Team:Edinburgh/GenBrick/Linker Designer


Linker designer

Linkers come in between the Bricks in an assembly. Typical linkers are around 45 base pairs in length, but they can be up to 80 base pairs or so. Each linker consist of 4 oligonucleotides. Following the Genabler terminology, we call these Eye Long, Eye Short, Hook Long, and Hook Short (EL, ES, HL and HS). The complete Linker looks like this:

  GCCNNN(Hook, Long)NNNNNNNNNNNNN          NN(Eye, Short)NN
     NNN(Hook, short)NNNNN         NNNNNNNNNN(Eye, Long)NNNAGC

The long single stranded regions are complementary. The double-stranded regions should have be at least ten bases in length, and the overlap region in the centre should be at around 15 to 18 bases in length with a melting temperature around 40˚C.

Linkers which go between two Coding Bricks can be of different types, eg: • Stop codon plus RBS plus start codon • C-terminal tag plus stop codon plus RBS plus start codon • Stop codon plus RBS plus start codon plus N-terminal tag • Flexible protein linker to join two domains in a fusion protein • other - your imagination is the limit!

Below is our Linker Designer, a program designed to facilitate the engineering of linkers. Included is a database of previous linkers used by the EdiGEM team 2013. Any linkers designed with the linker designer will be saved and can be accessed for future use.

If you want to open a full-page version of the tool, you can access it here.