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Engineering Structurally Interacting RNA (sxRNA).

Francis Doyle1, Sameer Lapsia2, Salvatore Spadaro2

  • 1Nanobioscience Constellation, College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, NY New York 12203, USA.

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|March 29, 2017
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Summary
This summary is machine-generated.

Structurally interacting RNA (sxRNA) are novel regulatory elements that form three-way junctions (3WJs) in trans. These sxRNAs can be designed to control gene expression by modulating microRNA binding and translation.

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Gene Regulation

Background:

  • RNA three-way junctions (3WJs) are common in functional RNAs.
  • Trans-acting 3WJs, formed between separate RNA molecules, can regulate RNA structure and function.
  • MicroRNAs (miRNAs) are key regulators of gene expression.

Purpose of the Study:

  • To introduce and characterize a new class of regulatory RNAs called structurally interacting RNA (sxRNA).
  • To demonstrate the rational design of sxRNAs based on cis-3WJ principles.
  • To show sxRNA's ability to modulate gene expression in response to specific miRNAs.

Main Methods:

  • Design of sxRNA
  • bait
  • sequences targeting specific miRNA
  • trigger
  • sequences.
  • Construction of chimeric RNAs incorporating sxRNA downstream of a coding sequence.
  • Assays to measure RNA-binding protein motif activity and translation levels.

Main Results:

  • sxRNAs can be rationally designed to form trans-3WJs with target miRNAs.
  • Designed sxRNAs create functional, regulatable RNA-binding protein motifs.
  • sxRNA can switch "ON" translation of downstream coding sequences in a miRNA-dependent manner.
  • Translation levels correlate with the amount of trigger miRNA present.

Conclusions:

  • Structurally interacting RNA (sxRNA) represents a novel class of RNA regulators.
  • sxRNAs offer a programmable platform for miRNA-mediated gene expression control.
  • This work expands the toolkit for synthetic biology and RNA-based therapeutics.