Team:Stanford/Notebook/mRNA sRNA

General Ideas

One Idea to measure [B] / [A] (assume [A] ≠ 0)

• input A induces expression of GFP mRNA

• input B induces expression of GFP sRNA (sRNA that targets the GFP mRNA transcript)

• so for a given [A],
  • if [B] = 0, we should see glowing bacteria
  • if 0 < [B] < [A], we should see some glow
  • if [B] > [A], we should see no glow

Another Idea to measure [B] / [A] (assume [A] ≠ 0)

• input A induces expression of GFP mRNA and YFP sRNA

• input B induces expression of YFP mRNA and GFP sRNA

• so for a given [A],
  • if [B] = 0, we should see GREEN glowing bacteria
  • if 0 < [B] < [A], we should see some glow that is more GREEN than YELLOW.
  • if [B] > [A], we should see some glow that is more YELLOW than GREEN.

References

• here's a good reference: [http://www.springerlink.com/content/x6p4lqn1608267r1/fulltext.pdf Engineering RNA-based circuits]. It discusses different methods of regulation by RNA:
  • via base-pairing (small RNA)
  • shape-based (riboswitches)
  • catalytic (ribozymes)

• engineered riboregulators (possible mechanism for us) [http://www.nature.com/nbt/journal/v22/n7/pdf/nbt986.pdf Engineered riboregulators enable post-transcriptional control of gene expression]
  • Note: apparently does not work well in practice

• engineering those aforementioned sRNA's:
  • vague article [http://www.nature.com/nmeth/journal/v4/n12/full/nmeth1207-986b.html Engineers meet small RNA]
  • some specifics [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1994261/pdf/pbio.0050229.pdf Quantitative Characteristics of Gene Regulation by Small RNA]