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Items: 1 to 20 of 195

1.

Riboswitch structure in the ligand-free state.

Liberman JA, Wedekind JE.

Wiley Interdiscip Rev RNA. 2012 May-Jun;3(3):369-84. doi: 10.1002/wrna.114. Epub 2011 Sep 28. Review.

2.

The dynamic nature of RNA as key to understanding riboswitch mechanisms.

Haller A, Soulière MF, Micura R.

Acc Chem Res. 2011 Dec 20;44(12):1339-48. doi: 10.1021/ar200035g. Epub 2011 Jun 16.

PMID:
21678902
3.

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure.

Suddala KC, Rinaldi AJ, Feng J, Mustoe AM, Eichhorn CD, Liberman JA, Wedekind JE, Al-Hashimi HM, Brooks CL 3rd, Walter NG.

Nucleic Acids Res. 2013 Dec;41(22):10462-75. doi: 10.1093/nar/gkt798. Epub 2013 Sep 3.

4.

Ligand recognition and helical stacking formation are intimately linked in the SAM-I riboswitch regulatory mechanism.

Dussault AM, Dubé A, Jacques F, Grondin JP, Lafontaine DA.

RNA. 2017 Oct;23(10):1539-1551. doi: 10.1261/rna.061796.117. Epub 2017 Jul 12.

PMID:
28701520
5.

ITC analysis of ligand binding to preQ₁ riboswitches.

Liberman JA, Bogue JT, Jenkins JL, Salim M, Wedekind JE.

Methods Enzymol. 2014;549:435-50. doi: 10.1016/B978-0-12-801122-5.00018-0.

6.

Atomic-scale characterization of conformational changes in the preQ₁ riboswitch aptamer upon ligand binding.

Petrone PM, Dewhurst J, Tommasi R, Whitehead L, Pomerantz AK.

J Mol Graph Model. 2011 Sep;30:179-85. doi: 10.1016/j.jmgm.2011.07.006. Epub 2011 Jul 22.

PMID:
21831681
7.

Linking aptamer-ligand binding and expression platform folding in riboswitches: prospects for mechanistic modeling and design.

Aboul-ela F, Huang W, Abd Elrahman M, Boyapati V, Li P.

Wiley Interdiscip Rev RNA. 2015 Nov-Dec;6(6):631-50. doi: 10.1002/wrna.1300. Epub 2015 Sep 11. Review.

8.

Comparison of a preQ1 riboswitch aptamer in metabolite-bound and free states with implications for gene regulation.

Jenkins JL, Krucinska J, McCarty RM, Bandarian V, Wedekind JE.

J Biol Chem. 2011 Jul 15;286(28):24626-37. doi: 10.1074/jbc.M111.230375. Epub 2011 May 18.

9.

Single-Molecule Approaches for the Characterization of Riboswitch Folding Mechanisms.

Boudreault J, Perez-Gonzalez DC, Penedo JC, Lafontaine DA.

Methods Mol Biol. 2015;1334:101-7. doi: 10.1007/978-1-4939-2877-4_6.

PMID:
26404145
10.

Folding of the SAM-I riboswitch: a tale with a twist.

Eschbach SH, St-Pierre P, Penedo JC, Lafontaine DA.

RNA Biol. 2012 May;9(5):535-41. doi: 10.4161/rna.19648. Epub 2012 Feb 21.

PMID:
22336759
11.

Structural studies of the purine and SAM binding riboswitches.

Gilbert SD, Montange RK, Stoddard CD, Batey RT.

Cold Spring Harb Symp Quant Biol. 2006;71:259-68. Review.

PMID:
17381305
12.

Basis for ligand discrimination between ON and OFF state riboswitch conformations: the case of the SAM-I riboswitch.

Boyapati VK, Huang W, Spedale J, Aboul-Ela F.

RNA. 2012 Jun;18(6):1230-43. doi: 10.1261/rna.032177.111. Epub 2012 Apr 27.

13.

Folding of a transcriptionally acting preQ1 riboswitch.

Rieder U, Kreutz C, Micura R.

Proc Natl Acad Sci U S A. 2010 Jun 15;107(24):10804-9. doi: 10.1073/pnas.0914925107. Epub 2010 Jun 1.

14.

Multiple conformations of SAM-II riboswitch detected with SAXS and NMR spectroscopy.

Chen B, Zuo X, Wang YX, Dayie TK.

Nucleic Acids Res. 2012 Apr;40(7):3117-30. doi: 10.1093/nar/gkr1154. Epub 2011 Dec 1.

15.

Conformational capture of the SAM-II riboswitch.

Haller A, Rieder U, Aigner M, Blanchard SC, Micura R.

Nat Chem Biol. 2011 Jun;7(6):393-400. doi: 10.1038/nchembio.562. Epub 2011 May 1.

PMID:
21532598
16.

Tuning riboswitch regulation through conformational selection.

Wilson RC, Smith AM, Fuchs RT, Kleckner IR, Henkin TM, Foster MP.

J Mol Biol. 2011 Jan 28;405(4):926-38. doi: 10.1016/j.jmb.2010.10.056. Epub 2010 Nov 12.

17.

Molecular insights into the ligand-controlled organization of the SAM-I riboswitch.

Heppell B, Blouin S, Dussault AM, Mulhbacher J, Ennifar E, Penedo JC, Lafontaine DA.

Nat Chem Biol. 2011 Jun;7(6):384-92. doi: 10.1038/nchembio.563. Epub 2011 May 1.

PMID:
21532599
18.

Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics.

Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE.

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3485-94. doi: 10.1073/pnas.1503955112. Epub 2015 Jun 23.

19.

The impact of a ligand binding on strand migration in the SAM-I riboswitch.

Huang W, Kim J, Jha S, Aboul-ela F.

PLoS Comput Biol. 2013;9(5):e1003069. doi: 10.1371/journal.pcbi.1003069. Epub 2013 May 16.

20.

SAM recognition and conformational switching mechanism in the Bacillus subtilis yitJ S box/SAM-I riboswitch.

Lu C, Ding F, Chowdhury A, Pradhan V, Tomsic J, Holmes WM, Henkin TM, Ke A.

J Mol Biol. 2010 Dec 17;404(5):803-18. doi: 10.1016/j.jmb.2010.09.059. Epub 2010 Oct 15.

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