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Items: 1 to 20 of 131

1.

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.

3.

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.

4.

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.

5.

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.

6.

The role of nucleobase interactions in RNA structure and dynamics.

Bottaro S, Di Palma F, Bussi G.

Nucleic Acids Res. 2014 Dec 1;42(21):13306-14. doi: 10.1093/nar/gku972. Epub 2014 Oct 29.

7.

DNA base dimers are stabilized by hydrogen-bonding interactions including non-Watson-Crick pairing near graphite surfaces.

Shankar A, Jagota A, Mittal J.

J Phys Chem B. 2012 Oct 11;116(40):12088-94. doi: 10.1021/jp304260t. Epub 2012 Sep 26.

PMID:
22967176
8.
10.

Analysis of RNA motifs.

Leontis NB, Westhof E.

Curr Opin Struct Biol. 2003 Jun;13(3):300-8. Review.

PMID:
12831880
11.

Sequence dependent variations in RNA duplex are related to non-canonical hydrogen bond interactions in dinucleotide steps.

Kailasam S, Bhattacharyya D, Bansal M.

BMC Res Notes. 2014 Feb 7;7:83. doi: 10.1186/1756-0500-7-83.

12.

Non-Watson-Crick base pairing in RNA. quantum chemical analysis of the cis Watson-Crick/sugar edge base pair family.

Sponer JE, Spackov√° N, Kulhanek P, Leszczynski J, Sponer J.

J Phys Chem A. 2005 Mar 17;109(10):2292-301.

PMID:
16838999
13.

RNA structure and dynamics: a base pairing perspective.

Halder S, Bhattacharyya D.

Prog Biophys Mol Biol. 2013 Nov;113(2):264-83. doi: 10.1016/j.pbiomolbio.2013.07.003. Epub 2013 Jul 23. Review.

PMID:
23891726
14.

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.

15.

Quantum chemical studies of structures and binding in noncanonical RNA base pairs: the trans Watson-Crick:Watson-Crick family.

Sharma P, Mitra A, Sharma S, Singh H, Bhattacharyya D.

J Biomol Struct Dyn. 2008 Jun;25(6):709-32.

PMID:
18399704
16.

Analysis of four-way junctions in RNA structures.

Laing C, Schlick T.

J Mol Biol. 2009 Jul 17;390(3):547-59. doi: 10.1016/j.jmb.2009.04.084. Epub 2009 May 13.

17.

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
18.

RNA structure at high resolution.

Shen LX, Cai Z, Tinoco I Jr.

FASEB J. 1995 Aug;9(11):1023-33. Review.

PMID:
7544309
19.

Principles of RNA base pairing: structures and energies of the trans Watson-Crick/sugar edge base pairs.

Sponer JE, Spackova N, Leszczynski J, Sponer J.

J Phys Chem B. 2005 Jun 9;109(22):11399-410.

PMID:
16852393
20.

Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA: analysis of the stem nucleotides.

Morosyuk SV, Lee K, SantaLucia J Jr, Cunningham PR.

J Mol Biol. 2000 Jun 30;300(1):113-26.

PMID:
10864503

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