Publications

2022

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Diversification of aminoacyl-tRNA synthetase activities via genomic duplication

Krahn N, Söll D, and  Vargas-Rodriguez O†

Frontiers in Physiology (2022) In press. (†Corresponding author)

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Uncovering translation roadblocks during the development of a synthetic tRNA

Prabhakar A, Krahn N, Zhang J, Vargas-Rodriguez O, Krupkin M, Fu Z, Acosta-Reyes FJ, Ge X, Choi J, Crnković A, Ehrenberg M, Puglisi EV, Söll D, and Puglisi J.

Nucleic Acid Research (2022) In press.

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The tRNA discriminator base defines the mutual orthogonality of two distinct pyrrolysyl-tRNA synthetase/tRNAPyl pairs in the same organism.

Zhang H, Gong X, Zhao Q, Mukai T, Vargas-Rodriguez O, Zhang H, Zhang Y, Wassel P, Amikura K, Maupin-Furlow J, Ren Y, Xu X, Wolf YI, Makarova KS, Koonin EV., Shen Y, Söll D, and Fu X.

Nucleic Acid Research (2022), 50(8), 4601-4615

 

2021

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Bacterial translation factor for deliberate mistranslation of the genetic code.

Vargas-Rodriguez O†, Badran AH, Hoffman KS, Chen M, Crnković A, Ding Y, Krieger JR, Westhof E, Söll D†, and Melnikov S. Proceedings of the National Academy of Sciences USA. (2021) 118(35). (†Co-corresponding author).

 

Genetic Encoding of Three Distinct Noncanonical Amino Acids Using Reprogrammed Initiator and Nonsense Codons.

Tharp JM, Vargas-Rodriguez O, Schepartz A, and Söll D.

ACS Chemical Biology (2021) 16, 766-744

 

2020

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Human trans-editing enzyme displays tRNA acceptor stem specificity and relaxed amino acid selectivity.

Vargas-Rodriguez O*, Bakhtina M*, McGowan D, Abid J, Goto Y, Suga H, and Musier-Forsyth K.

Journal of Biological Chemistry (2020). 295, 16180-16190. (*Equal contribution). JBC’s Editors’ Pick.

 

2019

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A cysteinyl-tRNA synthetase variant confers resistance against selenite toxicity and decreases selenocysteine misincorporation.

Hoffman KS*, Vargas-Rodriguez O*, Bak DW, Mukai T, Weerapana E, Söll D, and Reynolds, N. M.

Journal of Biological Chemistry (2019) 294 (34), 12855-12865. (*Equal contribution)

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Plasticity and constraints of tRNA aminoacylation define directed evolution of aminoacyl-tRNA synthetases.

Crnković A, Vargas-Rodriguez O, and Söll D.

International Journal of Molecular Sciences (2019) 20, 2294.

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Engineered aminoacyl-tRNA synthetases with improved selectivity towards non-canonical amino acids.

Kwok HS, Vargas-Rodriguez O, Melnikov SV, and Söll D.

ACS Chemical Biology (2019) 14, 603-612.

 

2018

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Structural basis for the slow peptide bond formation by d-amino acids in the ribosomal active site.

Melnikov SV, Khabibullina NF, Mairhofer E, Vargas-Rodriguez O, Reynolds NM, Micura R, Söll D, Polikanov YS.

Nucleic Acid Research (2018) 47, 2089-2100.

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Upgrading aminoacyl-tRNA synthetases for genetic code expansion.

Vargas-Rodriguez O†, Sevostyanova A, Söll D, and Crnković, A†.

Current Opinion in Chemical Biology (2018) 46, 115-112. (†Co-corresponding author).

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Recoding of the selenocysteine UGA codon by cysteine in the presence of a non-canonical tRNACys and elongation factor SelB.

Vargas-Rodriguez O*, Englert M*, Merkuryev A, Mukai T, and Söll D.

RNA Biology (2018) 15:4-5, 471-479. (*Equal contribution).

