DNA

Part:BBa_K4438811

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


MN4_trigger_6_midtrigger_phi29

MN4_trigger_6_midtrigger_phi29(BBa_K4438811) is single-stranded DNA having 10 nucleotides. Figure 1B) shows the secondary structure and minimum free energy. The sequence is complementary to the middle region of the Aptamer_MN4 (BBa_K4438800) with no mismatched bases.


Usage and Biology

The part MN4_trigger_6_midtrigger_phi29(BBa_K4438811) has complementarity to the part Aptamer_MN4 (BBa_K4438800) and disrupts its three-way junction. Figure 1D) Shows the secondary structure of both parts hybridised at 37° Celsius. Quinine binds with cocaine-binding aptamer MN4 [1] and displaces the MN4_trigger_6_midtrigger_phi29(BBa_K4438811) . This part has complete complementarity with MN4_Target_6(BBa_K4438812). Phi 29 DNA extension polymerase extends the template strand and in-vitro transcription of the duplex forms multiple broccoli light-up aptamers. Different levels of quinine can be detected using all these three parts.

T--IISER-Tirupati India--mn4structure6.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

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.

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