Composite

Part:BBa_K4245204:Design

Designed by: Akshaya Poonepalle, Shivaek Venkateswaran, Varnica Basavaraj, Manaswi Gorle, Sahana Ram Narayanan, Janet Standeven   Group: iGEM22_Lambert_GA   (2022-10-09)
Revision as of 21:40, 11 October 2022 by RichardJiang (Talk | contribs)


hsa-mir-133a-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). For miRNA 133a-3p, we designed two complementary arms, BBa_K4245103, the 3' arm for hsa-miR-133a-3p and BBa_K4245110, the 5' arm for hsa-miR-133a-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.

Source

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