoding groove. RNA, 2011. 17(7): p. 1258-73
 
Zhu, J., et al., 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. 108(5): p. 1839-44.
 
Vallejos, M., et al., 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.
 
Redzic, J.S., et al., The Retinal Specific CD147 Ig0 Domain: From Molecular Structure to Biological Activity. J Mol Biol, 2011.
 
Liu W, Jankowska-Anyszka M., Piecyk K., Dickson L., Wallace A., Niedzwiecka A., Stepinski J., Stolarski R., Darzynkiewicz E., Kieft .J, Zhao R., Jones D.N., Davis R.E. (2011)Structural basis for nematode eIF4E binding an m(2,2,7)G-Cap and its implications for translation initiation. Nucleic Acids Res. 39: 8820-8832
2

 2010

​Feser, J., et al., Elevated histone expression promotes life span extension. Mol Cell, 2010. 39(5): p. 724-35.
 
Pfingsten, J.S., A.E. Castile, and J.S. Kieft, Mechanistic role of structurally dynamic regions in Dicistroviridae IGR IRESs. J Mol Biol, 2010. 395(1): p. 205-17.
 
Constantineau, J., et al., A synonymous variant in scavenger receptor, class B, type I gene is associated with lower SR-BI protein expression and function. Atherosclerosis, 2010. 210(1): p. 177-82.
 
Hammond, J.A., R.P. Rambo, and J.S. Kieft, Multi-domain packing in the aminoacylatable 3' end of a plant viral RNA. J Mol Biol, 2010. 399(3): p. 450-63.
 
Kieft, J.S., et al., Identification and characterization of anion binding sites in RNA. RNA, 2010. 16(6): p. 1118-23.
3

 2009

Liu, W., et al., Structural insights into parasite eIF4E binding specificity for m7G and m2,2,7G mRNA caps. J Biol Chem, 2009. 284(45): p. 31336-49.
 
Hammond, J.A., et al., Comparison and functional implications of the 3D architectures of viral tRNA-like structures. RNA, 2009. 15(2): p. 294-307.
 
Lee, S.J., et al., An approach to the construction of tailor-made amphiphilic peptides that strongly and selectively bind to hairpin RNA targets. J Am Chem Soc, 2009. 131(6): p. 2224-30.
 
Kieft, J.S., Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures. Virus Res, 2009. 139(2): p. 148-56.
 
Filbin, M.E. and J.S. Kieft, Toward a structural understanding of IRES RNA function. Curr Opin Struct Biol, 2009. 19(3): p. 267-76.
 
Keel, A.Y., et al., Large-scale native preparation of in vitro transcribed RNA. Methods Enzymol, 2009. 469: p. 3-25.
4

 2008

​Costantino, D.A., et al., tRNA-mRNA mimicry drives translation initiation from a viral IRES. Nat Struct Mol Biol, 2008. 15(1): p. 57-64.
 
Timmerman, S.L., et al., The 5' leader of the mRNA encoding the mouse neurotrophin receptor TrkB contains two internal ribosomal entry sites that are differentially regulated. PLoS One, 2008. 3(9): p. e3242.
 
Kieft, J.S. Biophysical analysis of IRES RNAs from the Dicistroviridae: linking architecture to function, in Non-protein coding RNAs; Springer Series in Biophysics Vol 13., N. Walter, S.Woodson, and R. Batey, Eds. 2008, Springer Berlin, Heidelberg, p 317-333
 
Kieft, J.S., Viral IRES RNA structures and ribosome interactions. Trends Biochem Sci, 2008. 33(6): p. 274-83.
 
Pfingsten, J.S. and J.S. Kieft, RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes. RNA, 2008. 14(7): p. 1255-63.
5

 2007

​Pfingsten, J.S., D.A. Costantino, and J.S. Kieft, Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes. J Mol Biol, 2007. 370(5): p. 856-69.
 
Batey, R.T. and J.S. Kieft, Improved native affinity purification of RNA. RNA, 2007. 13(8): p. 1384-9.
 
Keel, A.Y., et al., A general strategy to solve the phase problem in RNA crystallography. Structure, 2007. 15(7): p. 761-72.
 
