Difference between revisions of "Part:BBa K2908555"
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This part is designed by miRNASong(an online software) and synthesized by company.It is used to down-regulate the level of miR141 in heterogenous TNBC cells. | This part is designed by miRNASong(an online software) and synthesized by company.It is used to down-regulate the level of miR141 in heterogenous TNBC cells. | ||
| + | https://2019.igem.org/wiki/images/c/cf/T--CSU_CHINA--2908555.jpg | ||
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===Usage and Biology=== | ===Usage and Biology=== | ||
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- Firstly, obtain the basic sequence information of miRNA from miRBASE, analyze which miRNA subtype is specifically described according to the literature table provided, obtain the sequence and identify the seed sequence.<br/> | - Firstly, obtain the basic sequence information of miRNA from miRBASE, analyze which miRNA subtype is specifically described according to the literature table provided, obtain the sequence and identify the seed sequence.<br/> | ||
- The miRNAsong website was used to design the basic sponge framework, the free energy cutoff was 25Kcal/mol, and the miss was checked by 2-8seed classic matching. Since more than one BS will be connected in the following experiments, spacer connection is directly designed between two BS in the design stage to facilitate the judgment of the overall change after spacer connection. Then manually annotate the mismatch site, spacer sequence. The website does not consider the off-target effect at all, and most of the results are so severe that the 9-12 base combination needs to be manually changed according to the site. Get the combination with lower miss, perform secondary structure verification, and record the passed combination in the table. | - The miRNAsong website was used to design the basic sponge framework, the free energy cutoff was 25Kcal/mol, and the miss was checked by 2-8seed classic matching. Since more than one BS will be connected in the following experiments, spacer connection is directly designed between two BS in the design stage to facilitate the judgment of the overall change after spacer connection. Then manually annotate the mismatch site, spacer sequence. The website does not consider the off-target effect at all, and most of the results are so severe that the 9-12 base combination needs to be manually changed according to the site. Get the combination with lower miss, perform secondary structure verification, and record the passed combination in the table. | ||
| − | + | -Results | |
| + | We test the efficiency of miR141-sponge inhibiting the miR-101, and the heat map shows as below (A); Picture B shows the sequence of this part. | ||
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<!-- Uncomment this to enable Functional Parameter display | <!-- Uncomment this to enable Functional Parameter display | ||
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===Functional Parameters=== | ===Functional Parameters=== | ||
<partinfo>BBa_K2908555 parameters</partinfo> | <partinfo>BBa_K2908555 parameters</partinfo> | ||
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Latest revision as of 14:10, 21 October 2019
miR141-sponge
This part is designed by miRNASong(an online software) and synthesized by company.It is used to down-regulate the level of miR141 in heterogenous TNBC cells.
Usage and Biology
- √ miRNA-sponge Design
- Firstly, obtain the basic sequence information of miRNA from miRBASE, analyze which miRNA subtype is specifically described according to the literature table provided, obtain the sequence and identify the seed sequence.
- The miRNAsong website was used to design the basic sponge framework, the free energy cutoff was 25Kcal/mol, and the miss was checked by 2-8seed classic matching. Since more than one BS will be connected in the following experiments, spacer connection is directly designed between two BS in the design stage to facilitate the judgment of the overall change after spacer connection. Then manually annotate the mismatch site, spacer sequence. The website does not consider the off-target effect at all, and most of the results are so severe that the 9-12 base combination needs to be manually changed according to the site. Get the combination with lower miss, perform secondary structure verification, and record the passed combination in the table.
-Results
We test the efficiency of miR141-sponge inhibiting the miR-101, and the heat map shows as below (A); Picture B shows the sequence of this part.
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]