Part:BBa_K3380151
DIR2s-Apt fluorescent RNA aptamer
DIR2s-Apt is a fluorescent RNA aptamer comprising a short ribonucleotide sequence that exhibits fluorescence upon binding to a specific fluorophore.
Characterization
The DIR2s-Apt fluorescent RNA aptamer was described by Tan et al. (2017). Figure 1 shows the DIR2s-Apt folding prediction as simulated by [http://www.nupack.org// NUPACK].
| DIR2s-Apt Characteristics | |||
|---|---|---|---|
| Fluorophore | DIR-PRO | OTB-SO3 | |
| Fluorescence colour | Red | Blue | |
| Excitation wavelength (nm) | 600 | 380 | |
| Emission wavelength (nm) | 658 | 421 | |
| Quantum Yield | 0.33 | 0.51 | |
| Extinction coefficient (M^-1 cm^-1) | 164000 | 73000 | |
| Source | [1] | ||
Figure 1: DIR2s-Apt secondary structure prediction. The adenine (A), cytosine (C), guanine (G) and uracil (U) nucleobases are shown in green, blue, black and red respectively.
Usage and Biology
It is usually used in live-cell imaging, however it can also be used in vitro. DIR2-Apt can be used for visualisation by gene fusion to the target of interest. Its fluorescent colour depends on the fluorophore it binds to. It can bind to DIR ( dimethylindole red) derivatives to give a red colour and OTB (oxazole thiazole blue) derivatives to give a blue colour. The emission spectra also depends on the bound fluorophore.
DIR2s-Apt promiscuity for multiple derivatives of fluorophores (DIR and OTB) allows its colour change just by addition of different fluorophores. Its short length also allows it to be synthesized rather than being cloned using a plasmid.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
| None |