DNA

Part:BBa_K4438800

Designed by: Shreyas Samir Parkhie   Group: iGEM22_IISER-Tirupati_India   (2022-10-12)


Aptamer_MN4

Aptamer_MN4 is a single-stranded DNA aptamer having 36 nucleotides. Figure 1A) shows the secondary structure and minimum free energy.


Usage and Biology

This part binds to cocaine with KD being 7 ± 1 uM (calculated using Isothermal Titration Calorimetry). It has three stems that are arranged around a three-way junction. Mostly used as a proof-of-concept aptamer. It also binds to other alkaloids. Its affinity for quinine is 30 times more than that of cocaine, with KD being 0.23 ± 0.03 uM. Since the same aptamer binds to many ligands, this part is unsuitable for biosensing applications [1,2]. T--IISER-Tirupati India--mn4structure7.png

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]


References

[1].Reinstein, O., Yoo, M., Han, C., Palmo, T., Beckham, S. A., Wilce, M. C., & Johnson, P. E. (2013). Quinine binding by the cocaine-binding aptamer. Thermodynamic and hydrodynamic analysis of high-affinity binding of an off-target ligand. Biochemistry, 52(48), 8652-8662. [2].Neves, M. A., Reinstein, O., & Johnson, P. E. (2010). Defining a stem length-dependent binding mechanism for the cocaine-binding aptamer. A combined NMR and calorimetry study. Biochemistry, 49(39), 8478-8487.

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Parameters
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