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For: Westhof E, Yusupov M, Yusupova G. The multiple flavors of GoU pairs in RNA. J Mol Recognit 2019;32:e2782. [PMID: 31033092 PMCID: PMC6617799 DOI: 10.1002/jmr.2782] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/02/2019] [Accepted: 03/14/2019] [Indexed: 11/10/2022]
Number Cited by Other Article(s)
1
Geng A, Roy R, Gu S, Guseva S, Pratihar S, Lee Y, Li L, Kimsey IJ, Wilson MA, Al-Hashimi HM. Insight into the Conformational Ensembles Formed by U-U and T-T Mismatches in RNA and DNA Duplexes From a Structure-based Survey, NMR, and Molecular Dynamics Simulations. J Mol Biol 2025;437:169197. [PMID: 40345379 DOI: 10.1016/j.jmb.2025.169197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2025] [Revised: 05/05/2025] [Accepted: 05/05/2025] [Indexed: 05/11/2025]
2
Ren Y, Lin X, Liao W, Peng X, Deng J, Zhang Z, Zhan J, Zhou Y, Westhof E, Lilley DMJ, Wang J, Huang L. A general strategy for engineering GU base pairs to facilitate RNA crystallization. Nucleic Acids Res 2025;53:gkae1218. [PMID: 39721592 PMCID: PMC11797044 DOI: 10.1093/nar/gkae1218] [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: 07/05/2024] [Revised: 11/07/2024] [Accepted: 11/26/2024] [Indexed: 12/28/2024]  Open
3
Timsit Y, Sergeant-Perthuis G, Bennequin D. The role of ribosomal protein networks in ribosome dynamics. Nucleic Acids Res 2025;53:gkae1308. [PMID: 39788545 PMCID: PMC11711686 DOI: 10.1093/nar/gkae1308] [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: 02/27/2024] [Revised: 12/12/2024] [Accepted: 01/02/2025] [Indexed: 01/12/2025]  Open
4
Srivastava Y, Akinyemi O, Rohe T, Pritchett E, Baker C, Sharma A, Jenkins J, Mathews D, Wedekind J. Two riboswitch classes that share a common ligand-binding fold show major differences in the ability to accommodate mutations. Nucleic Acids Res 2024;52:13152-13173. [PMID: 39413212 PMCID: PMC11602147 DOI: 10.1093/nar/gkae886] [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: 06/05/2024] [Revised: 09/09/2024] [Accepted: 09/25/2024] [Indexed: 10/18/2024]  Open
5
Kompatscher M, Bartosik K, Erharter K, Plangger R, Juen F, Kreutz C, Micura R, Westhof E, Erlacher M. Contribution of tRNA sequence and modifications to the decoding preferences of E. coli and M. mycoides tRNAGlyUCC for synonymous glycine codons. Nucleic Acids Res 2024;52:1374-1386. [PMID: 38050960 PMCID: PMC10853795 DOI: 10.1093/nar/gkad1136] [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: 09/13/2023] [Revised: 11/06/2023] [Accepted: 11/10/2023] [Indexed: 12/07/2023]  Open
6
Krahn N, Zhang J, Melnikov SV, Tharp JM, Villa A, Patel A, Howard R, Gabir H, Patel T, Stetefeld J, Puglisi J, Söll D. tRNA shape is an identity element for an archaeal pyrrolysyl-tRNA synthetase from the human gut. Nucleic Acids Res 2024;52:513-524. [PMID: 38100361 PMCID: PMC10810272 DOI: 10.1093/nar/gkad1188] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/23/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]  Open
7
Ojha M, Vogt J, Das NK, Redmond E, Singh K, Banna HA, Sadat T, Koirala D. Structure of saguaro cactus virus 3' translational enhancer mimics 5' cap for eIF4E binding. Proc Natl Acad Sci U S A 2024;121:e2313677121. [PMID: 38241435 PMCID: PMC10823258 DOI: 10.1073/pnas.2313677121] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 12/18/2023] [Indexed: 01/21/2024]  Open
8
