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For: DeBenedictis EA, Carver GD, Chung CZ, Söll D, Badran AH. Multiplex suppression of four quadruplet codons via tRNA directed evolution. Nat Commun 2021;12:5706. [PMID: 34588441 PMCID: PMC8481270 DOI: 10.1038/s41467-021-25948-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 09/10/2021] [Indexed: 11/20/2022]  Open
Number Cited by Other Article(s)
1
Kim D, Sung D, Lee JW. Expanding the genetic code: Strategies for noncanonical amino acid incorporation in biopolymer. BIORESOURCE TECHNOLOGY 2025;432:132691. [PMID: 40381810 DOI: 10.1016/j.biortech.2025.132691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2025] [Revised: 05/07/2025] [Accepted: 05/15/2025] [Indexed: 05/20/2025]
2
Biela AD, Nowak JS, Biela AP, Mukherjee S, Moafinejad SN, Maiti S, Chramiec-Głąbik A, Mehta R, Jeżowski J, Dobosz D, Dahate P, Arluison V, Wien F, Indyka P, Rawski M, Bujnicki JM, Lin TY, Glatt S. Determining the effects of pseudouridine incorporation on human tRNAs. EMBO J 2025:10.1038/s44318-025-00443-y. [PMID: 40301665 DOI: 10.1038/s44318-025-00443-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2025] [Revised: 03/18/2025] [Accepted: 04/02/2025] [Indexed: 05/01/2025]  Open
3
Casteleijn MG, Abendroth U, Zemella A, Walter R, Rashmi R, Haag R, Kubick S. Beyond In Vivo, Pharmaceutical Molecule Production in Cell-Free Systems and the Use of Noncanonical Amino Acids Therein. Chem Rev 2025;125:1303-1331. [PMID: 39841856 PMCID: PMC11826901 DOI: 10.1021/acs.chemrev.4c00126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 12/26/2024] [Accepted: 01/06/2025] [Indexed: 01/24/2025]
4
Huang Y, Zhang P, Wang H, Chen Y, Liu T, Luo X. Genetic Code Expansion: Recent Developments and Emerging Applications. Chem Rev 2025;125:523-598. [PMID: 39737807 PMCID: PMC11758808 DOI: 10.1021/acs.chemrev.4c00216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 12/02/2024] [Accepted: 12/09/2024] [Indexed: 01/01/2025]
5
Dakhnevich A, Kazakova A, Iliushin D, Ivanov RA. Pyrrolysine Aminoacyl-tRNA Synthetase as a Tool for Expanding the Genetic Code. Int J Mol Sci 2025;26:539. [PMID: 39859254 PMCID: PMC11764691 DOI: 10.3390/ijms26020539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2024] [Revised: 01/04/2025] [Accepted: 01/07/2025] [Indexed: 01/27/2025]  Open
6
Choi YN, Kim D, Lee S, Shin Y, Lee J. Quadruplet codon decoding-based versatile genetic biocontainment system. Nucleic Acids Res 2025;53:gkae1292. [PMID: 39777466 PMCID: PMC11705086 DOI: 10.1093/nar/gkae1292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Revised: 11/22/2024] [Accepted: 12/20/2024] [Indexed: 01/11/2025]  Open
7
Xu B, Liu LH, Lin H, Zhang Y, Huang Y, He Q, Wang F, Wu YR, Zhang Z, Jiang A. A cell-free bacteriophage synthesis system for directed evolution. Trends Biotechnol 2025;43:248-261. [PMID: 39462751 DOI: 10.1016/j.tibtech.2024.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Revised: 10/05/2024] [Accepted: 10/08/2024] [Indexed: 10/29/2024]
8
Kim JC, Kim Y, Cho S, Park HS. Noncanonical Amino Acid Incorporation in Animals and Animal Cells. Chem Rev 2024;124:12463-12497. [PMID: 39541258 DOI: 10.1021/acs.chemrev.3c00955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
9
Costello A, Peterson AA, Chen PH, Bagirzadeh R, Lanster DL, Badran AH. Genetic Code Expansion History and Modern Innovations. Chem Rev 2024;124:11962-12005. [PMID: 39466033 DOI: 10.1021/acs.chemrev.4c00275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
10
Niu W, Guo J. Cellular Site-Specific Incorporation of Noncanonical Amino Acids in Synthetic Biology. Chem Rev 2024;124:10577-10617. [PMID: 39207844 PMCID: PMC11470805 DOI: 10.1021/acs.chemrev.3c00938] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
11
