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For: Hart JM, Kennedy SD, Mathews DH, Turner DH. NMR-assisted prediction of RNA secondary structure: identification of a probable pseudoknot in the coding region of an R2 retrotransposon. J Am Chem Soc 2008;130:10233-9. [PMID: 18613678 PMCID: PMC2646634 DOI: 10.1021/ja8026696] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2008] [Indexed: 12/30/2022]
Number Cited by Other Article(s)
1
Deng P, Tan SQ, Yang QY, Fu L, Wu Y, Zhu HZ, Sun L, Bao Z, Lin Y, Zhang QC, Wang H, Wang J, Liu JJG. Structural RNA components supervise the sequential DNA cleavage in R2 retrotransposon. Cell 2023;186:2865-2879.e20. [PMID: 37301196 DOI: 10.1016/j.cell.2023.05.032] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/14/2023] [Accepted: 05/20/2023] [Indexed: 06/12/2023]
2
Moudgal N, Arhin G, Frank AT. Using Unassigned NMR Chemical Shifts to Model RNA Secondary Structure. J Phys Chem A 2022;126:2739-2745. [PMID: 35470661 DOI: 10.1021/acs.jpca.2c00456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
3
Mandal T, Dhara K, Parui N, Dash J. Domino Relay Olefin Metathesis of Triallyl Oxindole and Indole Precursors to Access Cyclic Indoxyls and Carbazoles. ChemCatChem 2020. [DOI: 10.1002/cctc.202000813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
4
Antunes D, Jorge NAN, Caffarena ER, Passetti F. Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. Front Genet 2018;8:231. [PMID: 29403526 PMCID: PMC5780412 DOI: 10.3389/fgene.2017.00231] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022]  Open
5
RNA Secondary Structure Determination by NMR. Methods Mol Biol 2018;1490:177-86. [PMID: 27665599 DOI: 10.1007/978-1-4939-6433-8_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
6
Kauffmann AD, Kennedy SD, Zhao J, Turner DH. Nuclear Magnetic Resonance Structure of an 8 × 8 Nucleotide RNA Internal Loop Flanked on Each Side by Three Watson-Crick Pairs and Comparison to Three-Dimensional Predictions. Biochemistry 2017;56:3733-3744. [PMID: 28700212 DOI: 10.1021/acs.biochem.7b00201] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
7
Xu ZZ, Mathews DH. Experiment-Assisted Secondary Structure Prediction with RNAstructure. Methods Mol Biol 2016;1490:163-176. [PMID: 27665598 DOI: 10.1007/978-1-4939-6433-8_10] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
8
Kennedy SD. NMR Methods for Characterization of RNA Secondary Structure. Methods Mol Biol 2016;1490:253-64. [PMID: 27665604 DOI: 10.1007/978-1-4939-6433-8_16] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
9
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]
10
Kierzek R, Turner DH, Kierzek E. Microarrays for identifying binding sites and probing structure of RNAs. Nucleic Acids Res 2014;43:1-12. [PMID: 25505162 PMCID: PMC4288193 DOI: 10.1093/nar/gku1303] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
11
Strulson CA, Boyer JA, Whitman EE, Bevilacqua PC. Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions. RNA (NEW YORK, N.Y.) 2014;20:331-47. [PMID: 24442612 PMCID: PMC3923128 DOI: 10.1261/rna.042747.113] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2013] [Accepted: 11/22/2013] [Indexed: 05/21/2023]
12
Tubbs J, Condon DE, Kennedy S, Hauser M, Bevilacqua P, Turner DH. The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry 2013;52:996-1010. [PMID: 23286901 PMCID: PMC3571207 DOI: 10.1021/bi3010347] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 12/27/2012] [Indexed: 12/29/2022]
13
Moss WN. Computational prediction of RNA secondary structure. Methods Enzymol 2013;530:3-65. [PMID: 24034313 DOI: 10.1016/b978-0-12-420037-1.00001-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
14
Chen J, Dishler AL, Kennedy SD, Yildirim I, Liu B, Turner DH, Serra MJ. Testing the nearest neighbor model for canonical RNA base pairs: revision of GU parameters. Biochemistry 2012;51:3508-22. [PMID: 22490167 PMCID: PMC3335265 DOI: 10.1021/bi3002709] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2012] [Indexed: 11/30/2022]
15
Bahrami A, Clos LJ, Markley JL, Butcher SE, Eghbalnia HR. RNA-PAIRS: RNA probabilistic assignment of imino resonance shifts. JOURNAL OF BIOMOLECULAR NMR 2012;52:289-302. [PMID: 22359049 PMCID: PMC3480180 DOI: 10.1007/s10858-012-9603-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Accepted: 01/08/2012] [Indexed: 05/13/2023]
16
Puglisi EV, Puglisi JD. Secondary structure of the HIV reverse transcription initiation complex by NMR. J Mol Biol 2011;410:863-74. [PMID: 21763492 DOI: 10.1016/j.jmb.2011.04.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/06/2011] [Accepted: 04/11/2011] [Indexed: 01/11/2023]
17
Lerman YV, Kennedy SD, Shankar N, Parisien M, Major F, Turner DH. NMR structure of a 4 x 4 nucleotide RNA internal loop from an R2 retrotransposon: identification of a three purine-purine sheared pair motif and comparison to MC-SYM predictions. RNA (NEW YORK, N.Y.) 2011;17:1664-77. [PMID: 21778280 PMCID: PMC3162332 DOI: 10.1261/rna.2641911] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2011] [Accepted: 05/08/2011] [Indexed: 05/31/2023]
18
Duchardt-Ferner E, Ferner J, Wöhnert J. Direkte Identifizierung von nichtkanonischen RNA-Strukturelementen durch den Nachweis von OH⋅⋅⋅OP-, NH⋅⋅⋅OP- und NH2⋅⋅⋅OP-Wasserstoffbrücken mit NMR-Spektroskopie in Lösung. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101743] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
