Difference between revisions of "Part:BBa K4245205:Design"

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===Design Notes===
 
===Design Notes===
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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.  
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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)
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<br>
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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 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. For the reporter, we decided on <partinfo>BBa_K3380153</partinfo>, the Broccoli fluorescent RNA aptamer, for its short length and function similar to GFP. In order to stabilize the folding of the Broccoli fluorescent RNA aptamer, we added <partinfo>BBa_K4245160</partinfo>, the padlock spacer sequence.
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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 miRNA 1, we designed two complementary arms, <partinfo>BBa_K4245103</partinfo>, the 3' arm for hsa-mir-133a-3p and <partinfo>BBa_K4245110</partinfo>, the 5' arm for hsa-mir-133a-3p. For the reporter, we decided on <partinfo>BBa_K3380153</partinfo>, the Broccoli fluorescent RNA aptamer, for its short length and function similar to GFP. In order to stabilize the folding of the Broccoli fluorescent RNA aptamer, we added <partinfo>BBa_K4245160</partinfo>, the padlock spacer sequence.
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<b>References</b>
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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
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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
  
 
===Source===
 
===Source===

Revision as of 19:36, 10 October 2022


hsa-mir-133a-3p RCT 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 1, 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 BBa_K3380153, the Broccoli fluorescent RNA aptamer, for its short length and function similar to GFP. In order to stabilize the folding of the Broccoli fluorescent RNA aptamer, we added BBa_K4245160, the padlock spacer sequence.
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

Source

hsa-mir-133a-3p RCT Padlock Probe

References