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Results: 1 to 20 of 89

Similar articles for PubMed (Select 23178934)

1.

RNA SHAPE analysis in living cells.

Spitale RC, Crisalli P, Flynn RA, Torre EA, Kool ET, Chang HY.

Nat Chem Biol. 2013 Jan;9(1):18-20. doi: 10.1038/nchembio.1131. Epub 2012 Nov 25.

2.

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11063-8. doi: 10.1073/pnas.1106501108. Epub 2011 Jun 3.

3.

RNA structure analysis at single nucleotide resolution by selective 2'-hydroxyl acylation and primer extension (SHAPE).

Merino EJ, Wilkinson KA, Coughlan JL, Weeks KM.

J Am Chem Soc. 2005 Mar 30;127(12):4223-31.

PMID:
15783204
5.

Selective 2'-hydroxyl acylation analyzed by protection from exoribonuclease.

Steen KA, Malhotra A, Weeks KM.

J Am Chem Soc. 2010 Jul 28;132(29):9940-3. doi: 10.1021/ja103781u.

6.

Exploring RNA structural codes with SHAPE chemistry.

Weeks KM, Mauger DM.

Acc Chem Res. 2011 Dec 20;44(12):1280-91. doi: 10.1021/ar200051h. Epub 2011 May 26.

7.
8.

Modeling and automation of sequencing-based characterization of RNA structure.

Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11069-74. doi: 10.1073/pnas.1106541108. Epub 2011 Jun 3.

9.

Analysis of the RNA backbone: structural analysis of riboswitches by in-line probing and selective 2'-hydroxyl acylation and primer extension.

Wakeman CA, Winkler WC.

Methods Mol Biol. 2009;540:173-91. doi: 10.1007/978-1-59745-558-9_13.

PMID:
19381560
10.
11.

RNA secondary structure prediction using high-throughput SHAPE.

Lusvarghi S, Sztuba-Solinska J, Purzycka KJ, Rausch JW, Le Grice SF.

J Vis Exp. 2013 May 31;(75):e50243. doi: 10.3791/50243.

PMID:
23748604
12.

Correlating SHAPE signatures with three-dimensional RNA structures.

Bindewald E, Wendeler M, Legiewicz M, Bona MK, Wang Y, Pritt MJ, Le Grice SF, Shapiro BA.

RNA. 2011 Sep;17(9):1688-96. doi: 10.1261/rna.2640111. Epub 2011 Jul 13.

13.

Use of SHAPE to select 2AP substitution sites for RNA-ligand interactions and dynamics studies.

Soulière MF, Micura R.

Methods Mol Biol. 2014;1103:227-39. doi: 10.1007/978-1-62703-730-3_17.

PMID:
24318898
14.

Local RNA structural changes induced by crystallization are revealed by SHAPE.

Vicens Q, Gooding AR, Laederach A, Cech TR.

RNA. 2007 Apr;13(4):536-48. Epub 2007 Feb 13.

15.

Strong correlation between SHAPE chemistry and the generalized NMR order parameter (S2) in RNA.

Gherghe CM, Shajani Z, Wilkinson KA, Varani G, Weeks KM.

J Am Chem Soc. 2008 Sep 17;130(37):12244-5. doi: 10.1021/ja804541s. Epub 2008 Aug 19.

16.

Time-resolved RNA SHAPE chemistry.

Mortimer SA, Weeks KM.

J Am Chem Soc. 2008 Dec 3;130(48):16178-80. doi: 10.1021/ja8061216.

PMID:
18998638
17.

Time-resolved RNA SHAPE chemistry: quantitative RNA structure analysis in one-second snapshots and at single-nucleotide resolution.

Mortimer SA, Weeks KM.

Nat Protoc. 2009;4(10):1413-21. doi: 10.1038/nprot.2009.126. Epub 2009 Sep 10.

PMID:
19745823
18.

Integrating chemical footprinting data into RNA secondary structure prediction.

Zarringhalam K, Meyer MM, Dotu I, Chuang JH, Clote P.

PLoS One. 2012;7(10):e45160. doi: 10.1371/journal.pone.0045160. Epub 2012 Oct 16.

19.

The mechanisms of RNA SHAPE chemistry.

McGinnis JL, Dunkle JA, Cate JH, Weeks KM.

J Am Chem Soc. 2012 Apr 18;134(15):6617-24. doi: 10.1021/ja2104075. Epub 2012 Apr 5. Erratum in: J Am Chem Soc. 2012 Jul 25;134(29):12319.

20.

Principles for understanding the accuracy of SHAPE-directed RNA structure modeling.

Leonard CW, Hajdin CE, Karabiber F, Mathews DH, Favorov OV, Dokholyan NV, Weeks KM.

Biochemistry. 2013 Jan 29;52(4):588-95. doi: 10.1021/bi300755u. Epub 2013 Jan 14.

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