Difference between revisions of "Part:BBa K4642035:Design"

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<partinfo>BBa_K4642035 SequenceAndFeatures</partinfo>
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===Design Notes===
 
===Design Notes===
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In order to design probes for miRPA, we designed another python script using Nupack’s design functions in its API to find probes which would bind to the miRNAs, but have overhangs which didn’t bind within themselves, to ensure primers could easily anneal to them. We then tested, using Nupack, the specificity of these probes and found that they had a less than 1% likelihood of binding to the closest human miRNA homologs in the correct shape. This demonstrated the increase in specificity that using miRPA could add to our test.
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In order to design probes for miRPA, we used NUPACK’s design functions in its API to find probes which would bind to the miRNAs, but have overhangs which didn’t bind within themselves, to ensure primers could easily anneal to them. We then tested, using NUPACK, the specificity of these probes and found that they had a less than 1% likelihood of binding to the closest human miRNA homologs in the correct shape. This demonstrated the increase in specificity that using miRPA could add to our test.
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===Source===
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Custom designed in-silico using NUPACK API.
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===References===

Latest revision as of 08:33, 9 October 2023


hsa-miR-145 Probe 1


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

In order to design probes for miRPA, we used NUPACK’s design functions in its API to find probes which would bind to the miRNAs, but have overhangs which didn’t bind within themselves, to ensure primers could easily anneal to them. We then tested, using NUPACK, the specificity of these probes and found that they had a less than 1% likelihood of binding to the closest human miRNA homologs in the correct shape. This demonstrated the increase in specificity that using miRPA could add to our test.


Source

Custom designed in-silico using NUPACK API.

References