Nov 25, 2012 · Here we design, synthesize and demonstrate two new chemical probes that enable selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) in living cells. …

Recent efforts have been focused on developing reagents that modify RNA as a function of RNA 2' hydroxyl group reactivity. Such RNA structure probing techniques can be read out by primer …

Mar 31, 2022 · We here introduce SHAPEwarp, a largely sequence-agnostic SHAPE-guided algorithm for the identification of structurally-similar regions in RNA molecules. Analysis of …

RNA structure plays important roles in practically every facet of gene regulation, but the paucity of structural probes that function in vivo has limited current understanding. Here we design, …

The simple SHAPE reaction is thus a robust, nucleotide-resolution, biophysical measurement of RNA structure. SHAPE can be used to provide an experimental correction to RNA folding …

RNA SHAPE chemistry exploits the discovery that conformationally dynamic nucleotides preferentially adopt conformations that facilitate reaction between the 2′-OH group and a …

May 5, 2018 · The selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) method probes RNA local structural and dynamic information at single nucleotide resolution.

Feb 5, 2025 · Unlike the static double helix of DNA, RNA can fold into complex three-dimensional shapes, each with distinct functional implications. These conformations are integral to RNA’s …

Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemistry is a powerful approach for measuring nucleotide structure and dynamics in diverse biological environments.

Jan 6, 2009 · Here, we demonstrate that quantitative, nucleotide-resolution information from a SHAPE experiment can be interpreted as a pseudo-free energy change term and used to …