IGEM:Stanford/2010/Notebook/mRNA sRNA: Difference between revisions

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General Idea:
==General Ideas==
input A induces expression of GFP mRNA
'''One Idea to measure [B] / [A]''' (assume [A] ≠ 0)
input B induces expression of sRNA that targets the GFP mRNA transcript


so for a given concentration of A,
*input A induces expression of GFP mRNA
if no B, we should see glowing bacteria
if [B] > [A], we should see no glow
if [B] is some fraction of [A], we should see some glow.


*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:
*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)
**via base-pairing (small RNA)
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**catalytic (ribozymes)
**catalytic (ribozymes)


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

Latest revision as of 19:53, 20 June 2010

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: Engineering RNA-based circuits. It discusses different methods of regulation by RNA:
    • via base-pairing (small RNA)
    • shape-based (riboswitches)
    • catalytic (ribozymes)
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