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Items: 1 to 20 of 110

1.

Differences between cotranscriptional and free riboswitch folding.

Lutz B, Faber M, Verma A, Klumpp S, Schug A.

Nucleic Acids Res. 2014 Feb;42(4):2687-96. doi: 10.1093/nar/gkt1213. Epub 2013 Nov 25.

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.

Using simulations and kinetic network models to reveal the dynamics and functions of riboswitches.

Lin JC, Yoon J, Hyeon C, Thirumalai D.

Methods Enzymol. 2015;553:235-58. doi: 10.1016/bs.mie.2014.10.062. Epub 2015 Feb 3.

PMID:
25726468
4.

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.

5.

Direct observation of cotranscriptional folding in an adenine riboswitch.

Frieda KL, Block SM.

Science. 2012 Oct 19;338(6105):397-400. doi: 10.1126/science.1225722.

6.

The regulation mechanism of yitJ and metF riboswitches.

Gong S, Wang Y, Zhang W.

J Chem Phys. 2015 Jul 28;143(4):045103. doi: 10.1063/1.4927390.

PMID:
26233166
7.

Cotranscriptional folding of a riboswitch at nucleotide resolution.

Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB.

Nat Struct Mol Biol. 2016 Dec;23(12):1124-1131. doi: 10.1038/nsmb.3316. Epub 2016 Oct 31.

8.

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
9.

Approach to the unfolding and folding dynamics of add A-riboswitch upon adenine dissociation using a coarse-grained elastic network model.

Li C, Lv D, Zhang L, Yang F, Wang C, Su J, Zhang Y.

J Chem Phys. 2016 Jul 7;145(1):014104. doi: 10.1063/1.4954992.

10.

A Highly Coupled Network of Tertiary Interactions in the SAM-I Riboswitch and Their Role in Regulatory Tuning.

Wostenberg C, Ceres P, Polaski JT, Batey RT.

J Mol Biol. 2015 Nov 6;427(22):3473-90. doi: 10.1016/j.jmb.2015.07.027. Epub 2015 Sep 3.

11.

Thermodynamic and kinetic folding of riboswitches.

Badelt S, Hammer S, Flamm C, Hofacker IL.

Methods Enzymol. 2015;553:193-213. doi: 10.1016/bs.mie.2014.10.060. Epub 2015 Feb 12.

PMID:
25726466
12.

Sequence-dependent folding landscapes of adenine riboswitch aptamers.

Lin JC, Hyeon C, Thirumalai D.

Phys Chem Chem Phys. 2014 Apr 14;16(14):6376-82. doi: 10.1039/c3cp53932f. Epub 2013 Dec 23.

PMID:
24366448
13.

Computational study of unfolding and regulation mechanism of preQ1 riboswitches.

Gong Z, Zhao Y, Chen C, Xiao Y.

PLoS One. 2012;7(9):e45239. doi: 10.1371/journal.pone.0045239. Epub 2012 Sep 17.

14.

Relative stability of helices determines the folding landscape of adenine riboswitch aptamers.

Lin JC, Thirumalai D.

J Am Chem Soc. 2008 Oct 29;130(43):14080-1. doi: 10.1021/ja8063638. Epub 2008 Oct 2.

PMID:
18828635
15.

Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine.

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

J Mol Biol. 2012 May 18;418(5):331-49. doi: 10.1016/j.jmb.2012.02.019. Epub 2012 Mar 13. Erratum in: J Mol Biol. 2012 Jul 13;420(3):258.

16.

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
17.

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.

18.

Using reweighted pulling simulations to characterize conformational changes in riboswitches.

Di Palma F, Colizzi F, Bussi G.

Methods Enzymol. 2015;553:139-62. doi: 10.1016/bs.mie.2014.10.055. Epub 2015 Feb 3.

PMID:
25726464
19.

Transcriptional pausing coordinates folding of the aptamer domain and the expression platform of a riboswitch.

Perdrizet GA 2nd, Artsimovitch I, Furman R, Sosnick TR, Pan T.

Proc Natl Acad Sci U S A. 2012 Feb 28;109(9):3323-8. doi: 10.1073/pnas.1113086109. Epub 2012 Feb 13.

20.

Kinetics of allosteric transitions in S-adenosylmethionine riboswitch are accurately predicted from the folding landscape.

Lin JC, Thirumalai D.

J Am Chem Soc. 2013 Nov 6;135(44):16641-50. doi: 10.1021/ja408595e. Epub 2013 Oct 22.

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