Publications: P.F. Agris

  • Scheunemann AE, Graham WD, Vendeix FA, Agris PF. (2010) Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA Nucleic Acids Res. 38(9):3094-105.
  • Bilbille, Y., Vendeix, F.A.P., Guenther, R., Malkiewicz, A., Arixa, X., Vilarrasa, J. and Agris, P.F. (2009) The structure of the human tRNALys3 anticodon bound to the HIV genome Loop I is stabilized by modified nucleosides. Nucleic Acids Research 37:3342-53.
  • Vendeix, F.A.P., Munoz, A. and Agris, P.F. (2009) Free energy calculation of modified base-pair formation in explicit solvent: A predictive model. RNA, 15:2278-87.
  • Gustilo, E.M., Vendeix, F.A.P. and Agris, P.F. (2008) tRNA’s modifications bring order to gene expression. Curr. Opin. Microb. 11:134-140.
  • Vendeix, F.A.P., Graham, W.D., Dziergowska, A., Gustilo, E., Sproat, B., Malkiewicz, A., and Agris, P.F. (2008) Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding. Biochemistry 47:6117-6129.
  • Agris, P.F. (2008) Bringing order to translation: Contributions of tRNA anticodon domain modifications. EMBO Reports 9:629-635.
  • Lusic, H. and Gustilo, E., Vendeix, F.A.P., Kaiser, R., Delany, M.O., Graham, W.D., Moye, V., Cantara, W.A., Agris, P.F. and Deiters, A. (2008) Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNAMet. Nucleic Acids Research, 36:6548-6557.
  • Jones, C.N., and Jones, C.I., Graham, W.D., Agris, P.F.,  and Spremulli, L.L. (2008) A single point mutation in human mitochondrial tRNAMet causes disease by disrupting Mg2+ binding leading to tRNA misfolding. J. Biol. Chem., 283: 34445-34456.
  • Eshete, M., Marchbank, M.T., Deutscher, S.L., and Agris, P.F. (2007) Specificity of phage display selected peptides as tools for recognition of modified vs. unmodified anticodon stem and loop domains of tRNA. The Protein J. 26: 61-73.
  • Weixlbaumer, A., Murphy, F. IV, Vendeix, F.A.P., Dziergowska, A., Malkiewicz, A., Agris, P.F. and Ramakrishnan, V. (2007) Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. Nature Struct. Mol. Biol. 14:498-502.
  • Gustilo, E.M., Dubois, D., Lapointe, J., and Agris P.F. (2007) E. coli glutamyl-tRNA synthetase is inhibited by anticodon stem-loop domains and a minihelix. RNA Biology 4:85-92.
  • Review: Agris, P.F. (2006) Wobble Decoding: 40 Years of modification, J. Mol. Biol. 366, 1-13.
  • Agris, P.F., Vendeix, F., and Graham, W.D. (2006) tRNA's wobble decoding of the genome: 40 years of modification. J. Mol. Biol., 366:1-13.
  • Nelson, A, Henkin, T., and Agris, P.F. (2006) Folding interactions of an mRNA 5’-UTR that regulates gene expression: Interaction with a regulatory tRNA. RNA 12:1254-1261.
  • Jones, C.I., Spencer, A.C., Hsu, J.L., Spremulli, L.L., Martinis, S.A. DeRider, M., and Agris, P.F. (2006) A counterintuitive Mg2+-dependent and modification-assisted functional folding of mitochondrial tRNAs. J. Mol. Biol., 362:771-786.
  • Gagnon, K., Zhang, X., Agris, P.F., and Maxwell, S.E. (2006) Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling. J. Mol. Biol., 362:1025-1042.
  • Dressman, H.K., Barley-Maloney, L., Rowlette, L-L., Agris, P.F., and Garcia-Blanco, M.A. (2006) Assessing incomplete deprotection of microarray oligonucleosides in situ. Nucl. Acids Res. 34, e131.
  • Barley-Maloney, L. and Agris, P.F. (2006) Quality assessment of commercial siRNA and DNA: monoclonal antibodies and a high through-put chemiluminescense assay. Analytical Biochemistry 360:172-174
  • Review: Agris, PF (2004) Decoding the Genome, A Modified View. Nucleic Acids Res. 32, 223-238.
  • Mucha, P, Szyk, A., Rekowski, P., and Agris, P.F. (2004) Sequence altered peptide adopts optimum conformation for modification-dependent binding of the yeast tRNAPhe anticodon domain.The Protein J. 23:33-38.
