{"id":18,"date":"2019-09-10T15:40:01","date_gmt":"2019-09-10T19:40:01","guid":{"rendered":"https:\/\/health.uconn.edu\/bae-lab\/?page_id=18"},"modified":"2026-03-20T06:31:35","modified_gmt":"2026-03-20T10:31:35","slug":"publications","status":"publish","type":"page","link":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Google Scholar<\/a>\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Pubmed<\/a>
\n<\/strong><\/p>\n<\/div><\/div><\/div><\/div>

2025<\/h3>
<\/div><\/div><\/div><\/div>
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Mechanistic and evolutionary insights into a family of aminoacyl-tRNA deacylases that protects against canavanine toxicity<\/span>
\n<\/strong><\/a>Maldonado J, Sepulveda S, <\/span>Karthikeyan\u00a0<\/span>S, Shirakawa KT, Merced I, Radecki A, Douglas J, Peti W, Page R, Vargas-Rodriguez O.<\/span>
\nNucleic Acids Research. (2025). 53(17). (2025). pre-print<\/a>.<\/span><\/p>\n<\/div><\/div><\/div><\/div>

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An engineered glutamic acid tRNA for efficient suppression of pathogenic nonsense mutations<\/strong><\/a>
\n<\/strong>Specht C<\/span>,<\/span> Tapia A<\/span>,<\/span> Penrod S<\/span>, <\/span>Soriano GA<\/span>,<\/span> Awawdeh A<\/span>,<\/span> <\/span>Alshawi SA<\/span>, <\/span>White CA<\/span>,<\/span> Beaudoin JD<\/span>,<\/span> Doud EH<\/span>,<\/span> Vargas-Rodriguez O<\/span>,<\/span> Huang Y<\/span>, Tharp JM.<\/span><\/span>
\nNucleic Acids Research. (2025). 53(12).<\/span><\/p>\n<\/div><\/div><\/div><\/div>

2024<\/h3>
<\/div><\/div><\/div><\/div>
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Efficient suppression of premature termination codons with alanine by engineered chimeric pyrrolysine tRNAs<\/span><\/a>
\n<\/strong>Awawdeh A<\/span>,<\/span> Tapia A<\/span>, <\/span>Alshawi SA<\/span>, Dawodu O<\/span>, Gaier SA<\/span>, <\/span>Specht C<\/span>, <\/span>Beaudoin J-D, Tharp JM\u2020\u00a0<\/span><\/span>and<\/span><\/span>\u00a0<\/span>Vargas-<\/span>Rodriguez O\u2020<\/span>.\u00a0<\/span><\/span>
\nNucleic Acids Research. (2024). 52(22):14244-14259 (\u2020Co-corresponding author)<\/span><\/p>\n<\/div><\/div><\/div><\/div>

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Coexisting <\/span>bacterial <\/span>a<\/span>minoacyl-tRNA synthetase <\/span>paralogs <\/span>exhibit<\/span> distinct phylogenetic <\/span>backgrounds <\/span>and<\/span> <\/span>functional <\/span>compatibility with <\/span>Escherichia <\/span>coli<\/span><\/em><\/a>
\n<\/strong>Radecki AA<\/span>,<\/span>\u00a0Fantasia-Davis A<\/span>, <\/span>Maldonado JS<\/span>, Mann JW<\/span>, Sepulveda-<\/span>Camacho\u00a0<\/span>S<\/span>, <\/span>Morosky P<\/span>, <\/span>Douglas J<\/span>, <\/span>and<\/span>\u00a0<\/span>Vargas-<\/span>Rodriguez O.\u00a0<\/span><\/span>
\nIUBMB Life (2024). 76(12):1139-1153<\/span><\/p>\n<\/div><\/div><\/div><\/div>

