Composite

Part:BBa_K4245207: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 22:14, 11 October 2022 by RichardJiang (Talk | contribs)

hsa-miR-208a-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 208a-3p, we designed two complementary arms, BBa_K4245105, the 3' arm for hsa-miR-208a-3p and BBa_K4245112, the 5' arm for hsa-miR-208a-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

hsa-miR-208a-3p RCA Padlock Probe

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