Shape chemical probing

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August undefined, 2024

Webb26 juli 2024 · SHAPE chemical probes react with the 2′-hydroxyl of flexible nucleotides, but not conformationally restrained nucleotides such as those found in A-form helices . The … Webb3 maj 2024 · The SHAPE protocol works by applying a SHAPE chemical probe to a sample to facilitate the addition of bulky adducts to RNA bases that are not engaged in a binding arrangements with other...

SnapShot: RNA Structure Probing Technologies - Cell

WebbExperimental probing data can be used to improve the accuracy of RNA secondary structure prediction. The software package RNAstructure can take advantage of … Webb4 jan. 2024 · Nuc-SHAPE-Structure-Seq generates in vivo RNA structure landscape of Arabidopsis nuclear RNAs with high coverage and accuracy. To investigate the role of … bitc ni awards 2022

3D Structural Analysis of Long Noncoding RNA by Small Angle

Webb10 okt. 2014 · In SHAPE-Seq ( 6, 7 ), RNAs are modified with chemical probes, such as 1M7 ( 24 ), or any probe that covalently modifies the RNA in a structure-dependent fashion ( … WebbSHAPE probing allows for studying the flexibility of RNA backbone, based on the susceptibility of nucleotides to chemical modification. RNA-modifying agents, such as … Webb1 juli 2016 · The resulting structures are composed of two fundamental building blocks: paired regions (mostly A-form helices), and unpaired loops. Interaction partners such as proteins, small ligands or other RNAs recognize specific structural motifs and can trigger refolding, cleavage, and chemical modifications upon binding. bitcni awards 2023

Dr. Kevin Weeks: a MaP of RNA structural landscapes - MiSciWriters

Webb3 maj 2024 · SHAPE probing (Steps 1–13). SHAPE experiments are inherently ensemble measurements of RNA structure. It is critical that the SHAPE reagent be rapidly and … Webb14 juni 2024 · SHAPE + chemical probing: Somarowthu et al. 2015. MALAT1: H. sapiens: 8,415: SHAPE: Brown et al. 2014. ROX2: D. melanogaster: 573: SHAPE + PARS: Ilik et al. … bitc newsWebb26 jan. 2024 · Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing provides local RNA flexibility information at single-nucleotide … bitcni awards 2022

"Webb3 juni 2011 · In the SHAPE-seq approach used by Lucks et al. (10), three processing steps are used to detect modification sites: (i) reverse transcriptase-mediated primer extension, for which there is now an authoritative approach for extracting the probability of RNA modification (9); (ii) a single-stranded DNA ligation step; and (iii) PCR. " - Shape chemical probing

Shape chemical probing

Guidelines for SHAPE Reagent Choice and Detection Strategy for …

Webb1 juli 2016 · SHAPE-Seq combines chemical probing with next-generation sequencing. • SHAPE-Seq accesses high-resolution RNA structural information in vivo and in vitro. • … WebbChemical probing coupled to high-throughput sequencing offers a flexible approach to uncover many aspects of RNA structure relevant to its cellular function and interac-tions. …

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WebbChemical probing is an important tool for characterizing the complex folded structures of RNA molecules, many of which play key cellular roles. Electrophilic SHAPE reagents … Webb20 maj 2015 · The SHAPE structure probing approach [ 7, 8] interrogates virtually all nucleotides of any RNA target. The adaptation of RNA chemical probing approaches to readout by massively parallel sequencing allows for high-throughput analysis and is rapidly advancing toward transcriptome-scale assays [ 9, 10 ].

Webb26 mars 2024 · Where the previous approaches used ‘per nucleotide’ probing, RING-MaP used ‘correlative’ chemical probing. As an example of RING-MaP’s utility, Dr. Weeks … WebbSHAPE-Seq and the derivative technique SHAPE-MaP can be used to investigate RNA structure using short-read sequencing approaches; however, while useful, these …

Webb22 maj 2024 · Chemical probing is an important tool for characterizing the complex folded structures of RNA molecules, many of which play key cellular roles. Electrophilic SHAPE reagents create adducts at... Webb19 nov. 2024 · SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) reagents, dimethyl sulfate (DMS), or other chemical probes are used to selectively …

WebbQuShape. QuShape is a comprehensive, platform-independent, user-friendly, and complete software package that enables efficient, reliable, highly automated, and accurate …

Webb在shape数据的分析中，如何合理地将shape数据整合进结构预测算法是一个关键的问题。常用的工具，如RNAstructure，通常将SHAPE值转化成每个配对核苷酸各自的伪自由能 … darwin\u0027s expeditionWebb10 aug. 2024 · Finally, this study increased the accuracy and signal-to-noise ratio (SNR) of selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing … darwin\u0027s finches activityWebbWe have developed a model for the secondary structure of the 1058-nucleotide plus-strand RNA genome of the icosahedral satellite tobacco mosaic virus (STMV) using nucleotide-resolution SHAPE chemical probing of the viral RNA isolated from virions and within the virion, perturbation of interactions distant in the primary sequence, and atomic force … darwin\u0027s expedition took how many yearsWebb28 juli 2024 · The selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) method is a convenient and efficient RNA structure probing technology with single … darwin\u0027s finchesWebb28 juli 2024 · Abstract and Figures Selective 2′-hydroxyl acylation analyzed by primer extension (SHAPE) chemical probing serves as a convenient and efficient experiment … bitcni climate action pledgeWebb14 jan. 2016 · In SHAPE-seq 16, a pool of in vitro–transcribed RNAs are subjected to SHAPE chemical probing and deep sequencing. This approach has revealed structural … bitcni shops challengeWebbIn this work, a selective and sensitive non-enzymatic electrochemical glucose sensor was developed using cobalt oxide nanoflowers (NF). Herein, for the first time, shape-specific … darwin\u0027s finch beaks