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Effects of heterologous tRNA modifications on the production of proteins containing noncanonical amino acids.

Crnković A*, Vargas-Rodriguez O*, Merkuryev A, and Söll D.

Bioengineering (2018) 5(1), 11. (*Equal contribution). Featured in cover.

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Engineering post-translational proofreading to discriminate non-standard amino acids.

Kunjapur AM, Stork DA, Kuru E, Vargas-Rodriguez O, Landon M, Söll D, and Church GM.

Proceedings of the National Academy of Sciences USA. ​(2018) 115(3), 619-624.

 

2017

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Double mimicry evades tRNA synthetase editing by toxic vegetable-sourced non-proteinogenic amino acid.

Song Y, Zhou H, Vo MN, Shi Y, Nawaz MH, Vargas-Rodriguez O, Diedrich JK, Yates JR, Kishi S, Musier-Forsyth K, and Schimmel P. Nature Communications (2017) 8(1), 2281.

 

The central role of tRNA in genetic code expansion.

Reynolds NM, Vargas-Rodriguez O, Söll D, and Crnković A.

Biochimica et Biophysica Acta (2017) 1861, 3001-3008.

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A genomically modified Escherichia coli strain carrying an orthogonal E. coli histidyl-tRNA synthetase-tRNAHis pair.

Englert M*, Vargas-Rodriguez O*, Reynolds NM, Wang YS, Söll D, and Umehara T.

Biochimica et Biophysica Acta (2017) 1861, 3009-3015. (*Equal contribution).

 

Conformational and chemical selection by a trans-acting editing domain.

Danhart EM, Bakhtina M, Cantara WA, Kuzmishin AB, Ma X, Sanford BL, Vargas-Rodriguez O, Košutić M, Goto Y, Suga H, Nakanishi K, Micura R, Foster MP, and Musier-Forsyth K.

Proceedings of the National Academy of Sciences USA. (2017) 114(33), E6774-6783.

 

Transfer RNAs with novel cloverleaf structures.

Mukai T, Vargas-Rodriguez O, Englert M, Tripp HJ, Ivanova NN, Rubin EM, KyrpidesNC, and Söll D.

Nucleic Acid Research (2017) 45(5), 2776-2785.

 

2016

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Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli.

Napolitano MG, Landon M, Gregg CJ, Lajoie MJ, Govindarajan L, Mosberg JA, Kuznetsov G, Goodman DB, Vargas-Rodriguez O, Isaacs FJ, Söll D, and Church, GM.

Proceedings of the National Academy of Sciences USA. (2016) 113(38), 5588-5597.

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2015

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Homologous ProXp trans-editing factors with broad tRNA specificity prevent mistranslation caused by serine/threonine misactivation.

Liu Z*, Vargas-Rodriguez O*, Goto Y, Novoa EM, Ribas de Pouplana L, Suga H, and Musier-Forsyth K.

Proceedings of the National Academy of Sciences USA (2015) 112(19), 6027-6032. (*Equal contribution)

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Ancestral AlaX editing enzymes for control of genetic code fidelity are not tRNA specific.

Novoa EM, Vargas-Rodriguez O, Lange S, Goto Y, Suga H, Musier-Forsyth K, and Ribas de Pouplana L.

Journal of Biological Chemistry (2015) 290(16), 10495-10503.

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2014

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Wobble puts RNA on target

Vargas-Rodriguez O and Musier-Forsyth, K.

Nature (2014) 510(7506), 480-481. News and Views.

 

Distinct tRNA recognition strategies used by a homologous family of editing domains prevent mistranslation.

Das M*, Vargas-Rodriguez O*, Goto Y, Suga H, Musier-Forsyth K.

Nucleic Acid Research (2014) 42(6), 3943-3953. (*Equal contribution).

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2013

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Exclusive use of trans-editing domains prevents proline mistranslation.

Vargas-Rodriguez O and Musier-Forsyth K.

Journal of Biological Chemistry (2013) 288(20), 14391-14399.