Difference between revisions of "Part:BBa K1970001:Design"

 
 
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===Design Notes===
 
===Design Notes===
 
Designing the deoxyribozyme ribonucleases so that they bound more tightly to each other than to CI repressor mRNA was challenging. Additionally, choosing which promoters to place in front of either gene required some thought on desired expression levels and controlability of the system.
 
Designing the deoxyribozyme ribonucleases so that they bound more tightly to each other than to CI repressor mRNA was challenging. Additionally, choosing which promoters to place in front of either gene required some thought on desired expression levels and controlability of the system.
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The sequences of the catalytic ssDNAs produced by the retrons in this biobrick were designed in order to maximize the ssDNAs' inhibitive effect on each other while keeping their affinities for their target cutting site the same. This was done using a combination of the ViennaRNA library and self-written scripts and programs that can be found here: https://github.com/TheAngryFox/retron_design.
  
  

Latest revision as of 13:17, 26 October 2016


XOR gate like repressor of CI repressor expression


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal SpeI site found at 1374
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 337
    Illegal NheI site found at 1589
    Illegal SpeI site found at 1374
    Illegal NotI site found at 1381
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal XhoI site found at 615
    Illegal XhoI site found at 1867
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal SpeI site found at 1374
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal SpeI site found at 1374
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

Designing the deoxyribozyme ribonucleases so that they bound more tightly to each other than to CI repressor mRNA was challenging. Additionally, choosing which promoters to place in front of either gene required some thought on desired expression levels and controlability of the system.

The sequences of the catalytic ssDNAs produced by the retrons in this biobrick were designed in order to maximize the ssDNAs' inhibitive effect on each other while keeping their affinities for their target cutting site the same. This was done using a combination of the ViennaRNA library and self-written scripts and programs that can be found here: https://github.com/TheAngryFox/retron_design.


Source

De novo DNA.

References