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The central role of transfer RNAs in mistranslation<\/a>
\n<\/strong>Schuntermann DB, Jaskolowski M, Reynolds NM, <\/span>and<\/span><\/span>\u00a0<\/span>Vargas-<\/span>Rodriguez O.\u00a0<\/span><\/span>
\nJournal of Biological Chemistry (2024). <\/span>300(9) 107679.<\/p>\n

.<\/span><\/p>\n<\/div><\/div><\/div><\/div>

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The role of tRNA identity elements in aminoacyl-tRNA editing<\/span><\/a>
\n<\/strong>Cruz E and<\/span><\/span>\u00a0<\/span>Vargas<\/span> Rodriguez O.\u00a0<\/span><\/span>
\nFront. Microbiol. <\/span><\/span>(2024).<\/span><\/p>\n<\/div><\/div><\/div><\/div>

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AARS Online: a collaborative database on the structure, function, and evolution of the aminoacyl-tRNA synthetases<\/span><\/a>
\n<\/strong>Douglas J<\/span><\/span>,<\/span> Cui H<\/span><\/span>,<\/span> <\/span>Perona JJ<\/span><\/span>, <\/span>Vargas<\/span> Rodriguez O<\/span><\/span>,<\/span>\u00a0Tyynismaa H<\/span><\/span>,<\/span>\u00a0Alvarez-Carreno C<\/span><\/span>, <\/span>Ling J<\/span><\/span>, <\/span>Ribas-de-Pouplana L<\/span><\/span>, <\/span>Yang XL<\/span><\/span>, <\/span>Michael<\/span> Ibba<\/span><\/span>, <\/span>Becker H<\/span><\/span>,<\/span> Fischer F<\/span><\/span>, <\/span>Sissler S<\/span><\/span>, C<\/span>arter<\/span> Jr CW, <\/span><\/span>Wills P.<\/span><\/span>
\nIUBMB Life\u00a0<\/span><\/span>(2024).<\/span><\/p>\n<\/div><\/div><\/div><\/div>

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Suppressor tRNAs at the interface of genetic code expansion and medicine<\/span>
\n<\/strong><\/a>*Awawdeh<\/span>\u00a0A, *Radecki<\/span> AA, Vargas-Rodriguez O.
\nFrontiers in Genetics. (2024). (*Equal contribution)<\/span><\/p>\n<\/div><\/div><\/div><\/div>

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Engineered mRNA-ribosome fusions for facile biosynthesis of selenoproteins<\/a>
\n<\/strong>*<\/span>Thaenert A, *<\/span>Sevostyanova A, *<\/span>Chung CZ, *<\/span>Vargas-Rodriguez O<\/strong>, Melnikov SV, and S\u00f6ll D.
\nProceedings of the National Academy of Sciences USA. (2024). (*Equal contribution)<\/span><\/p>\n<\/div><\/div><\/div><\/div>

2023<\/h3>
<\/div><\/div><\/div><\/div>
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Mistranslation of the genetic code by a new family of bacterial transfer RNAs.\u00a0<\/span><\/a>
\n<\/strong>Schuntermann DB, Fischer JT, Bile J, Gaier SA, Shelley BA, Awawdeh A, Jahn M, Hoffman KS, Westhof E, S\u00f6ll D\u2020, Clarke CR, Vargas-Rodriguez O<\/strong>\u2020.<\/strong>
\nJournal of Biological Chemistry (2023). (\u2020Co-corresponding author) - Editors' Pick. JBC Highlight<\/a><\/span><\/p>\n<\/div><\/div><\/div><\/div>

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Dual incorporation of noncanonical amino acids enables production of post-translationally modified selenoproteins.<\/span><\/a>
\n<\/strong>Morosky P, Comyns C, Nunes LGA, Chung CZ, Hoffmann PR, S\u00f6ll D, Vargas-Rodriguez O<\/strong>, and Krahn N.
\nFrontiers in Molecular Biosciences (2023).\u00a0<\/span><\/p>\n<\/div><\/div><\/div><\/div>