Jann C, Giofré S, Bhattacharjee R, Lemke EA. Cracking the Code: Reprogramming the Genetic Script in Prokaryotes and Eukaryotes to Harness the Power of Noncanonical Amino Acids. Chem Rev 2024;124:10281-10362. [PMID: 39120726 PMCID: PMC11441406 DOI: 10.1021/acs.chemrev.3c00878] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 06/10/2024] [Accepted: 06/27/2024] [Indexed: 08/10/2024]
12
Recoded gene circuits for multiplexed genetic code expansion. Nat Biotechnol 2024:10.1038/s41587-024-02387-w. [PMID: 39261593 DOI: 10.1038/s41587-024-02387-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/13/2024]
13
Costello A, Peterson AA, Lanster DL, Li Z, Carver GD, Badran AH. Efficient genetic code expansion without host genome modifications. Nat Biotechnol 2024:10.1038/s41587-024-02385-y. [PMID: 39261591 DOI: 10.1038/s41587-024-02385-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 08/13/2024] [Indexed: 09/13/2024]
14
Koch NG, Budisa N. Evolution of Pyrrolysyl-tRNA Synthetase: From Methanogenesis to Genetic Code Expansion. Chem Rev 2024;124:9580-9608. [PMID: 38953775 PMCID: PMC11363022 DOI: 10.1021/acs.chemrev.4c00031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 05/22/2024] [Accepted: 05/28/2024] [Indexed: 07/04/2024]
15
Ishida S, Ngo PHT, Gundlach A, Ellington A. Engineering Ribosomal Machinery for Noncanonical Amino Acid Incorporation. Chem Rev 2024;124:7712-7730. [PMID: 38829723 DOI: 10.1021/acs.chemrev.3c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2024]
16
Weiss JL, Decker JC, Bolano A, Krahn N. Tuning tRNAs for improved translation. Front Genet 2024;15:1436860. [PMID: 38983271 PMCID: PMC11231383 DOI: 10.3389/fgene.2024.1436860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024]  Open
17
Sigal M, Matsumoto S, Beattie A, Katoh T, Suga H. Engineering tRNAs for the Ribosomal Translation of Non-proteinogenic Monomers. Chem Rev 2024;124:6444-6500. [PMID: 38688034 PMCID: PMC11122139 DOI: 10.1021/acs.chemrev.3c00894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 02/21/2024] [Accepted: 04/10/2024] [Indexed: 05/02/2024]
18
Awawdeh A, Radecki AA, Vargas-Rodriguez O. Suppressor tRNAs at the interface of genetic code expansion and medicine. Front Genet 2024;15:1420331. [PMID: 38798701 PMCID: PMC11116698 DOI: 10.3389/fgene.2024.1420331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 04/29/2024] [Indexed: 05/29/2024]  Open
19
Butler ND, Kunjapur AM. Selective and Site-Specific Incorporation of Nonstandard Amino Acids Within Proteins for Therapeutic Applications. Methods Mol Biol 2024;2720:35-53. [PMID: 37775656 DOI: 10.1007/978-1-0716-3469-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
20
Anastassiadis T, Köhrer C. Ushering in the era of tRNA medicines. J Biol Chem 2023;299:105246. [PMID: 37703991 PMCID: PMC10583094 DOI: 10.1016/j.jbc.2023.105246] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 09/03/2023] [Accepted: 09/06/2023] [Indexed: 09/15/2023]  Open
21
Jewel D, Pham Q, Chatterjee A. Virus-assisted directed evolution of biomolecules. Curr Opin Chem Biol 2023;76:102375. [PMID: 37542745 PMCID: PMC10870257 DOI: 10.1016/j.cbpa.2023.102375] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/01/2023] [Accepted: 07/02/2023] [Indexed: 08/07/2023]
22
McFeely CAL, Shakya B, Makovsky CA, Haney AK, Ashton Cropp T, Hartman MCT. Extensive breaking of genetic code degeneracy with non-canonical amino acids. Nat Commun 2023;14:5008. [PMID: 37591858 PMCID: PMC10435567 DOI: 10.1038/s41467-023-40529-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/26/2023] [Indexed: 08/19/2023]  Open
23
Lahiri P, Martin MS, Lino BR, Scheck RA, Van Deventer JA. Dual Noncanonical Amino Acid Incorporation Enabling Chemoselective Protein Modification at Two Distinct Sites in Yeast. Biochemistry 2023;62:2098-2114. [PMID: 37377426 PMCID: PMC11146674 DOI: 10.1021/acs.biochem.2c00711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2023]