  • Agris, P.F. (2004) Decoding the genome, A modified view. Nucl. Acids Res. 32:223-238.
  • Phelps, S., Joseph, S., Malkiewicz, A., and Agris, P.F. (2004) Modification-dependent tRNA translocation on the ribosome. J. Mol. Biol. 338:439-444.
  • Guenther, R.H., Sit, T.L., Gracz, H.S., Dolan, M.A., Townsend, H.L., Liu, G, Newman, W.H., Agris, P.F., and Lommel, S. (2004) Structural characterization of an intermolecular RNA–RNA interaction involved in the transcription regulation element of a bipartite plant virus. Nucl. Acids. Res. 32:2819-2828.
  • Murphy, F.V., IV, Ramakrishnan, V., Malkiewicz, A., and Agris, P.F. (2004) The role of modifications in codon recognition and discrimination: tRNALysUUU. Nature Struct. Biol. 11:1186-1191. (Accompanying Commentary by Dr. Rachel Green)
  • Mucha, P., Szyk, A., Rekowski, P., and Agris, P.F. (2003) Using capillary electrophoresis to study methylation effect on RNA-peptide interaction. Acta Biochimica Polinica 50:57-64.
  • Stuart, J.W., and Koshlap, K.M., Guenther, R., and Agris, P.F. (2003) Naturally-occurring modification restricts the anticodon domain conformational space of tRNAPhe. J. Mol. Biol. 334:901-918.
  • Agris, P. F., Simkins, S. G., Smith, S., and Fu, C (2002) Quality control in antisense oligonucleotide synthesis. Nature Biotechnology, 20, 871-872.
  • Yarian, C., Townsend, H., Czestkowski, W., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., and Agris P.F. (2002) Accurate translation of the genetic code depends on tRNA's modified nucleosides. J. Biol. Chem. 277:16391-16395.
  • Mucha, P., Agnieszka, A., Rekowski, P., Guenther, R., and Agris, P.F. (2002) Interaction of RNA with phage display selected peptides analyzed by capillary electrophoresis mobility shift assay. RNA 8:698-704.
  • Fu, C., Smith, S., Simkins, S.G., Guenther, R., and Agris, P.F. (2002) Oligonucleotide quality control: monoclonal antibody identification and quantification of protecting groups remaining in commercial products. Analytical Biochemistry, 306:135-143.
  • Nobles, K.N. and Yarian, C.S., Guenther, R.H., and Agris, P.F. (2001) Highly conserved modified nucleosides influence Mg2+_dependent tRNA folding. Nucl Acids Res. 30:4751-4760.
  • Mucha, P., Szyk, A., Rekowski, P., Weiss, P.A. and Agris, P.F. (2001) Anticodon domain methylated nucleosides of yeast tRNAPhe are significant recognition determinants in the binding of a phage display selected peptide. Biochemistry, 40: 14191-14199.
  • Sengupta, R. Vainauskas, S., Yarian, C., Sochacka, E., Malkiewicz, A., Guenther, R.H., Koshlap, K.M., Agris P.F. (2000) Modified constructs of tRNA's TYC-domain to probe substrate conformational requirements of m1A58 and m5U54-tRNA methyltransferases. Nucl. Acids Res. 28:1374-1380.
  • Sochacka, E., Czerwinska, G., Guenther, R., Ansari, H., Cain, C. Yarian, H., Agris P.F., and Malkiewicz, A. (2000) Synthesis and properties of uniquely modified oligoribonucleotides of yeast tRNAPhe fragments with 6-methyluridine and 5,6-dimethyluridine at site -specific positions. Nucleosides and Nucleotides and Nucleic Acids 19:515-531
  • Ashraf, S.S., Guenther, R.H., Ansari, G., Malkiewicz, A., Sochacka, E., and Agris, P.F. (2000) Role of modified nucleosides of yeast tRNAPhe in ribosomal binding. Cell Biochem. Biophys.33:241-252.
  • Stuart, J.W., Gdaniec, Z., Guenther, R., Marszalek, M., Sochacka, E., Malkiewicz, A., and Agris, P.F. (2000) Functional anticodon architecture of human tRNALys3 includes disruption of intra-loop hydrogen bonding by the naturally occurring amino acid modification, t6A. Biochemistry39:13396-13404.
  • Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, M., Guenther, R., Miskiewicz, A., and Agris, P.F. (2000) tRNALysUUU species require anticodon domain modified nucleosides for Watson-Crick and wobble codon binding. Biochemistry 39:13390-13395.