Paul F. Agris

Vendeix, F. A. P., Murphy, F. V., Cantara, W. A., Leszczynska, G., Gustilo, E. M., Sproat, B., … Agris, P. F. (2012). Human tRNA(UUU)(LYs3) Is Pre-Structured by Natural Modifications for Cognate and Wobble Codon Binding through Keto-Enol Tautomerism. JOURNAL OF MOLECULAR BIOLOGY, 416(4), 467–485. https://doi.org/10.1016/j.jmb.2011.12.048

Harris, K. A., Jones, V., Bilbille, Y., Swairjo, M. A., & Agris, P. F. (2011). YrdC exhibits properties expected of a subunit for a tRNA threonylcarbamoyl transferase. RNA, 17(9), 1678–1687.

Scheunemann, A. E., Graham, W. D., Vendeix, F. A. P., & Agris, P. F. (2010). Binding of aminoglycoside antibiotics to helix 69 of 23S rRNA. Nucleic Acids Research, 38(9), 3094–3105.

Vendeix, F. A. P., Munoz, A. M., & Agris, P. F. (2009). Free energy calculation of modified base-pair formation in explicit solvent: A predictive model. RNA, 15(12), 2278–2287. https://doi.org/10.1261/rna.1734309

Bilbille, Y., Vendeix, F. A. P., Guenther, R., Malkiewicz, A., Ariza, X., Vilarrasa, J., & Agris, P. F. (2009). The structure of the human tRNA(Lys3) anticodon bound to the HIV genome is stabilized by modified nucleosides and adjacent mismatch base pairs. NUCLEIC ACIDS RESEARCH, 37(10), 3342–3353. https://doi.org/10.1093/nar/gkp187

Jones, C. N., Jones, C. I., Graham, W. D., Agris, P. F., & Spremulli, L. L. (2008). A Disease-causing Point Mutation in Human Mitochondrial tRNA(Met) Results in tRNA Misfolding Leading to Defects in Translational Initiation and Elongation. JOURNAL OF BIOLOGICAL CHEMISTRY, 283(49), 34445–34456. https://doi.org/10.1074/jbc.M806992200

Vendeix, F. A. P., Dziergowska, A., Gustilo, E. M., Graham, W. D., Sproat, B., Malkiewicz, A., & Agris, P. F. (2008). Anticodon domain modifications contribute order to tRNA for ribosome-mediated codon binding. BIOCHEMISTRY, 47(23), 6117–6129. https://doi.org/10.1021/bi702356j

Agris, P. F. (2008). Bringing order to translation: the contributions of transfer RNA anticodon-domain modifications. EMBO REPORTS, 9(7), 629–635. https://doi.org/10.1038/embor.2008.104

Lusic, H., Gustilo, E. M., Vendeix, F. A. P., Kaiser, R., Delaney, M. O., Graham, W. D., … Deiters, A. (2008). Synthesis and investigation of the 5-formylcytidine modified, anticodon stem and loop of the human mitochondrial tRNA(Met). NUCLEIC ACIDS RESEARCH, 36(20), 6548–6557. https://doi.org/10.1093/nar/gkn703

Gustilo, E. M., Franck, A. P. F., & Agris, P. F. (2008). [Review of tRNA's modifications bring order to gene expression]. Current Opinion in Microbiology, 11(2), 134–140.

Gustilo, E. M., Dubois, D. Y., Lapointe, J., & Agris, P. F. (2007). E-coli glutamyl-tRNA synthetase is inhibited by anticodon stem-loop domains and a minihelix. RNA BIOLOGY, 4(2), 85–92. https://doi.org/10.4161/rna.4.2.4736

Weixlbaumer, A., Murphy, F. V., Dziergowska, A., Malkiewicz, A., Vendeix, F. A. P., Agris, P. F., & Ramakrishnan, V. (2007). Mechanism for expanding the decoding capacity of transfer RNAs by modification of uridines. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 14(6), 498–502. https://doi.org/10.1038/nsmb1242

Barley-Maloney, L., & Agris, P. F. (2007). Quality assessment of commercial small interfering RNA and DNA: Monoclonal antibodies and a high-throughput chemiluminescence assay. Analytical Biochemistry, 360(1), 172–174.

