Biology Faculty: Paul Agris

Paul Agris

Professor of Biological Sciences and Chemistry; Director of the RNA Institute
Ph.D., Massachusetts Institute of Technology

Office LS1076
Telephone (518) 437-4448
Fax (518) 437-4456
Email pagris@albany.edu

Areas of Interest

  • Molecular Biology and Biophysics
  • Structure-function relationships of nucleic acids
  • Introduction of modified nucleosides into RNA and DNA
  • Chemical synthesis of oligonucleotides with phosphoramidite chemistries
  • RNA-based drug therapeutics




Research

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Structure-function relationships of nucleic acids, such as that of tRNA in protein synthesis, are fundamental to all cell and molecular biology. In order to probe the structure-function relationships of RNAs as potential targets or tools, we have developed methods for the introduction of native, non-natural, and stable isotope labeled nucleosides. We have found that modified nucleosides in tRNA play an important structural and functional role both within the tRNA molecules and in tRNA anticodon recognition of select codons at the wobble position. Modified nucleosides alter codon "wobble", enhance ribosome binding, explain programmed translational frameshifting, are determinants for aminoacyl-tRNA synthetase recognition, and are involved in human immunodeficiency virus selection of a specific human tRNA to prime reverse transcription.

The introduction of modified nucleosides into RNA and DNA produces tight metal ion binding sites. The sites are formed either directly by the modification providing ligands for the metal, or indirectly by the modification inducing a structural transition in the nucleic acid, thereby exposing ligands not previously available. Mg2+ is the metal of choice, in vivo. However, we have found that heavy, toxic metal compete effectively for the same binding site as Mg2+.

Chemical synthesis of oligonucleotides with phosphoramidite chemistries is used for the site-specific placement of these RNA or DNA nucleosides. The chemical synthesis of oligonucleotides also permits the design of new nucleic acids by introduction of uncommon, modified and non-natural nucleosides for investigations of new functions. Transfer RNA is actually a large set of molecules which we tend to speak of as the generic tRNA structure, and for which one of the most common features are the modified nucleosides. The biophysical aspects of tRNA function are relatively unknown. Our studies of tRNA and other RNAs utilize molecular genetic, microbiological, biochemical and chemical and biophysical (nuclear magnetic resonance, NMR) methods to more clearly and precisely define the site-specific structure-function relationships and design new nucleic acids. For instance, many aspects of tRNA structure have now been found to exist in DNA. Our technologies have permitted us to design a DNA analog to an RNA, and for that DNA to have the same function as the RNA in protein synthesis. The newly designed DNA prevents native tRNA from binding the ribosome. Other DNAs we have designed block aminoacylation of tRNA and posttranslational modification of tRNA.

Publications

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  • 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.

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