Difference between revisions of "Part:BBa K4245209:Design"

Latest revision as of 22:31, 11 October 2022

hsa-mir-451a 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 hsa-miR-451a, we designed two complementary arms, BBa_K4245106, the 3' arm for hsa-miR-451a and BBa_K4245113, the 5' arm for hsa-miR-451a. 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-451a 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

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 __NOTOC__
 <partinfo>BBa_K4245209 short</partinfo>
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 ===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)
 <br>
-Lambert iGEM found three specific miRNAs — hsa-miR-1-3p (BBa_K4245006), hsa-mir-133a-3p (BBa_K4245009), and hsa-miR-451a (BBa_K4245012))— to be upregulated in correlation to CAD (Kaur et al., 2020). For miRNA 1, we designed two complementary arms, BBa_K4245106, the 3' arm for hsa-miR-451a and BBa_K4245113, the 5' arm for hsa-miR-451a. 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.
+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).
+<br>
+<br>
+Lambert iGEM found three specific miRNAs — hsa-miR-1-3p (<partinfo>BBa_K4245006</partinfo>), hsa-mir-133a-3p (<partinfo>BBa_K4245009</partinfo>), and hsa-miR-208a-3p (<partinfo>BBa_K4245011</partinfo>) — to be upregulated in correlation to CAD (Kaur et al., 2020). For hsa-miR-451a, we designed two complementary arms, <partinfo>BBa_K4245106</partinfo>, the 3' arm for hsa-miR-451a and <partinfo>BBa_K4245113</partinfo>, the 5' arm for hsa-miR-451a. For the reporter, we decided on both <partinfo>BBa_K4245130</partinfo>/<partinfo>BBa_K4245132</partinfo> the FAM and BHQ1 labeled linear probes, and <partinfo>BBa_K4245134</partinfo>/<partinfo>BBa_K4245135</partinfo>, the DNA fluorescent aptamer split lettuce, due to their frugality and similar wavelength to GFP.
+<br>
 <br>
 ===Source===
+hsa-miR-451a 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
+<br>
 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