Eshete, M., Marchbank, M. T., Deutscher, S. L., Sproat, B., Leszczynska, G., Malkiewicz, A., & Agris, P. F. (2007). Specificity of phage display selected peptides for modified anticodon stem and loop domains of tRNA. PROTEIN JOURNAL, 26(1), 61–73. https://doi.org/10.1007/s10930-006-9046-z

Agris, P. F., Vendeix, F. A. P., & Graham, W. D. (2007). [Review of tRNA's wobble decoding of the genome: 40 years of modification]. Journal of Molecular Biology, 366(1), 1–13.

Jones, C. I., Spencer, A. C., Hsu, J. L., Spremulli, L. L., Martinis, S. A., DeRider, M., & Agris, P. F. (2006). A counterintuitive Mg2+-dependent and modification-assisted functional folding of mitochondrial tRNAs. JOURNAL OF MOLECULAR BIOLOGY, 362(4), 771–786. https://doi.org/10.1016/j.jmb.2006.07.036

Gagnon, K. T., Zhang, X. X., Agris, P. F., & Maxwell, E. S. (2006). Assembly of the archaeal box C/D sRNP can occur via alternative pathways and requires temperature-facilitated sRNA remodeling. Journal of Molecular Biology, 362(5), 1025–1042. https://doi.org/10.1016/j.jmb.2006.07.091

Dressman, H. K., Barley-Maloney, L., Rowlette, L. L., Agris, P. F., & Garcia-Blanco, M. A. (2006). Assessing incomplete deprotection of microarray oligonucleotides in situ. Nucleic Acids Research, 34(19).

Nelson, A. R., Henkin, T. M., & Agris, P. F. (2006). tRNA regulation of gene expression: Interactions of an mRNA 5 '-UTR with a regulatory tRNA. RNA, 12(7), 1254–1261. https://doi.org/10.1261/rna.29906

Agris, P. F., & Ashraf, S. (2005). Antibacterial and antiviral agents and methods of screening for the same. Washington, DC: U.S. Patent and Trademark Office.

Agris, P. F. (2005). Methods and compositions for determining the purity of chemically synthesized nucleic acids. Washington, DC: U.S. Patent and Trademark Office.

Agris, P. F. (2004). [Review of Decoding the genome: a modified view]. NUCLEIC ACIDS RESEARCH, 32(1), 223–238. https://doi.org/10.1093/nar/gkh185

Phelps, S. S., Malkiewicz, A., Agris, P. F., & Joseph, S. (2004). Modified nucleotides in tRNA(Lys) and tRNA(Val) are important for translocation. JOURNAL OF MOLECULAR BIOLOGY, 338(3), 439–444. https://doi.org/10.1016/j.jmb.2004.02.070

Mucha, P., Szyk, A., Rekowski, P., & Agris, P. F. (2004). Sequence-altered peptide adopts optimum conformation for modification-dependent binding of the yeast tRNA(Phe) anticodon domain. PROTEIN JOURNAL, 23(1), 33–38. https://doi.org/10.1023/B:JOPC.0000016256.20648.0f

Guenther, R. H., Sit, T. L., Gracz, H. S., Dolan, M. A., Townsend, H. L., Liu, G. H., … Lommel, S. A. (2004). Structural characterization of an intermolecular RNA-RNA interaction involved in the transcription regulation element of a bipartite plant virus. NUCLEIC ACIDS RESEARCH, 32(9), 2819–2828. https://doi.org/10.1093/nar/gkh585

Murphy, F. V., Ramakrishnan, V., Malkiewicz, A., & Agris, P. F. (2004). The role of modifications in codon discrimination by tRNA(Lys) UUU. NATURE STRUCTURAL & MOLECULAR BIOLOGY, 11(12), 1186–1191. https://doi.org/10.1038/nsmb861

