Difference between revisions of "Part:BBa K4245201:Design"
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===Design Notes=== | ===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. | + | 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. |
| − | Lambert iGEM found three specific miRNAs — hsa-miR-1-3p (BBa_K4245006), hsa-mir-133a-3p (BBa_K4245009), 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 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. | + | 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. |
Revision as of 17:31, 10 October 2022
hsa-miR-1-3p RCT Padlock Probe
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE 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.
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_K4245100, the 3' arm for hsa-miR-1-3p and BBa_K4245107, the 5' arm for hsa-miR-1-3p. 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.
Source
The sequence was ordered as DNA oligos from Integrated DNA Technologies.