2022<\/h3>
<\/div><\/div><\/div><\/div>
\"Diversification<\/div><\/div><\/div>

Diversification of aminoacyl-tRNA synthetase activities via genomic duplication.<\/a>
\n<\/strong>Krahn N, S\u00f6ll D, and Vargas-Rodriguez O<\/strong>\u2020
\nFrontiers in Physiology (2022) 13:983245. (\u2020Corresponding author)<\/p>\n<\/div><\/div><\/div><\/div>

\"Uncovering<\/div><\/div><\/div>

Uncovering translation roadblocks during the development of a synthetic tRNA.<\/a>
\n<\/strong>Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O<\/strong>, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnkovi\u0107 A, Ehrenberg M, Puglisi EV, S\u00f6ll D, and Puglisi J.
\nNucleic Acid Research (2022) 50(18):10201-10211.<\/p>\n<\/div><\/div><\/div><\/div>

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The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase\/tRNAPyl pairs in the same organism.<\/a>
\n<\/strong>Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O<\/strong>, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova KS, Koonin EV., Shen Y, S\u00f6ll D, and Fu X.
\nNucleic Acid Research (2022), 50(8):4601-4615<\/p>\n<\/div><\/div><\/div><\/div>

2021<\/h3>
<\/div><\/div><\/div><\/div>
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Bacterial translation factor for deliberate mistranslation of the genetic code.<\/span><\/a>
\nVargas-Rodriguez O<\/strong>\u2020, Badran AH, Hoffman KS, Chen M, Crnkovi\u0107 A, Ding Y, Krieger JR, Westhof E, S\u00f6ll D\u2020, and Melnikov S.
\nProceedings of the National Academy of Sciences USA. (2021) 118(35). (\u2020Co-corresponding author).<\/span><\/p>\n<\/div><\/div><\/div><\/div>

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Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons.<\/span><\/a>
\n<\/strong>Tharp JM, Vargas-Rodriguez O<\/strong>, Schepartz A, and S\u00f6ll D.
\nACS Chemical Biology (2021) 16, 766-744<\/p>\n<\/div><\/div><\/div><\/div>

2020<\/h3>
<\/div><\/div><\/div><\/div>
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Human trans-editing enzyme displays tRNA acceptor stem specificity and relaxed amino acid selectivity.<\/a>
\nVargas-Rodriguez O<\/strong>*, Bakhtina M*, McGowan D, Abid J, Goto Y, Suga H, and Musier-Forsyth K.
\nJournal of Biological Chemistry (2020). 295, 16180-16190. (*Equal contribution). JBC\u2019s Editors\u2019 Pick.<\/p>\n<\/div><\/div><\/div><\/div>

2019<\/h3>

A cysteinyl-tRNA synthetase variant confers resistance against selenite toxicity and decreases selenocysteine misincorporation.<\/a>
\n<\/strong>Hoffman KS*, <\/span>Vargas-Rodriguez O<\/strong>*, Bak DW, Mukai T, Weerapana E, S\u00f6ll D, and Reynolds, N. M.<\/span>
\nJournal of Biological Chemistry (2019) 294 (34), 12855-12865. (*Equal contribution)<\/span><\/p>\n

Plasticity and constraints of tRNA aminoacylation define directed evolution of aminoacyl-tRNA synthetases.<\/a><\/strong>
\nCrnkovi\u0107 A, <\/span>Vargas-Rodriguez O<\/strong>, and S\u00f6ll D.<\/span>
\nInternational Journal of Molecular Sciences (2019) 20, 2294.<\/span><\/p>\n

Engineered aminoacyl-tRNA synthetases with improved selectivity towards non-canonical amino acids.<\/a>
\n<\/strong>Kwok HS, Vargas-Rodriguez O<\/strong>, Melnikov SV, and S\u00f6ll D.
\nACS Chemical Biology (2019) 14, 603-612.<\/span><\/p>\n<\/div><\/div>

