Temporary

Part:BBa_J70033:Design

Designed by: Julie Norville   Group: Knight Lab   (2008-12-12)

A BioMortar Part for Creating GSGS Protein Fusions (see Design page)


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 6
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Design Notes

First determine what sequence you need on the ends of your BioMortar part (your sequence will probably not need 5 a's on either side):
BBa_J70033 Template Part
               GGA TCC GGG TCC aaaaa
         aaaaa CCT AGG CCC AGG 
(translates to)G   S   G   S

In order to see what you need, first place a BioScaffold Part between your proteins of interest:

Example: BioScaffold Part BBa_J70032, between parts BBa_I714891 and BBa_K133133

In order to see what you need, first place a BioScaffold Part between your proteins of interest.  Use the BBa_J70032 design page to show you where the PsrI and PpiI enzymes will cut.
      BBa_I714891         Scar     BBa_J70032       Scar
. . . gag ctg tac aag taa TACTAGAG BioScaffold Part TACTAGAT cac cac cac cac . . .
. . . ctc gac atg ttc att ATGATCTC                  ATGATCTA gtg gtg gtg gtg . . .
      E   L   Y   K   Stop                                   H   H   H   H

Cutting with PsrI and PpiI 
      BBa_I714891         Scar     BBa_J70032       Scar
. . . gag ctg t ac aag^taa TACTAGAG BioScaffold Part TACTAGAT ca c cac c^ac cac . . .
. . . ctc gac a^tg ttc att ATGATCTC                  ATGATCTA gt^g gtg g tg gtg . . .
      E   L   Y    K   Stop                                   H   H   H   H

Removing the BioScaffold Part 
. . . gag ctg t ac aag^                                                  ^ac cac . . .
. . . ctc gac a^                                                 ^g gtg g tg gtg . . .

Adding a BBa_J70033 Type BioMortar Part
. . . gag ctg t ac aag^          GGA TCC GGG TCC xxxxx                ^ac cac . . .
. . . ctc gac a^           xxxxx CCT AGG CCC AGG              ^g gtg g tg gtg . . .

Now you can see how to design your oligos in order to create you BioMortar Part 
                                 BioMortar Part
. . . gag ctg t ac aag^          GGA TCC GGG TCC ccacc                ^ac cac . . .
. . . ctc gac a^           tgttc CCT AGG CCC AGG              ^g gtg g tg gtg . . .

Notice that in this case (since the second part does not begin with ATG) it would have been easier to use BBa_J70030 as your BioScaffold part (since it requires cutting with PpiI and MabI rather than PpiI, PsrI, and MabI)

Simpler example: BioScaffold Part BBa_J70030, between parts BBa_I714891 and BBa_K133133

Design for BioMortar Part when BBa_J70030 is your BioScaffold Part 
      BBa_I714891          Scar     BBa_J70030       Scar
. . . gag ctg t ac aag^taa TACTAGAG BioScaffold Part TACTAGAT cac ca^c cac cac . . .
. . . ctc gac a^tg ttc att ATGATCTC                  ATGATCTA^gtg gt g gtg gtg . . .
      E   L   Y    K   Stop                                   H   H    H   H

Result
                                 BioMortar Part
. . . gag ctg t ac aag^          GGA TCC GGG TCC cacca               ^c cac . . .
. . . ctc gac a^           tgttc CCT AGG CCC AGG              ^gtg gt g gtg . . .

Source

Designed

References