SHAPE

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Revision as of 19:32, 2 September 2013 by Omei (talk | contribs)

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 ==

Experimental methods exists for determining, at the level of individual atoms, the various inter-atomic bindings that determine how an RNA molecule folds.  However, this type of experiment cam take months to perform, for a single RNA sequence.  The EteRNA cloud lab process is now synthesizing more than 1000 novel RNA molecules per month, and as players/scientists, we expect the results for all 1000 sequences to be available in weeks, if not days.  To meet this need, the EteRNA biochemistry team is pioneering the development of high-throughput RNA analysis, and well as high-throughput RNA synthesis.

== 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 ==

SHAPE reaction.png

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 ==