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 ==
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 ==
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.