Difference between revisions of "Part:BBa K4683002:Design"
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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) | 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) | ||
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| − | Lambert iGEM found hsa-miR-1-3p (<partinfo>BBa_K4245006</partinfo>) to be upregulated in correlation to CAD (Kaur et al., 2020). For miRNA 1, we designed two complementary arms, <partinfo>BBa_K4245100</partinfo>, the 3' arm for hsa-miR-1-3p and <partinfo>BBa_K4245107</partinfo>, the 5' arm for hsa-miR-1-3p, with Nb.BbvCI nicking sites <partinfo> | + | Lambert iGEM found hsa-miR-1-3p (<partinfo>BBa_K4245006</partinfo>) to be upregulated in correlation to CAD (Kaur et al., 2020). For miRNA 1, we designed two complementary arms, <partinfo>BBa_K4245100</partinfo>, the 3' arm for hsa-miR-1-3p and <partinfo>BBa_K4245107</partinfo>, the 5' arm for hsa-miR-1-3p, with Nb.BbvCI nicking sites <partinfo>BBa_M31961</partinfo> before the 3' arm and after the 5' arm. For the reporter, we decided on the complement of the Lettuce Aptamer <partinfo>BBa_K4683000</partinfo> so that during the amplification process, Lettuce Aptamers would be produced (see fig). |
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[[File:group-11.png|thumb|center|500px|<i>Figure. eRCA padlock design</i>]] | [[File:group-11.png|thumb|center|500px|<i>Figure. eRCA padlock design</i>]] | ||
Revision as of 02:31, 11 October 2023
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 hsa-miR-1-3p (BBa_K4245006) to be upregulated in correlation to CAD (Kaur et al., 2020). 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, with Nb.BbvCI nicking sites BBa_M31961 before the 3' arm and after the 5' arm. For the reporter, we decided on the complement of the Lettuce Aptamer BBa_K4683000 so that during the amplification process, Lettuce Aptamers would be produced (see fig).
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