Help:BioBrick Prefix and 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.
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If the following part is a coding sequence or any other part that starts "ATG", the BioBrick prefix is: |
gaattcgcggccgcttctagATG... |
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Otherwise, the BioBrick prefix is: |
gaattcgcggccgcttctagagCA... |
BioBrick Suffix
Similarly, the standard BioBrick prefix depends on the part that preceeds it (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.]
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The standard BioBrick suffix for most parts: |
...ACtactagtagcggccgctgcag |
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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.
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If the second part starts "AT", the scar is: |
tactag |
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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.