19
Duchardt-Ferner E, Ferner J, Wöhnert J. Rapid identification of noncanonical RNA structure elements by direct detection of OH···O=P, NH···O=P, and NH2···O=P hydrogen bonds in solution NMR spectroscopy. Angew Chem Int Ed Engl 2011;50:7927-30. [PMID: 21837618 DOI: 10.1002/anie.201101743] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/31/2011] [Indexed: 12/24/2022]
20
Moss WN, Eickbush DG, Lopez MJ, Eickbush TH, Turner DH. The R2 retrotransposon RNA families. RNA Biol 2011;8:714-8. [PMID: 21734471 DOI: 10.4161/rna.8.5.16033] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]  Open
21
Andronescu M, Condon A, Hoos HH, Mathews DH, Murphy KP. Computational approaches for RNA energy parameter estimation. RNA (NEW YORK, N.Y.) 2010;16:2304-18. [PMID: 20940338 PMCID: PMC2995392 DOI: 10.1261/rna.1950510] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
22
Liang R, Kierzek E, Kierzek R, Turner DH. Comparisons between chemical mapping and binding to isoenergetic oligonucleotide microarrays reveal unexpected patterns of binding to the Bacillus subtilis RNase P RNA specificity domain. Biochemistry 2010;49:8155-68. [PMID: 20557101 PMCID: PMC2938832 DOI: 10.1021/bi100286n] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2010] [Revised: 06/16/2010] [Indexed: 11/29/2022]
23
Mathews DH, Moss WN, Turner DH. Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol 2010;2:a003665. [PMID: 20685845 DOI: 10.1101/cshperspect.a003665] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
24
Hammond NB, Tolbert BS, Kierzek R, Turner DH, Kennedy SD. RNA internal loops with tandem AG pairs: the structure of the 5'GAGU/3'UGAG loop can be dramatically different from others, including 5'AAGU/3'UGAA. Biochemistry 2010;49:5817-27. [PMID: 20481618 PMCID: PMC2900907 DOI: 10.1021/bi100332r] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
25
Wachowius F, Höbartner C. Chemical RNA modifications for studies of RNA structure and dynamics. Chembiochem 2010;11:469-80. [PMID: 20135663 DOI: 10.1002/cbic.200900697] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
26
Quarrier S, Martin JS, Davis-Neulander L, Beauregard A, Laederach A. Evaluation of the information content of RNA structure mapping data for secondary structure prediction. RNA (NEW YORK, N.Y.) 2010;16:1108-17. [PMID: 20413617 PMCID: PMC2874162 DOI: 10.1261/rna.1988510] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2009] [Accepted: 02/20/2010] [Indexed: 05/21/2023]
27
Liu B, Shankar N, Turner DH. Fluorescence competition assay measurements of free energy changes for RNA pseudoknots. Biochemistry 2010;49:623-34. [PMID: 19921809 PMCID: PMC2808147 DOI: 10.1021/bi901541j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
28
Reuter JS, Mathews DH. RNAstructure: software for RNA secondary structure prediction and analysis. BMC Bioinformatics 2010;11:129. [PMID: 20230624 PMCID: PMC2984261 DOI: 10.1186/1471-2105-11-129] [Citation(s) in RCA: 1271] [Impact Index Per Article: 90.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 03/15/2010] [Indexed: 11/16/2022]  Open
29
Puffer B, Kreutz C, Rieder U, Ebert MO, Konrat R, Micura R. 5-Fluoro pyrimidines: labels to probe DNA and RNA secondary structures by 1D 19F NMR spectroscopy. Nucleic Acids Res 2010;37:7728-40. [PMID: 19843610 PMCID: PMC2794194 DOI: 10.1093/nar/gkp862] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
30
Liu B, Mathews DH, Turner DH. RNA pseudoknots: folding and finding. F1000 BIOLOGY REPORTS 2010;2:8. [PMID: 20495679 PMCID: PMC2873773 DOI: 10.3410/b2-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
31
Kierzek E. Binding of short oligonucleotides to RNA: studies of the binding of common RNA structural motifs to isoenergetic microarrays. Biochemistry 2009;48:11344-56. [PMID: 19835418 DOI: 10.1021/bi901264v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Rieder U, Lang K, Kreutz C, Polacek N, Micura R. Evidence for pseudoknot formation of class I preQ1 riboswitch aptamers. Chembiochem 2009;10:1141-4. [PMID: 19382115 DOI: 10.1002/cbic.200900155] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
33
Harmanci AO, Sharma G, Mathews DH. Stochastic sampling of the RNA structural alignment space. Nucleic Acids Res 2009;37:4063-75. [PMID: 19429694 PMCID: PMC2709569 DOI: 10.1093/nar/gkp276] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
34
Kierzek E, Christensen SM, Eickbush TH, Kierzek R, Turner DH, Moss WN. Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraints. J Mol Biol 2009;390:428-42. [PMID: 19397915 DOI: 10.1016/j.jmb.2009.04.048] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 04/17/2009] [Accepted: 04/21/2009] [Indexed: 12/24/2022]
35
Cao S, Chen SJ. Predicting structures and stabilities for H-type pseudoknots with interhelix loops. RNA (NEW YORK, N.Y.) 2009;15:696-706. [PMID: 19237463 PMCID: PMC2661829 DOI: 10.1261/rna.1429009] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2008] [Accepted: 01/10/2009] [Indexed: 05/20/2023]
36
Nucleic Acids: Expanding the Structural and Functional Horizons. J Am Chem Soc 2009;131:3791-3. [DOI: 10.1021/ja9012485] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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