2018<\/h3>

Mechanistic insights into the slow peptide bond formation by d-amino acids in the ribosomal active site.<\/a>
\n<\/strong>Melnikov SV, Khabibullina NF, Mairhofer E, Vargas-Rodriguez O<\/strong>, Reynolds NM, Micura R, S\u00f6ll D, Polikanov YS.\u00a0<\/span>
\nNucleic Acid Research (2018) 47, 2089-2100.<\/p>\n

Upgrading aminoacyl-tRNA synthetases for genetic code expansion.<\/a><\/strong>
\nVargas-Rodriguez O<\/strong>\u2020, Sevostyanova A, S\u00f6ll D, and Crnkovi\u0107, A\u2020.<\/span>
\nCurrent Opinion in Chemical Biology (2018) 46, 115-112. (\u2020Co-corresponding author).<\/span><\/p>\n

Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNACys and elongation factor SelB.<\/a><\/strong>
\nVargas-Rodriguez O<\/strong>*, Englert M*, Merkuryev A, Mukai T, and S\u00f6ll D.<\/span>
\nRNA Biology (2018) 15:4-5, 471-479. (*Equal contribution)<\/span>.<\/span><\/p>\n

Effects of heterologous tRNA modifications on the production of proteins containing noncanonical amino acids.<\/a><\/strong>
\nCrnkovi\u0107 A*, <\/span>Vargas-Rodriguez O<\/strong>*, Merkuryev A, and S\u00f6ll D.<\/span>
\nBioengineering\u00a0<\/span>(2018) 5(1), 11. (*Equal contribution). Featured in cover.<\/span><\/p>\n

Engineering post-translational proofreading to discriminate non-standard amino acids.<\/a><\/strong>
\nKunjapur AM, Stork DA, Kuru E, <\/span>Vargas-Rodriguez O<\/strong>, Landon M, S\u00f6ll D, and Church GM.<\/span>
\nProceedings of the National Academy of Sciences USA. \u200b(2018) 115(3), 619-624.<\/span><\/p>\n<\/div><\/div>

2017<\/h3>

Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.<\/span><\/a>
\n<\/strong>Song Y, Zhou H, Vo MN, Shi Y, Nawaz MH, <\/span>Vargas-Rodriguez O<\/strong>, Diedrich JK, Yates JR, Kishi S, Musier-Forsyth K, and Schimmel P.<\/span>
\nNature Communications (2017) 8(1), 2281.<\/span><\/p>\n

The central role of tRNA in genetic code expansion.<\/a><\/strong>
\nReynolds NM, <\/span>Vargas-Rodriguez<\/strong>\u00a0O<\/strong>, S\u00f6ll D, and Crnkovi\u0107 A.<\/span>
\nBiochimica et Biophysica Acta (2017) 1861, 3001-3008.<\/span><\/p>\n

A genomically modified Escherichia coli strain carrying an orthogonal E. coli histidyl-tRNA synthetase-tRNAHis pair.<\/a><\/strong>
\nEnglert M*, <\/span>Vargas-Rodriguez O<\/strong>*, Reynolds NM, Wang YS, S\u00f6ll D, and Umehara T.<\/span>
\nBiochimica et Biophysica Acta (2017) 1861, 3009-3015. (*Equal contribution).<\/span><\/p>\n

Conformational and chemical selection by a trans-acting editing domain.<\/a><\/strong>
\nDanhart EM, Bakhtina M, Cantara WA, Kuzmishin AB, Ma X, Sanford BL,\u00a0<\/span>Vargas-Rodriguez O<\/strong>, Ko\u0161uti\u0107 M, Goto Y, Suga H, Nakanishi K, Micura R, <\/span>Foster MP, and Musier-Forsyth K.<\/span>
\nProceedings of the National Academy of Sciences USA. (2017) 114(33), E6774-6783.<\/span><\/p>\n

