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For: Donghi D, Pechlaner M, Finazzo C, Knobloch B, Sigel RKO. The structural stabilization of the κ three-way junction by Mg(II) represents the first step in the folding of a group II intron. Nucleic Acids Res 2012;41:2489-504. [PMID: 23275550 PMCID: PMC3575829 DOI: 10.1093/nar/gks1179] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Senft MD, Maier R, Hiremath A, Zhang F, Schreiber F. Effective interactions and phase behavior of protein solutions in the presence of hexamine cobalt(III) chloride. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2023;46:119. [PMID: 38051398 PMCID: PMC10698144 DOI: 10.1140/epje/s10189-023-00376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023]
2
Zhuo B, Ou X, Li J. Structure and Mechanical Stabilities of the Three-Way Junction Motifs in Prohead RNA. J Phys Chem B 2021;125:12125-12134. [PMID: 34719230 DOI: 10.1021/acs.jpcb.1c04681] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
3
Assembly factors chaperone ribosomal RNA folding by isolating helical junctions that are prone to misfolding. Proc Natl Acad Sci U S A 2021;118:2101164118. [PMID: 34135123 DOI: 10.1073/pnas.2101164118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]  Open
4
Zhang Q, Ma C, Duan Y, Heinrich B, Rosato U, Diggs LP, Ma L, Roy S, Fu Q, Brown ZJ, Wabitsch S, Thovarai V, Fu J, Feng D, Ruf B, Cui LL, Subramanyam V, Frank KM, Wang S, Kleiner DE, Ritz T, Rupp C, Gao B, Longerich T, Kroemer A, Wang XW, Ruchirawat M, Korangy F, Schnabl B, Trinchieri G, Greten TF. Gut Microbiome Directs Hepatocytes to Recruit MDSCs and Promote Cholangiocarcinoma. Cancer Discov 2020;11:1248-1267. [PMID: 33323397 DOI: 10.1158/2159-8290.cd-20-0304] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 10/14/2020] [Accepted: 12/10/2020] [Indexed: 02/07/2023]
5
Dong X, Qu G, Piazza CL, Belfort M. Group II intron as cold sensor for self-preservation and bacterial conjugation. Nucleic Acids Res 2020;48:6198-6209. [PMID: 32379323 PMCID: PMC7293003 DOI: 10.1093/nar/gkaa313] [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: 12/15/2019] [Revised: 04/01/2020] [Accepted: 04/20/2020] [Indexed: 01/18/2023]  Open
6
Zhang K, Frank AT. Conditional Prediction of Ribonucleic Acid Secondary Structure Using Chemical Shifts. J Phys Chem B 2019;124:470-478. [DOI: 10.1021/acs.jpcb.9b09814] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
7
Nikolaev Y, Ripin N, Soste M, Picotti P, Iber D, Allain FHT. Systems NMR: single-sample quantification of RNA, proteins and metabolites for biomolecular network analysis. Nat Methods 2019;16:743-749. [PMID: 31363225 PMCID: PMC6837886 DOI: 10.1038/s41592-019-0495-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 06/17/2019] [Indexed: 12/14/2022]
8
Stasiewicz J, Mukherjee S, Nithin C, Bujnicki JM. QRNAS: software tool for refinement of nucleic acid structures. BMC STRUCTURAL BIOLOGY 2019;19:5. [PMID: 30898165 PMCID: PMC6429776 DOI: 10.1186/s12900-019-0103-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Accepted: 03/05/2019] [Indexed: 01/03/2023]
9
Covalent and non-covalent binding of platinated vitamin B12-derivatives to a B12 responsive riboswitch. Inorganica Chim Acta 2018. [DOI: 10.1016/j.ica.2017.09.018] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
10
Specific phosphorothioate substitution within domain 6 of a group II intron ribozyme leads to changes in local structure and metal ion binding. J Biol Inorg Chem 2017;23:167-177. [DOI: 10.1007/s00775-017-1519-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 11/14/2017] [Indexed: 10/18/2022]
11
Zhao C, Pyle AM. Structural Insights into the Mechanism of Group II Intron Splicing. Trends Biochem Sci 2017;42:470-482. [PMID: 28438387 PMCID: PMC5492998 DOI: 10.1016/j.tibs.2017.03.007] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 03/28/2017] [Accepted: 03/30/2017] [Indexed: 12/19/2022]
12
Guha TK, Hausner G. Insertion of Group II Intron-Based Ribozyme Switches into Homing Endonuclease Genes. Methods Mol Biol 2017;1498:135-152. [PMID: 27709573 DOI: 10.1007/978-1-4939-6472-7_9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
13