24
Gerecht K, Freund N, Liu W, Liu Y, Fürst MJLJ, Holliger P. The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. Annu Rev Biophys 2023;52:413-432. [PMID: 37159296 DOI: 10.1146/annurev-biophys-111622-091203] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
25
Hu Z, Liang J, Su T, Zhang D, Li H, Gao X, Yao W, Song X. Minimizing the Anticodon-Recognized Loop of Methanococcus jannaschii Tyrosyl-tRNA Synthetase to Improve the Efficiency of Incorporating Noncanonical Amino Acids. Biomolecules 2023;13:biom13040610. [PMID: 37189358 DOI: 10.3390/biom13040610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/23/2023] [Accepted: 03/25/2023] [Indexed: 03/31/2023]  Open
26
Mohanta TK, Mohanta YK, Sharma N. Anticodon table of the chloroplast genome and identification of putative quadruplet anticodons in chloroplast tRNAs. Sci Rep 2023;13:760. [PMID: 36641535 PMCID: PMC9840617 DOI: 10.1038/s41598-023-27886-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 01/10/2023] [Indexed: 01/16/2023]  Open
27
McFeely CAL, Dods KK, Patel SS, Hartman MCT. Expansion of the genetic code through reassignment of redundant sense codons using fully modified tRNA. Nucleic Acids Res 2022;50:11374-11386. [PMID: 36300637 PMCID: PMC9638912 DOI: 10.1093/nar/gkac846] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 09/09/2022] [Accepted: 09/23/2022] [Indexed: 11/21/2022]  Open
28
Allen GL, Grahn AK, Kourentzi K, Willson RC, Waldrop S, Guo J, Kay BK. Expanding the chemical diversity of M13 bacteriophage. Front Microbiol 2022;13:961093. [PMID: 36003937 PMCID: PMC9393631 DOI: 10.3389/fmicb.2022.961093] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 07/04/2022] [Indexed: 11/21/2022]  Open
29
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, Puglisi J. Uncovering translation roadblocks during the development of a synthetic tRNA. Nucleic Acids Res 2022;50:10201-10211. [PMID: 35882385 PMCID: PMC9561287 DOI: 10.1093/nar/gkac576] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/14/2022] [Accepted: 07/22/2022] [Indexed: 11/24/2022]  Open
30
Shakya B, Joyner OG, Hartman MCT. Hyperaccurate Ribosomes for Improved Genetic Code Reprogramming. ACS Synth Biol 2022;11:2193-2201. [PMID: 35549158 PMCID: PMC10100576 DOI: 10.1021/acssynbio.2c00150] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
31
Siddika T, Heinemann IU, O'Donoghue P. Expanding codon size. eLife 2022;11:78869. [PMID: 35543705 PMCID: PMC9094744 DOI: 10.7554/elife.78869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
32
DeBenedictis EA, Söll D, Esvelt KM. Measuring the tolerance of the genetic code to altered codon size. eLife 2022;11:76941. [PMID: 35293861 PMCID: PMC9094753 DOI: 10.7554/elife.76941] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/13/2022]  Open
33
McLure RJ, Radford SE, Brockwell DJ. High-throughput directed evolution: a golden era for protein science. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.02.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
34
Gamper H, Masuda I, Hou YM. Genome Expansion by tRNA +1 Frameshifting at Quadruplet Codons. J Mol Biol 2022;434:167440. [PMID: 34995554 PMCID: PMC9643101 DOI: 10.1016/j.jmb.2021.167440] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 12/27/2021] [Accepted: 12/30/2021] [Indexed: 11/29/2022]
35
DeBenedictis EA, Chory EJ, Gretton DW, Wang B, Golas S, Esvelt KM. Systematic molecular evolution enables robust biomolecule discovery. Nat Methods 2022;19:55-64. [PMID: 34969982 PMCID: PMC11655129 DOI: 10.1038/s41592-021-01348-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 11/09/2021] [Indexed: 11/09/2022]
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