Riboregulator

In molecular biology, a riboregulator is a ribonucleic acid (RNA) that responds to a signal nucleic acid molecule by Watson-Crick base pairing. A riboregulator may respond to a signal molecule in any number of manners including, translation (or repression of translation) of the RNA into a protein, activation of a ribozyme, release of silencing RNA (siRNA), conformational change, and/or binding other nucleic acids. Riboregulators contain two canonical domains, a sensor domain and an effector domain. These domains are also found on riboswitches, but unlike riboswitches, the sensor domain only binds complementary RNA or DNA strands as opposed to small molecules. Because binding is based on base-pairing, a riboregulator can be tailored to differentiate and respond to individual genetic sequences and combinations thereof.

Translational riboregulators regulate the ability of a ribosome complex to scan, assemble, and/or translate an RNA molecule into a protein. In translational riboregulators, the RNA molecule is repressed or de-repressed depending on the secondary structure of the RNA molecule. Signal-responsive structures are usually introduced into the 5' untranslated region (5' UTR) of the RNA molecules using standard molecular biological techniques.

As discovered by Marilyn Kozak, the small (40S) ribosome complex scans an RNA molecule from 5' untranslated region to the start codon. When the complex encounters secondary structure, it must melt the structure to reach the start codon or it will fall off the molecule. The complex moves along through the untranslated region until it stalls just prior to reaching the start codon because it encounters a highly conserved sequence (a Kozak consensus sequence in eukaryotes, or Shine-Dalgarno sequence in prokaryotes). The stalled complex then combines with the large ribosome (60S) to begin translating the RNA into protein.

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