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For: Zagryadskaya EI, Doyon FR, Steinberg SV. Importance of the reverse Hoogsteen base pair 54-58 for tRNA function. Nucleic Acids Res 2003;31:3946-53. [PMID: 12853610 PMCID: PMC165963 DOI: 10.1093/nar/gkg448] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
Number Cited by Other Article(s)
1
Wu D, Li X, Khan FA, Yuan C, Pandupuspitasari NS, Huang C, Sun F, Guan K. tRNA modifications and tRNA-derived small RNAs: new insights of tRNA in human disease. Cell Biol Toxicol 2024;40:76. [PMID: 39276283 PMCID: PMC11401796 DOI: 10.1007/s10565-024-09919-9] [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: 06/10/2024] [Accepted: 09/04/2024] [Indexed: 09/16/2024]
2
Xuan Y, Wang L, Zhang L, Lv M, Li F, Gong Q. Structural basis of pri-let-7 recognition by human pseudouridine synthase TruB1. Biochem Biophys Res Commun 2024;721:150122. [PMID: 38776834 DOI: 10.1016/j.bbrc.2024.150122] [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: 01/30/2024] [Revised: 04/29/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
3
Banazadeh M, Abiri A, Poortaheri MM, Asnaashari L, Langarizadeh MA, Forootanfar H. Unexplored power of CRISPR-Cas9 in neuroscience, a multi-OMICs review. Int J Biol Macromol 2024;263:130413. [PMID: 38408576 DOI: 10.1016/j.ijbiomac.2024.130413] [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: 02/03/2023] [Revised: 05/27/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024]
4
de Jesus V, Biedenbänder T, Vögele J, Wöhnert J, Fürtig B. NMR assignment of non-modified tRNAIle from Escherichia coli. BIOMOLECULAR NMR ASSIGNMENTS 2022;16:165-170. [PMID: 35275364 PMCID: PMC9068674 DOI: 10.1007/s12104-022-10075-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/24/2022] [Indexed: 06/14/2023]
5
Fukuda H, Chujo T, Wei FY, Shi SL, Hirayama M, Kaitsuka T, Yamamoto T, Oshiumi H, Tomizawa K. Cooperative methylation of human tRNA3Lys at positions A58 and U54 drives the early and late steps of HIV-1 replication. Nucleic Acids Res 2021;49:11855-11867. [PMID: 34642752 PMCID: PMC8599865 DOI: 10.1093/nar/gkab879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 09/15/2021] [Accepted: 09/20/2021] [Indexed: 11/17/2022]  Open
6
Bandyopadhyay D, Mishra PP. Decoding the Structural Dynamics and Conformational Alternations of DNA Secondary Structures by Single-Molecule FRET Microspectroscopy. Front Mol Biosci 2021;8:725541. [PMID: 34540899 PMCID: PMC8446445 DOI: 10.3389/fmolb.2021.725541] [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] [Received: 06/15/2021] [Accepted: 07/30/2021] [Indexed: 12/02/2022]  Open
7
Post-Transcriptional Modifications of Conserved Nucleotides in the T-Loop of tRNA: A Tale of Functional Convergent Evolution. Genes (Basel) 2021;12:genes12020140. [PMID: 33499018 PMCID: PMC7912444 DOI: 10.3390/genes12020140] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 12/30/2022]  Open
8
De Novo Nucleic Acids: A Review of Synthetic Alternatives to DNA and RNA That Could Act as Bio-Information Storage Molecules. Life (Basel) 2020;10:life10120346. [PMID: 33322642 PMCID: PMC7764398 DOI: 10.3390/life10120346] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/04/2020] [Accepted: 12/09/2020] [Indexed: 01/30/2023]  Open
9
Yamagami R, Miyake R, Fukumoto A, Nakashima M, Hori H. Consumption of N5, N10-methylenetetrahydrofolate in Thermus thermophilus under nutrient-poor condition. J Biochem 2018. [PMID: 29538705 DOI: 10.1093/jb/mvy037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
10
Non-dissociative structural transitions of the Watson-Crick and reverse Watson-Crick А·Т DNA base pairs into the Hoogsteen and reverse Hoogsteen forms. Sci Rep 2018;8:10371. [PMID: 29991693 PMCID: PMC6039495 DOI: 10.1038/s41598-018-28636-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Accepted: 06/21/2018] [Indexed: 11/08/2022]  Open
11
Brovarets' OO, Tsiupa KS, Hovorun DM. Surprising Conformers of the Biologically Important A·T DNA Base Pairs: QM/QTAIM Proofs. Front Chem 2018;6:8. [PMID: 29536003 PMCID: PMC5835050 DOI: 10.3389/fchem.2018.00008] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/11/2018] [Indexed: 11/22/2022]  Open
12
Yamagami R, Tomikawa C, Shigi N, Kazayama A, Asai SI, Takuma H, Hirata A, Fourmy D, Asahara H, Watanabe K, Yoshizawa S, Hori H. Folate-/FAD-dependent tRNA methyltransferase from Thermus thermophilus regulates other modifications in tRNA at low temperatures. Genes Cells 2016;21:740-54. [PMID: 27238446 DOI: 10.1111/gtc.12376] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 04/19/2016] [Indexed: 11/29/2022]
13
Ashkenazy H, Abadi S, Martz E, Chay O, Mayrose I, Pupko T, Ben-Tal N. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res 2016;44:W344-50. [PMID: 27166375 PMCID: PMC4987940 DOI: 10.1093/nar/gkw408] [Citation(s) in RCA: 2105] [Impact Index Per Article: 233.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 05/03/2016] [Indexed: 12/12/2022]  Open
14
