Difference between revisions of "Part:BBa K3905015:Design"

 
 
Line 7: Line 7:
  
 
===Design Notes===
 
===Design Notes===
−
We ensured the structure formed when both probes have annealed to the miRNA have a high probability to have unbound ends. We designed a python script to do this using Nupack's API.  
+
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.
−
We ensured GC content is 40-60%
+
  
  
Line 15: Line 14:
 
===Source===
 
===Source===
  
−
CACACGCACAGCTATAGTGAGTCGTATTATCCTGTTTCTTGTTT
+
Synthetic, designed with NUPACK
  
 
===References===
 
===References===

Latest revision as of 21:27, 21 October 2021


210-3p 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 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.



Source

Synthetic, designed with NUPACK

References