Part:BBa_K4245200:Design

hsa-miR-1-3p RCA Padlock Probe

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

A padlock probe, which is often 30-150 nucleotides in length, is a single-stranded DNA sequence designed to recognize a specific target sequence. The “arms” of a padlock probe are the ends of the ssDNA that are complementary to a specific target sequence. The middle sequence (the sequence between the arms) can be specifically designed to perform a function once amplified. (Nilsson et al., 1994)
Lambert iGEM found three specific miRNAs — hsa-miR-1-3p (BBa_K4245006), hsa-mir-133a-3p (BBa_K4245009), and hsa-miR-208a-3p (BBa_K4245011)— to be upregulated in correlation to CAD (Kaur et al., 2020). However, hsa-miR-208a-3p was not experimented with. For miRNA 1, we designed two complementary arms, BBa_K4245100, the 3' arm for hsa-miR-1-3p and BBa_K4245107, the 5' arm for hsa-miR-1-3p. For the reporter, we decided on both (BBa_K4245130/BBa_K4245132) the FAM and BHQ1 labeled linear probes, and (BBa_K4245134/BBa_K4245135), the DNA fluorescent aptamer split lettuce, due to their frugality and similar wavelength to GFP.

References

Kaur, A., Mackin, S. T., Schlosser, K., Wong, F. L., Elharram, M., Delles, C., Stewart, D. J., Dayan, N., Landry, T., & Pilote, L. (2019). Systematic review of microrna biomarkers in acute coronary syndrome and stable coronary artery disease. Cardiovascular Research, 116(6), 1113–1124. https://doi.org/10.1093/cvr/cvz302 Nilsson, M., Malmgren, H., Samiotaki, M., Kwiatkowski, M., Chowdhary, B. P., & Landegren, U. (1994). Padlock probes: Circularizing oligonucleotides for localized DNA detection. Science, 265(5181), 2085–2088. https://doi.org/10.1126/science.7522346