Lu XJ, Bussemaker HJ, Olson WK. DSSR: an integrated software tool for dissecting the spatial structure of RNA. Nucleic Acids Res 2015;43:e142. [PMID: 26184874 PMCID: PMC4666379 DOI: 10.1093/nar/gkv716] [Citation(s) in RCA: 151] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Accepted: 07/02/2015] [Indexed: 12/16/2022]  Open
15
Brovarets' OO. [Structural and energetic properties of the four configurations of the A.T and G.C DNA base pairs]. UKRAINIAN BIOCHEMICAL JOURNAL 2013;85:104-10. [PMID: 24319980 DOI: 10.15407/ubj85.04.104] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
16
Brovarets' OO. [Under what conditions does G.C Watson-Crick DNA base pair acquire all four configurations characteristic for A.T Watson-Crick DNA base pair?]. UKRAINIAN BIOCHEMICAL JOURNAL 2013;85:98-103. [PMID: 24319979 DOI: 10.15407/ubj85.04.098] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]  Open
17
Brovarets’ OO, Yurenko YP, Hovorun DM. Intermolecular CH···O/N H-bonds in the biologically important pairs of natural nucleobases: a thorough quantum-chemical study. J Biomol Struct Dyn 2013;32:993-1022. [PMID: 23730732 DOI: 10.1080/07391102.2013.799439] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
18
Ishii TM, Kotlova N, Tapsoba F, Steinberg SV. The long D-stem of the selenocysteine tRNA provides resilience at the expense of maximal function. J Biol Chem 2013;288:13337-44. [PMID: 23525102 DOI: 10.1074/jbc.m112.434704] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]  Open
19
Kraut S, Bebenroth D, Nierth A, Kobitski AY, Nienhaus GU, Jäschke A. Three critical hydrogen bonds determine the catalytic activity of the Diels-Alderase ribozyme. Nucleic Acids Res 2011;40:1318-30. [PMID: 21976731 PMCID: PMC3273808 DOI: 10.1093/nar/gkr812] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
20
Schlitt KM, Millen AL, Wetmore SD, Manderville RA. An indole-linked C8-deoxyguanosine nucleoside acts as a fluorescent reporter of Watson-Crick versus Hoogsteen base pairing. Org Biomol Chem 2011;9:1565-71. [PMID: 21240404 DOI: 10.1039/c0ob00883d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
21
Zhang S, Wang T. A Complexity-based Method to Compare RNA Secondary Structures and its Application. J Biomol Struct Dyn 2010;28:247-58. [PMID: 20645657 DOI: 10.1080/07391102.2010.10507357] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
22
Liu Q, Yang Y, Chen C, Bu J, Zhang Y, Ye X. RNACompress: Grammar-based compression and informational complexity measurement of RNA secondary structure. BMC Bioinformatics 2008;9:176. [PMID: 18373878 PMCID: PMC2335284 DOI: 10.1186/1471-2105-9-176] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2007] [Accepted: 03/31/2008] [Indexed: 11/10/2022]  Open
23
Kotlova N, Ishii TM, Zagryadskaya EI, Steinberg SV. Active suppressor tRNAs with a double helix between the D- and T-loops. J Mol Biol 2007;373:462-75. [PMID: 17822715 DOI: 10.1016/j.jmb.2007.07.058] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Revised: 07/25/2007] [Accepted: 07/26/2007] [Indexed: 10/23/2022]
24
Bessho Y, Shibata R, Sekine SI, Murayama K, Higashijima K, Hori-Takemoto C, Shirouzu M, Kuramitsu S, Yokoyama S. Structural basis for functional mimicry of long-variable-arm tRNA by transfer-messenger RNA. Proc Natl Acad Sci U S A 2007;104:8293-8. [PMID: 17488812 PMCID: PMC1895943 DOI: 10.1073/pnas.0700402104] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
25
Ghosal G, Muniyappa K. Hoogsteen base-pairing revisited: resolving a role in normal biological processes and human diseases. Biochem Biophys Res Commun 2006;343:1-7. [PMID: 16540083 DOI: 10.1016/j.bbrc.2006.02.148] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2006] [Accepted: 02/24/2006] [Indexed: 01/21/2023]
26
Oliva R, Cavallo L, Tramontano A. Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions. Nucleic Acids Res 2006;34:865-79. [PMID: 16461956 PMCID: PMC1361619 DOI: 10.1093/nar/gkj491] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
27
Kelly NJ, Morrow CD. Structural elements of the tRNA TPsiC loop critical for nucleocytoplasmic transport are important for human immunodeficiency virus type 1 primer selection. J Virol 2005;79:6532-9. [PMID: 15858038 PMCID: PMC1091683 DOI: 10.1128/jvi.79.10.6532-6539.2005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
28
Doyon FR, Zagryadskaya EI, Chen J, Steinberg SV. Specific and non-specific purine trap in the T-loop of normal and suppressor tRNAs. J Mol Biol 2004;343:55-69. [PMID: 15381420 DOI: 10.1016/j.jmb.2004.08.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Revised: 08/09/2004] [Accepted: 08/09/2004] [Indexed: 11/18/2022]
29
Ray WC. MAVL and StickWRLD: visually exploring relationships in nucleic acid sequence alignments. Nucleic Acids Res 2004;32:W59-63. [PMID: 15215351 PMCID: PMC441607 DOI: 10.1093/nar/gkh469] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
30
Zagryadskaya EI, Kotlova N, Steinberg SV. Key elements in maintenance of the tRNA L-shape. J Mol Biol 2004;340:435-44. [PMID: 15210345 DOI: 10.1016/j.jmb.2004.05.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2004] [Revised: 04/28/2004] [Accepted: 05/01/2004] [Indexed: 11/29/2022]
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