Stuart, J. W., Koshlap, K. M., Guenther, R., & Agris, P. F. (2003). Naturally-occurring modification restricts the anticodon domain conformational space of tRNA(Phe). JOURNAL OF MOLECULAR BIOLOGY, 334(5), 901–918. https://doi.org/10.1016/j.jmb.2003.09.058

Mucha, P., Szyk, A., Rekowski, P., & Agris, P. F. (2003). Using capillary electrophoresis to study methylation effect on RNA-peptide interaction. Acta Biochimica Polonica, 50(3), 857–864.

Yarian, C., Townsend, H., Czestkowski, W., Sochacka, E., Malkiewicz, A. J., Guenther, R., … Agris, P. F. (2002). Accurate translation of the genetic code depends on tRNA modified nucleosides. JOURNAL OF BIOLOGICAL CHEMISTRY, 277(19), 16391–16395. https://doi.org/10.1074/jbc.M200253200

Nobles, K. N., Yarian, C. S., Liu, G., Guenther, R. H., & Agris, P. F. (2002). Highly conserved modified nucleosides influence Mg2+-dependent tRNA folding. NUCLEIC ACIDS RESEARCH, 30(21), 4751–4760. https://doi.org/10.1093/nar/gkf595

Fu, C., Smith, S., Simkins, S. G., & Agris, P. F. (2002). Identification and quantification of protecting groups remaining in commercial oligonucleotide products using monoclonal antibodies. ANALYTICAL BIOCHEMISTRY, 306(1), 135–143. https://doi.org/10.1006/abio.2002.5687

Mucha, P., Szyk, A., Rekowski, P., Guenther, R., & Agris, P. F. (2002). Interaction of RNA with phage display selected peptides analyzed by capillary electrophoresis mobility shift assay. RNA, 8(5), 698–704. https://doi.org/10.1017/S1355838202020319

Agris, P. F., Smith, S., Fu, C., & Simkins, S. G. (2002). QC in antisense oligo synthesis.

Mucha, P., Szyk, A., Rekowski, P., Weiss, P. A., & Agris, P. F. (2001). Anticodon domain methylated nucleosides of yeast tRNA(Phe) are significant recognition determinants in the binding of a phage display selected peptide. BIOCHEMISTRY, 40(47), 14191–14199. https://doi.org/10.1021/bi010978o

Stuart, J. W., Gdaniec, Z., Guenther, R., Marszalek, M., Sochacka, E., Malkiewicz, A., & Agris, P. F. (2000). Functional anticodon architecture of human tRNA(Lys3) includes disruption of intraloop hydrogen bonding by the naturally occurring amino acid modification, t(6)A. BIOCHEMISTRY, 39(44), 13396–13404. https://doi.org/10.1021/bi0013039

Sengupta, R., Vainauskas, S., Yarian, C., Sochacka, E., Malkiewicz, A., Guenther, R. H., … Agris, P. F. (2000). Modified constructs of the tRNA T Psi C domain to probe substrate conformational requirements of m(1)A(58) and m(5)U(54) tRNA methyltransferases. NUCLEIC ACIDS RESEARCH, 28(6), 1374–1380. https://doi.org/10.1093/nar/28.6.1374

Yarian, C., Marszalek, M., Sochacka, E., Malkiewicz, A., Guenther, R., Miskiewicz, A., & Agris, P. F. (2000). Modified nucleoside dependent Watson-Crick and wobble codon binding by tRNA(UUU)(Lys) species. BIOCHEMISTRY, 39(44), 13390–13395. https://doi.org/10.1021/bi001302g

Ashraf, S. S., Guenther, R. H., Ansari, G., Malkiewicz, A., Sochacka, E., & Agris, P. F. (2000). Role of modified nucleosides of yeast tRNA(Phe) in ribosomal binding. CELL BIOCHEMISTRY AND BIOPHYSICS, 33(3), 241–252. https://doi.org/10.1385/CBB:33:3:241

