SHAPE-Seq provides structural information about RNA. In this method, a unique barcode is first added to the 3' end of RNA, and the RNA is allowed to fold under pre-established in vitro conditions.

Oct 10, 2014 · As part of this optimization, we present SHAPE-Seq v2.0, a ‘universal’ method that can obtain reactivity information for every nucleotide of an RNA without having to use or introduce a specific reverse transcriptase priming site within the RNA.

Dec 1, 2012 · This article contains a protocol for selective 2'-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq) that, through a combination of structure-dependent chemical probing and next-generation sequencing technologies, achieves structural characterization of hundreds of RNAs in a single experiment.

Jun 3, 2011 · We demonstrate the ability of SHAPE-Seq to accurately infer secondary and tertiary structural information, detect subtle conformational changes due to single nucleotide point mutations, and simultaneously measure the structures of a complex pool of …

Selective 2 -hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) is a technique that combines advances in structure-dependent chemical probing of RNAs (Weeks and Mauger, 2011) with the throughput of next-generation sequencing (NGS)

Dec 1, 2012 · This article contains a protocol for selective 2′-hydroxyl acylation analyzed by primer extension and sequencing (SHAPE-Seq) that, through a combination of structure-dependent chemical probing and next-generation sequencing technologies, achieves structural characterization of hundreds of RNAs in a single experiment.

SHAPE-Seq provides structural information about RNA (Lucks et al., 2011) (Watters et al., 2016). In this method, a unique barcode is first added to the 3′ end of RNA, and the RNA is allowed to fold under pre-established in vitro conditions.

Apr 12, 2016 · We outline the process of designing and performing a SHAPE-Seq experiment and describe methods for using experimental SHAPE-Seq data to restrain computational folding algorithms to generate more accurate predictions of RNA secondary structure.

Collectively, these new sequencing-based SHAPE technologies have opened the door for scientists to make single-nucleotide resolution measurements of RNA structure across entire transcriptomes and full-length RNA molecules (Siegfried …

Dec 1, 2014 · As part of this optimization, we present SHAPE-Seq v2.0, a ‘universal’ method that can obtain reactivity information for every nucleotide of an RNA without having to use or introduce a specific reverse transcriptase priming site within the RNA.