Part:BBa_K3380101:Design
F30 Upstream RNA aptamer scaffold
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
Design Notes
We ordered the synthesized sequence. Originally ordered sequence: forward (5’ TCCCttgccatgtgtatgtggg 3’) and (5’AGTAcccacatacacatggcaa 3’) with TCCC and AGTA 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 Upstream F30 scaffold should be used with the Downstream F30 scaffold (BBa_K3380102), 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.