Bartova S, Alberti E, Sigel RK, Donghi D. Metal ion binding to an RNA internal loop. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.02.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
14
Bermejo GA, Clore GM, Schwieters CD. Improving NMR Structures of RNA. Structure 2016;24:806-815. [PMID: 27066747 DOI: 10.1016/j.str.2016.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 01/27/2023]
15
Guha TK, Hausner G. Using Group II Introns for Attenuating the In Vitro and In Vivo Expression of a Homing Endonuclease. PLoS One 2016;11:e0150097. [PMID: 26909494 PMCID: PMC4801052 DOI: 10.1371/journal.pone.0150097] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 02/09/2016] [Indexed: 01/09/2023]  Open
16
Bartova S, Pechlaner M, Donghi D, Sigel RKO. Studying metal ion binding properties of a three-way junction RNA by heteronuclear NMR. J Biol Inorg Chem 2016;21:319-28. [PMID: 26880094 DOI: 10.1007/s00775-016-1341-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Accepted: 01/25/2016] [Indexed: 10/22/2022]
17
Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. Biochemistry 2015;54:6769-82. [PMID: 26451676 PMCID: PMC4666457 DOI: 10.1021/acs.biochem.5b00833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
18
Skilandat M, Sigel RKO. The role of Mg(II) in DNA cleavage site recognition in group II intron ribozymes: solution structure and metal ion binding sites of the RNA-DNA complex. J Biol Chem 2015;289:20650-63. [PMID: 24895129 DOI: 10.1074/jbc.m113.542381] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
19
Bonneau E, Legault P. Nuclear magnetic resonance structure of the III-IV-V three-way junction from the Varkud satellite ribozyme and identification of magnesium-binding sites using paramagnetic relaxation enhancement. Biochemistry 2014;53:6264-75. [PMID: 25238589 DOI: 10.1021/bi500826n] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
20
Jiang T, Kennedy SD, Moss WN, Kierzek E, Turner DH. Secondary structure of a conserved domain in an intron of influenza A M1 mRNA. Biochemistry 2014;53:5236-48. [PMID: 25026548 PMCID: PMC4139153 DOI: 10.1021/bi500611j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
21
Marcia M, Pyle AM. Principles of ion recognition in RNA: insights from the group II intron structures. RNA (NEW YORK, N.Y.) 2014;20:516-27. [PMID: 24570483 PMCID: PMC3964913 DOI: 10.1261/rna.043414.113] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2013] [Accepted: 01/29/2014] [Indexed: 05/20/2023]
22
Sripakdeevong P, Cevec M, Chang AT, Erat MC, Ziegeler M, Zhao Q, Fox GE, Gao X, Kennedy SD, Kierzek R, Nikonowicz EP, Schwalbe H, Sigel RKO, Turner DH, Das R. Structure determination of noncanonical RNA motifs guided by ¹H NMR chemical shifts. Nat Methods 2014;11:413-6. [PMID: 24584194 PMCID: PMC3985481 DOI: 10.1038/nmeth.2876] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Accepted: 01/06/2014] [Indexed: 12/31/2022]
23
Solution structure and metal ion binding sites of the human CPEB3 ribozyme's P4 domain. J Biol Inorg Chem 2014;19:903-12. [PMID: 24652468 DOI: 10.1007/s00775-014-1125-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2014] [Accepted: 03/05/2014] [Indexed: 01/18/2023]
24
Comparison of the π-stacking properties of purine versus pyrimidine residues. Some generalizations regarding selectivity. J Biol Inorg Chem 2014;19:691-703. [PMID: 24464134 DOI: 10.1007/s00775-013-1082-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 12/18/2013] [Indexed: 10/25/2022]
25
Somarowthu S, Legiewicz M, Keating KS, Pyle AM. Visualizing the ai5γ group IIB intron. Nucleic Acids Res 2013;42:1947-58. [PMID: 24203709 PMCID: PMC3919574 DOI: 10.1093/nar/gkt1051] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
26
Rowinska-Zyrek M, Skilandat M, Sigel RKO. Hexaamminecobalt(III) - Probing Metal Ion Binding Sites in Nucleic Acids by NMR Spectroscopy. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300123] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
27
Complex formation of cadmium with sugar residues, nucleobases, phosphates, nucleotides, and nucleic acids. Met Ions Life Sci 2013;11:191-274. [PMID: 23430775 DOI: 10.1007/978-94-007-5179-8_8] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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