Difference between revisions of "Part:BBa K3380102:Design"

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===Design Notes===
 
===Design Notes===
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The F30 downstream RNA aptamer scaffold needs to be placed after the RNA aptamer sequence followed by the 4bp overhang. It should be used in conjunction with the F30 Upstream RNA aptamer scaffold (BBa_K3380101) for proper functioning.
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We ordered the synthesized sequence. Originally ordered sequence: forward (5’ AATGcccacatactctgatgatccttcgggatcattcatggcaa 3’) and (5’ AAGCttgccatgaatgatcccgaaggatcatcagagtatgtggg 3’) with AATG and AAGC respectively being a linker, to facilitate further manipulations (swapping of the part or attaching to different promoters).
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The forward and reverse sequences were phosphorylated, annealed and ligated to other parts using T4 DNA ligase.
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The Downstream F30 scaffold should be used with the Upstream F30 scaffold (BBa_K3380101), both flanking a fluorescent RNA aptamer.
  
 
===Source===
 
===Source===
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===References===
 
===References===
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Filonov, G.S., Kam, C.W., Song, W. and Jaffrey, S.R., 2015. In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. Chemistry & biology, 22(5), pp.649-660.
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Shu, D., Khisamutdinov, E.F., Zhang, L. and Guo, P., 2014. Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor. Nucleic acids research, 42(2), pp.e10-e10.

Latest revision as of 09:02, 10 October 2020


F30 Downstream RNA aptamer scaffold


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]


Design Notes

We ordered the synthesized sequence. Originally ordered sequence: forward (5’ AATGcccacatactctgatgatccttcgggatcattcatggcaa 3’) and (5’ AAGCttgccatgaatgatcccgaaggatcatcagagtatgtggg 3’) with AATG and AAGC respectively being a linker, to facilitate further manipulations (swapping of the part or attaching to different promoters).

The forward and reverse sequences were phosphorylated, annealed and ligated to other parts using T4 DNA ligase.

The Downstream F30 scaffold should be used with the Upstream F30 scaffold (BBa_K3380101), both flanking a fluorescent RNA aptamer.

Source

The F30 scaffold was engineered by Filonov et al. in 2015. It is based on the Φ29 RNA three-way junction motif studied by Shu et al. in 2014.

References

Filonov, G.S., Kam, C.W., Song, W. and Jaffrey, S.R., 2015. In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. Chemistry & biology, 22(5), pp.649-660.

Shu, D., Khisamutdinov, E.F., Zhang, L. and Guo, P., 2014. Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor. Nucleic acids research, 42(2), pp.e10-e10.