Borovská I, Vořechovský I, Královičová J. Alu RNA fold links splicing with signal recognition particle proteins. Nucleic Acids Res 2023;51:8199-8216. [PMID: 37309897 PMCID: PMC10450188 DOI: 10.1093/nar/gkad500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 05/23/2023] [Accepted: 05/31/2023] [Indexed: 06/14/2023]  Open
9
Westhof E, Watson ZL, Zirbel CL, Cate JHD. Anionic G•U pairs in bacterial ribosomal rRNAs. RNA (NEW YORK, N.Y.) 2023;29:1069-1076. [PMID: 37068913 DOI: 10.1261/rna.079583.123] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 04/05/2023] [Indexed: 06/18/2023]
10
Souza TML, Pinho VD, Setim CF, Sacramento CQ, Marcon R, Fintelman-Rodrigues N, Chaves OA, Heller M, Temerozo JR, Ferreira AC, Mattos M, Momo PB, Dias SSG, Gesto JSM, Pereira-Dutra F, Viola JPB, Queiroz-Junior CM, Guimarães LC, Chaves IM, Guimarães PPG, Costa VV, Teixeira MM, Bou-Habib DC, Bozza PT, Aguillón AR, Siqueira-Junior J, Macedo-Junior S, Andrade EL, Fadanni GP, Tolouei SEL, Potrich FB, Santos AA, Marques NF, Calixto JB, Rabi JA. Preclinical development of kinetin as a safe error-prone SARS-CoV-2 antiviral able to attenuate virus-induced inflammation. Nat Commun 2023;14:199. [PMID: 36639383 PMCID: PMC9837764 DOI: 10.1038/s41467-023-35928-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 01/09/2023] [Indexed: 01/15/2023]  Open
11
L’ARNm et ses modifications chez les eucaryotes*. BULLETIN DE L'ACADÉMIE NATIONALE DE MÉDECINE 2022. [DOI: 10.1016/j.banm.2022.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
12
Kiliszek A, Pluta M, Bejger M, Rypniewski W. Structure and thermodynamics of a UGG motif interacting with Ba2+ and other metal ions: accommodating changes in the RNA structure and the presence of a G(syn)-G(syn) pair. RNA (NEW YORK, N.Y.) 2022;29:rna.079414.122. [PMID: 36319090 PMCID: PMC9808570 DOI: 10.1261/rna.079414.122] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
13
Yarus M. A crescendo of competent coding (c3) contains the Standard Genetic Code. RNA (NEW YORK, N.Y.) 2022;28:1337-1347. [PMID: 35868841 PMCID: PMC9479743 DOI: 10.1261/rna.079275.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
14
Hassler HB, Probert B, Moore C, Lawson E, Jackson RW, Russell BT, Richards VP. Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies. MICROBIOME 2022;10:104. [PMID: 35799218 PMCID: PMC9264627 DOI: 10.1186/s40168-022-01295-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 05/23/2022] [Indexed: 05/02/2023]
15
Zuber J, Schroeder SJ, Sun H, Turner DH, Mathews DH. Nearest neighbor rules for RNA helix folding thermodynamics: improved end effects. Nucleic Acids Res 2022;50:5251-5262. [PMID: 35524574 PMCID: PMC9122537 DOI: 10.1093/nar/gkac261] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/29/2022] [Accepted: 04/08/2022] [Indexed: 12/26/2022]  Open
16
Westhof E, Thornlow B, Chan PP, Lowe TM. Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures. Nucleic Acids Res 2022;50:4100-4112. [PMID: 35380696 PMCID: PMC9023262 DOI: 10.1093/nar/gkac222] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 11/18/2022]  Open
17
Fractional 2'-O-methylation in the ribosomal RNA of Dictyostelium discoideum supports ribosome heterogeneity in Amoebozoa. Sci Rep 2022;12:1952. [PMID: 35121764 PMCID: PMC8817022 DOI: 10.1038/s41598-022-05447-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 01/07/2022] [Indexed: 12/02/2022]  Open
18
