SHAPE

The SHAPE acronym stands for "Selective 2′ hydroxyl acylation analyzed by primer extension". It is the primary method used to evaluate designs in EteRNA lab experiments.

== Overview ==

== Background: The high-level structure of RNA ==

== Background: Laboratory procedures ==

=== PCR ===

=== Transcription (DNA to RNA) ===

=== Reverse transcription (RNA to DNA ) ===

== A more detailed explanation of the SHAPE process ==

== To be incorprated ==

This chemical probing strategy assesses local flexibility in RNA via accessibility of the ribose 2′-OH group to acylation by the electrophilic reagent NMIA or 1M7. In flexible regions (such as loops, bulges, and junctions), RNA adopts conformations that will promote formation of a nucleophilic 2′-oxyanion which reacts with NMIA or 1M7 to form a bulky 2′-O-adduct. Modified RNAs are subsequently evaluated by primer extension with an RNase H-deficient reverse transcriptase, creating a cDNA library corresponding to stops at sites of adduct formation in the RNA.

 

 

== External links ==

• http://www.chem.unc.edu/rna/pdf-files/2005_em_jacs.pdf the original 2005 scientific paper
• The figure 1 of 'Probing Retroviral and Retrotransposon Genome Structures: The "SHAPE" of Things to Come.' presents a good overview of this method.