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03-310 Sigma-Aldrich

In Vivo SHAPE Reagent for Live Cell RNA Structure Analysis

In Vivo SHAPE Reagent contains 2-methylnicotinic acid imidazolide (NAI). This reagent has very low toxicity and permits the analysis of RNA structure in living cells using Selective 2’-Hydroxyl Acylation and Primer Extension (SHAPE).

  •  eCl@ss 32161000

  •  NACRES NA.32

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Properties

Quality Level   100
mfr. no.   Upstate®
concentration   2 M
application(s)   activity assay: suitable (reverse transcriptase)
shipped in   dry ice

Description

General description

Features & Advantages

  • Ready-to-use RNase-free solution
  • Low toxicity allows use with live cells
  • High cell-permeability for rapid modification of RNA
  • Reacts with all RNA nucleotides without bias for high resolution mapping


In Vivo SHAPE Reagent is used for the determination of RNA structure. This reagent contains a highly pure form of 2-methylnicotinic acid imidazolide (NAI). This compound forms 2’-O-adducts on single stranded regions of RNA that can be detected by Selective 2’-Hydroxyl Acylation and Primer Extension (SHAPE).

In contrast to other reagents used for the SHAPE method, the NAI–based In Vivo SHAPE Reagent is rapidly absorbed into cells and is formulated to have low levels of toxicity making it ideal for use with live cells. Unlike other reagents used for SHAPE analysis, In Vivo SHAPE Reagent reacts in an unbiased fashion with all four RNA nucleotides. This combination of low toxicity, rapid uptake and lack of nucleotide bias enables high resolution RNA structure analysis in a variety of living systems.

Folding into higher-order structures allows RNAs to function inside living cells and form dynamic complexes with effector proteins. Predicting these 3D structures is challenging and therefore a number of probing techniques have been developed to study RNA folding.

Compounds such as 2-methylnicotinic acid imidazolide (NAI) contained the In Vivo SHAPE Reagent result in the formation of 2-O-adducts. These adducts form rapidly on single stranded unpaired RNA and much more slowly on based paired (double stranded) RNA. Modified RNA can then be analyzed by primer extension. Modified nucleotides are not extended by RNA dependent DNA polymerases thus allowing sites of modification to be detected.

Components

2-methylnicotinic acid imidazolide (NAI) in DMSO

Quality

Purity of NAI compound is tested by HPLC.

Physical form

0.5 mL vial containing 2M NAI (>97% pure) in DMSO solution

2M NAI in DMSO

Storage and Stability

Store NAI at -20°C in a non-frost-free freezer protected from light. With proper storage (protect from light and avoid excessive freeze-thaw cycles) this product is stable for up to 6 months from the date of receipt.

Disclaimer

Unless otherwise stated in our catalog or other company documentation accompanying the product(s), our products are intended for research use only and are not to be used for any other purpose, which includes but is not limited to, unauthorized commercial uses, in vitro diagnostic uses, ex vivo or in vivo therapeutic uses or any type of consumption or application to humans or animals.

Safety & Documentation

Safety Information

Safety Information for this product is unavailable at this time.
Protocols & Articles
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Description

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913839 2-Methylnicotinic acid imidazolide

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