Ruszkowska A, Zheng YY, Mao S, Ruszkowski M, Sheng J. Structural Insights Into the 5′UG/3′GU Wobble Tandem in Complex With Ba2+ Cation. Front Mol Biosci 2022;8:762786. [PMID: 35096964 PMCID: PMC8793689 DOI: 10.3389/fmolb.2021.762786] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 11/24/2021] [Indexed: 11/25/2022]  Open
19
Fitting the standard genetic code into its triplet table. Proc Natl Acad Sci U S A 2021;118:2021103118. [PMID: 34462348 PMCID: PMC8433516 DOI: 10.1073/pnas.2021103118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
20
An RNA-centric historical narrative around the Protein Data Bank. J Biol Chem 2021;296:100555. [PMID: 33744291 PMCID: PMC8080527 DOI: 10.1016/j.jbc.2021.100555] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/17/2021] [Accepted: 03/16/2021] [Indexed: 01/06/2023]  Open
21
Auffinger P, Ennifar E, D'Ascenzo L. Deflating the RNA Mg2+ bubble. Stereochemistry to the rescue! RNA (NEW YORK, N.Y.) 2020;27:rna.076067.120. [PMID: 33268500 PMCID: PMC7901845 DOI: 10.1261/rna.076067.120] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 11/20/2020] [Indexed: 05/03/2023]
22
Wolff P, Villette C, Zumsteg J, Heintz D, Antoine L, Chane-Woon-Ming B, Droogmans L, Grosjean H, Westhof E. Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea. RNA (NEW YORK, N.Y.) 2020;26:1957-1975. [PMID: 32994183 PMCID: PMC7668247 DOI: 10.1261/rna.077537.120] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/09/2020] [Indexed: 05/22/2023]
23
Schäck MA, Jablonski KP, Gräf S, Klassen R, Schaffrath R, Kellner S, Hammann C. Eukaryotic life without tQCUG: the role of Elongator-dependent tRNA modifications in Dictyostelium discoideum. Nucleic Acids Res 2020;48:7899-7913. [PMID: 32609816 PMCID: PMC7430636 DOI: 10.1093/nar/gkaa560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/16/2020] [Accepted: 06/18/2020] [Indexed: 12/23/2022]  Open
24
Rangadurai A, Szymanski ES, Kimsey I, Shi H, Al-Hashimi HM. Probing conformational transitions towards mutagenic Watson-Crick-like G·T mismatches using off-resonance sugar carbon R relaxation dispersion. JOURNAL OF BIOMOLECULAR NMR 2020;74:457-471. [PMID: 32789613 PMCID: PMC7508749 DOI: 10.1007/s10858-020-00337-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 07/13/2020] [Indexed: 05/30/2023]
25
C5-Substituted 2-Selenouridines Ensure Efficient Base Pairing with Guanosine; Consequences for Reading the NNG-3' Synonymous mRNA Codons. Int J Mol Sci 2020;21:ijms21082882. [PMID: 32326096 PMCID: PMC7216251 DOI: 10.3390/ijms21082882] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/16/2020] [Accepted: 04/18/2020] [Indexed: 12/14/2022]  Open
26
Cornish-Bowden A, Cárdenas ML. Contrasting theories of life: Historical context, current theories. In search of an ideal theory. Biosystems 2020;188:104063. [DOI: 10.1016/j.biosystems.2019.104063] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/10/2019] [Accepted: 10/10/2019] [Indexed: 12/18/2022]
27
Antoine L, Wolff P, Westhof E, Romby P, Marzi S. Mapping post-transcriptional modifications in Staphylococcus aureus tRNAs by nanoLC/MSMS. Biochimie 2019;164:60-69. [PMID: 31295507 DOI: 10.1016/j.biochi.2019.07.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 07/03/2019] [Indexed: 02/06/2023]
28
Westhof E, Yusupov M, Yusupova G. The multiple flavors of GoU pairs in RNA. J Mol Recognit 2019;32:e2782. [PMID: 31033092 PMCID: PMC6617799 DOI: 10.1002/jmr.2782] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 03/02/2019] [Accepted: 03/14/2019] [Indexed: 11/10/2022]
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