Kieft, J.S., et al., Structural methods for studying IRES function. Methods Enzymol, 2007. 430: p. 333-71.
6

 2002-2006

​Pfingsten, J.S., D.A. Costantino, and J.S. Kieft, Structural basis for ribosome recruitment and manipulation by a viral IRES RNA. Science, 2006. 314(5804): p. 1450-4.
 
Costantino, D. and J.S. Kieft, A preformed compact ribosome-binding domain in the cricket paralysis-like virus IRES RNAs. RNA, 2005. 11(3): p. 332-43.
 
Kieft, J.S. and R.T. Batey, A general method for rapid and nondenaturing purification of RNAs. RNA, 2004. 10(6): p. 988-959.
 
Kieft, J.S. and J.S. Pfingsten, Weapons in the molecular arms race. Nat Struct Mol Biol, 2005. 12(11): p. 938-9
7

 From J.S. Kieft as graduate student and post-doc

​Kieft, J.S., et al., Crystal structure of an RNA tertiary domain essential to HCV IRES-mediated translation initiation. Nat Struct Biol, 2002. 9(5): p. 370-4.
 
Kieft, J.S., et al., Mechanism of ribosome recruitment by hepatitis C IRES RNA. RNA, 2001. 7(2): p. 194-206.
 
Spahn, C.M., et al., Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science, 2001. 291(5510): p. 1959-62.
 
Rijnbrand, R., et al., The influence of downstream protein-coding sequence on internal ribosome entry on hepatitis C virus and other flavivirus RNAs. RNA, 2001. 7(4): p. 585-97.
 
Kieft, J.S., et al., Mechanisms of internal ribosome entry in translation initiation. Cold Spring Harb Symp Quant Biol, 2001. 66: p. 277-83.
 
Jubin, R., et al., Hepatitis C virus internal ribosome entry site (IRES) stem loop IIId contains a phylogenetically conserved GGG triplet essential for translation and IRES folding. J Virol, 2000. 74(22): p. 10430-7.
 
Kieft, J.S., et al., The hepatitis C virus internal ribosome entry site adopts an ion-dependent tertiary fold. J Mol Biol, 1999. 292(3): p. 513-29.
 
Kieft, J.S. and I. Tinoco, Jr., Solution structure of a metal-binding site in the major groove of RNA complexed with cobalt (III) hexammine. Structure, 1997. 5(5): p. 713-21.
 
Tinoco, I., Jr. and J.S. Kieft, The ion core in RNA folding. Nat Struct Biol, 1997. 4(7): p. 509-12.
8

 Reviews, Book Chapters, and Commentaries

Plank, T-D., and Kieft, J.S., The structures of nonprotein-coding RNAs that driven internal ribosome entry site function. Wiley Interdiscip Rev RNA, 2012. 3: 195-212.
 
Kieft, J.S., Comparing the three-dimensional structures of Dicistroviridae IGR IRES RNAs with other viral RNA structures. Virus Res, 2009. 139(2): p. 148-56.
 
Filbin, M.E. and J.S. Kieft, Toward a structural understanding of IRES RNA function. Curr Opin Struct Biol, 2009. 19(3): p. 267-76.
 
Keel, A.Y., et al., Large-scale native preparation of in vitro transcribed RNA. Methods Enzymol, 2009. 469: p. 3-25.
 
Kieft, J.S. Biophysical analysis of IRES RNAs from the Dicistroviridae: linking architecture to function, in Non-protein coding RNAs; Springer Series in Biophysics Vol 13., N. Walter, S.Woodson, and R. Batey, Eds. 2008, Springer Berlin, Heidelberg, p 317-333
 
Kieft, J.S., Viral IRES RNA structures and ribosome interactions. Trends Biochem Sci, 2008. 33(6): p. 274-83.
 
Pfingsten, J.S. and J.S. Kieft, RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes. RNA, 2008. 14(7): p. 1255-63.
 
Kieft, J.S., et al., Structural methods for studying IRES function. Methods Enzymol, 2007. 430: p. 333-71.
 
Kieft, J.S. and J.S. Pfingsten, Weapons in the molecular arms race. Nat Struct Mol Biol, 2005. 12(11): p. 938-9
 
Tinoco, I., Jr. and J.S. Kieft, The ion core in RNA folding. Nat Struct Biol, 1997. 4(7): p. 509-12.
9