Sochacka, E., Czerwinska, G., Guenther, R., Cain, R., Agris, P. F., & Malkiewicz, A. (2000). Synthesis and properties of uniquely modified oligoribonucleotides: Yeast tRNA(Phe) fragments with 6-methyluridine and 5,6-dimethyluridine at site-specific positions. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS, 19(3), 515–531. https://doi.org/10.1080/15257770008035004

Koshlap, K. M., Guenther, R., Sochacka, E., Malkiewicz, A., & Agris, P. F. (1999). A distinctive RNA fold: The solution structure of an analogue of the yeast tRNA(Phe) T psi C domain. BIOCHEMISTRY, 38(27), 8647–8656. https://doi.org/10.1021/bi990118w

Agris, P. F., & Ashraf, S. (1999). Antibacterial agents and methods of screening for the same. Washington, DC: U.S. Patent and Trademark Office.

Agris, P. F., Marchbank, M. T., Newman, W., Guenther, R., Ingram, P., Swallow, J., … Deutscher, S. L. (1999). Experimental models of protein-RNA interaction: Isolation and analyses of tRNA(Phe) and U1 snRNA-binding peptides from bacteriophage display libraries. JOURNAL OF PROTEIN CHEMISTRY, 18(4), 425–435. https://doi.org/10.1023/A:1020688609121

Ashraf, S. S., Guenther, R., & Agris, P. F. (1999). Orientation of the tRNA anticodon in the ribosomal P-site: Quantitative footprinting with U-33-modified, anticodon stem and loop domains. RNA, 5(9), 1191–1199. https://doi.org/10.1017/S1355838299990933

Ashraf, S. S., Sochacka, E., Cain, R., Guenther, R., Malkiewicz, A., & Agris, P. F. (1999). Single atom modification (O -> S) of tRNA confers ribosome binding. RNA, 5(2), 188–194. https://doi.org/10.1017/S1355838299981529

Yarian, C. S., Basti, M. M., Cain, R. J., Ansari, G., Guenther, R. H., Sochacka, E., … Agris, P. F. (1999). Structural and functional roles of the N1-and N3-protons of Psi at tRNA's position 39. NUCLEIC ACIDS RESEARCH, 27(17), 3543–3549. https://doi.org/10.1093/nar/27.17.3543

Ashraf, S. S., Ansari, G., Guenther, R., Sochacka, E., Malkiewicz, A., & Agris, P. F. (1999). The uridine in "U-turn": Contributions to tRNA-ribosomal binding. RNA, 5(4), 503–511. https://doi.org/10.1017/S1355838299981931

Agris, P. F., Guenther, R., Sochacka, E., Newman, W., Czerwinska, G., Liu, G. H., … Malkiewicz, A. (1999). Thermodynamic contribution of nucleoside modifications to yeast tRNA(Phe) anticodon stem loop analogs. Acta Biochimica Polonica, 46(1), 163–172.

Guenther, R., Forrest, B., Newman, W., Malkiewicz, A., & Agris, P. F. (1998). Modified RNAs as potential drug targets. Acta Biochimica Polonica, 45(1), 13–18.

Ashraf, S. S., Guenther, R., Ye, W., Lee, Y., Malkiewicz, A., & Agris, P. F. (1997). Ribosomal binding of modified tRNA anticodons related to thermal stability. Symposium on RNA Biology II. RNA: Tool and Target (1997: North Carolina Biotechnology Center) Research Triangle Park, North Carolina, USA, October 17-19, 1997  (Nucleic acids symposium series; no. 36), 36, 58–60. Oxford: Oxford University Press.

Agris, P. F., Guenther, R. H., Ingram, P. C., Basti, M. M., Stuart, J. W., Sochacka, E., & Malkiewicz, A. (1997). Unconventional structure of tRNA(Lys)SUU anticodon explains tRNA's role in bacterial and mammalian ribosomal frameshifting and primer selection by HIV-1. RNA, 3(4), 420–428.