Help:BioBrick Prefix and Suffix

Revision as of 22:40, 20 November 2006 by Scmohr (Talk | contribs) (→‎BioBrick Suffix)

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For more information about how the prefix and suffix were determined and the special case of coding regions, see Assembly:RBS-CDS_issues.

Part Sequence

The DNA sequence for parts in the Registry starts with the first base of the part itself and ends with its last base. For example, a protein coding sequence is like this "ATG----------TAATAA". The sequence in the Registry does not include any bases of the BioBrick Prefix or Suffix.

Plasmids (see below) and primers or tags that explicitly specify prefix or suffix bases are exceptions to this rule.


BioBrick Prefix

The standard BioBrick prefix depends on the part that follows it (part in grey, EcoRI, XbaI). YOUR SEQUENCE as it should be entered into the database is in uppercase letters.

If the following part is a coding sequence or any other part that starts "ATG", the BioBrick prefix is:

gaattcgcggccgcttctagATG...

Otherwise, the BioBrick prefix is:

gaattcgcggccgcttctagagCA...

BioBrick Suffix

Similarly, the standard BioBrick suffix depends on the part that precedes it. Whenever possible, the transcriptional start site of a promoter part should lie 2bp upstream of the SpeI site. (part in grey, PstI, SpeI). YOUR SEQUENCE as it should be entered into the database is in uppercase letters. For help locating the transcription initiation site in your promoter part, try [http://www.fruitfly.org/seq_tools/promoter.html promoter prediction.]

The standard BioBrick suffix for most parts:

...ACtactagtagcggccgctgcag

For promoter parts, the transcriptional initiation site (in green) is placed 2 bp upstream of the SpeI site:

...CACtactagtagcggccgctgcag

BioBrick Scar

When BioBricks with these prefix and suffix sequencees are assembled, there is a "scar" between these parts.

If the second part starts "AT", the scar is:

tactag

Otherwise, the scar is:

tactagag


Plasmid Sequences

Since plasmids are circular pieces of DNA, the specification of the "first" base is arbitrary. Furthermore, plasmids often hold BioBrick parts, leading to a question of how the plasmid itself is defined.

In the Registry, we define the plasmid as starting with the first base of the suffix and ending with the last base of the BioBrick prefix. That definition keeps the plasmid continuous and breaks it where parts will be inserted.