Richard Lab:Bio-Brick Formats

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Introduction

In general the Richard Lab uses the standard Bio-Brick format. However occasionally this format is incompatible with our goals (e.g. making protein fusions) or is unnecessarilly cumbersome (e.g. PCR overlap extension). To have a review on why (and how) we use these sites see the our New Standard Assembly page.

Formats

Biobrick Standard

This standard uses the typical biobrick assembly enzymes [EcoRI (GAATTC), XbaI (TCTAGA), SpeI (ACTAGT), and PstI (CTGCAG)] as well as NotI sites (GCGGCCGC) flanking the part. There is a slightly different prefix for protein coding parts to put the start codon in a better spot in relation to the RBS. During assembly the XbaI site of the "rear part" and the SpeI site of the "front" part eliminate eachother and form a "scar" which forever binds the two parts together.

  • Prefix
  • GAATTCgcggccgctTCTAGAg
  • The EcoRI and XbaI sites are in CAPS while the NotI site is in bold.
  • Protein Coding Prefix
  • GAATTCgcggccgctTCTAG
  • using this prefix the first base of the start codon (i.e. the "A" in "ATG") will complete the XbaI site.
  • Suffix
  • tACTAGTagcggccgCTGCAG
  • Scar
  • Tactagag for non coding parts and Tactag between coding parts and Ribosome binding sites.

Short Biobrick

Because the NotI sites in the biobricks are rarely used a shortened biobrick system can be employed. This is especailly usefull when adding "flanking" restriction sites to sequences via overlap extention PCR. The shortened sequences are thus:

Protein Fusions

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