Difference between revisions of "Part:BBa K3017003"

 
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<partinfo>BBa_K3017003 short</partinfo>
 
<partinfo>BBa_K3017003 short</partinfo>
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[[File:T--Hong Kong HKUST--as_GFP_white.jpeg|thumb|Secondary structure of the transcription product of this part, predicted by NUPACK]]
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<p>asRNA is the key to the reversibility of the CRISPRi switch. The asRNA binds to the artificial linker loop of the sgRNA, and extend the loop to become a linear structure. It is proven that this linearization of the loop causes derepression.</p>
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<p>The synthetic asRNA is composed of 2 functional domains, extensor, for linearizing the loop, and Spot 42, aiding the stability of the asRNA.</p>
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<h2>Extensor</h2>
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[[File:T--Hong Kong HKUST--as_GFP_white.jpeg|thumb|Secondary structure of the transcription product of this part, predicted by NUPACK]]
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<p>The extensor sequence is complementary to the artificial linker loop. By forming a duplex, the loop is extended. It was thought in the study that an asRNA complementary to the spacer would displace the DNA target and yield a higher depression effect. But after optimization, the study found out that changing the sgRNA’s secondary structure by extending a loop formed by the artificial linker would maximize the derepression effect to at least 95%, compared to only 15-55% of complementing the spacer.</p>
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<p>The derepression is specific to the <i>gfp</i> gene BBa_E0040. Therefore asRNA extensor in the transcription product of this part targets sgRNA artificial linker of transcription product of part K3017001.</p>
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<h2>Spot 42</h2>
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[[File:T--Hong Kong HKUST--assgDNA_GFP_white.jpeg|thumb|Complex formation between asRNA, sgRNA and target DNA is depicted]]
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<p>Bacterial Hfq protein is known to modulate the stability or the translation of mRNAs and interact with small regulatory RNAs. A study provides evidence that Hfq strongly cooperates in intermolecular base pairing between the asRNA and its target RNA. Spot 42 is an RNA antisense regulator that has several A/U-rich regions that provide specificity to Hfq protein. Hfq protein also provide protection to the asRNA at these A/U-rich regions.</p>
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<p>Same Spot 42 sequence is present in every asRNA we have designed as it is highly specific to Hfq protein and the duplex is necessary for the asRNA to work. Hfq is endogenous to <i>E.coli</i>, therefore the protein is not encoded in any part of the circuit.</p>
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Revision as of 06:06, 17 October 2019


CRISPRi antisense RNA for derepressing gfp - transcription template

Secondary structure of the transcription product of this part, predicted by NUPACK

asRNA is the key to the reversibility of the CRISPRi switch. The asRNA binds to the artificial linker loop of the sgRNA, and extend the loop to become a linear structure. It is proven that this linearization of the loop causes derepression.

The synthetic asRNA is composed of 2 functional domains, extensor, for linearizing the loop, and Spot 42, aiding the stability of the asRNA.

Extensor

Secondary structure of the transcription product of this part, predicted by NUPACK

The extensor sequence is complementary to the artificial linker loop. By forming a duplex, the loop is extended. It was thought in the study that an asRNA complementary to the spacer would displace the DNA target and yield a higher depression effect. But after optimization, the study found out that changing the sgRNA’s secondary structure by extending a loop formed by the artificial linker would maximize the derepression effect to at least 95%, compared to only 15-55% of complementing the spacer.

The derepression is specific to the gfp gene BBa_E0040. Therefore asRNA extensor in the transcription product of this part targets sgRNA artificial linker of transcription product of part K3017001.

Spot 42

Complex formation between asRNA, sgRNA and target DNA is depicted

Bacterial Hfq protein is known to modulate the stability or the translation of mRNAs and interact with small regulatory RNAs. A study provides evidence that Hfq strongly cooperates in intermolecular base pairing between the asRNA and its target RNA. Spot 42 is an RNA antisense regulator that has several A/U-rich regions that provide specificity to Hfq protein. Hfq protein also provide protection to the asRNA at these A/U-rich regions.

Same Spot 42 sequence is present in every asRNA we have designed as it is highly specific to Hfq protein and the duplex is necessary for the asRNA to work. Hfq is endogenous to E.coli, therefore the protein is not encoded in any part of the circuit.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]