Transfer RNAs with novel cloverleaf structures.<\/span><\/a><\/strong>
\nMukai T, <\/span>Vargas-Rodriguez O<\/strong>, Englert M, Tripp HJ, Ivanova NN, Rubin EM, KyrpidesNC, and S\u00f6ll D.<\/span>
\nNucleic Acid Research (2017) 45(5), 2776-2785.<\/span><\/p>\n<\/div><\/div>

2016<\/h3>

Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.<\/span><\/a>
\n<\/strong>Napolitano MG, Landon M, Gregg CJ, Lajoie MJ, Govindarajan L, Mosberg JA, Kuznetsov G, Goodman DB, <\/span>
\nVargas-Rodriguez O<\/strong>, Isaacs FJ, S\u00f6ll D, and <\/span>Church, GM.<\/span>
\nProceedings of the National Academy of Sciences USA. (2016) 113(38), 5588-5597.<\/span><\/p>\n<\/div><\/div>

2015<\/h3>

Homologous ProXp trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine\/threonine misactivation.<\/span><\/a>
\n<\/strong>Liu Z*, <\/span>Vargas-Rodriguez O<\/strong>*, Goto Y, Novoa EM, Ribas de Pouplana L, Suga H, and Musier-Forsyth K.<\/span>
\nProceedings of the National Academy of Sciences USA (2015) 112(19), 6027-6032. (*Equal contribution)<\/span><\/p>\n

Ancestral AlaX editing enzymes for control of genetic code fidelity are not tRNA specific.<\/span><\/a>
\n<\/strong>Novoa EM, <\/span>Vargas-Rodriguez O<\/strong>, Lange S, Goto Y, Suga H, Musier-Forsyth K, and Ribas de Pouplana L.<\/span>
\nJournal of Biological Chemistry (2015) 290(16), 10495-10503.<\/span><\/p>\n<\/div><\/div>

2014<\/h3>

Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation<\/a>.<\/span>
\n<\/strong>Das M*, Vargas-Rodriguez O*<\/strong>, Goto Y, Suga H, Musier-Forsyth K.<\/span>
\nNucleic Acids Research (2014) 42(6):3943-53.<\/span><\/p>\n

Structural biology: wobble puts RNA on target<\/a>.<\/strong>
\nVargas-Rodriguez O<\/strong> and Musier-Forsyth K.
\nNature. (2014) 510(7506):480-1.<\/p>\n<\/div><\/div>

2013<\/h3>

Exclusive use of trans-editing domains prevents proline mistranslation.<\/span><\/a>
\nVargas-Rodriguez O<\/strong> and Musier-Forsyth K.<\/span>
\nJournal of Biological Chemistry (2013) 288(20), 14391-14399.<\/span><\/p>\n<\/div><\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"

Google Scholar\u00a0 \u00a0 \u00a0 \u00a0 \u00a0 \u00a0 Pubmed<\/p>\n","protected":false},"author":38,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_acf_changed":false,"footnotes":""},"acf":[],"publishpress_future_action":{"enabled":false,"date":"2026-04-12 04:44:11","action":"change-status","newStatus":"draft","terms":[],"taxonomy":""},"_links":{"self":[{"href":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/wp-json\/wp\/v2\/pages\/18"}],"collection":[{"href":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/wp-json\/wp\/v2\/users\/38"}],"replies":[{"embeddable":true,"href":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/wp-json\/wp\/v2\/comments?post=18"}],"version-history":[{"count":91,"href":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/wp-json\/wp\/v2\/pages\/18\/revisions"}],"predecessor-version":[{"id":680,"href":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/wp-json\/wp\/v2\/pages\/18\/revisions\/680"}],"wp:attachment":[{"href":"https:\/\/health.uconn.edu\/vargas-rodriguez-lab\/wp-json\/wp\/v2\/media?parent=18"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}