Part:BBa_K3425031
RBS for Type IIS iGEM Standard Assembly
BBa_K3425031 is an RBS (BBa_B0032) modified for Type IIS iGEM Standard assembly (RFC1000) by adding a five-nucleotide spacer (TACTA) to the end of the sequence.
Aligned Spacing
The distance between an RBS and a start codon is an important factor affecting the strength of an RBS. Whereas BioBrick assembly generates six-nucleotide scar between the RBS and the start codon, Type IIS iGEM Standard assembly generates only one-nucleotide scar. Therefore, five nucleotides were added to the BBa_B0032 for its use in Type IIS assembly. However, note that the nucleotides of the spacer are different from the BioBrick scar, which might influence the performance of RBS.
Sequence Context Dependence
Generally, the strength of an RBS depends heavily on 1) the sequence of the RBS 2) the aligned spacing and 3) the upstream and downstream genetic context. Therefore, the same RBS element performs differently in different sequence context. This means, that identical RBS element results in different expression levels for different genes. An interesting solution to this problem might be implementation of bicistronic architecture [1], for example BCD2
BBa_K1114107 or
BBa_J364100.
Characterization Issues
The ancestral RBS of this part,
BBa_B0032,
was characterized as strong. However, due to the inherent dependence on the sequence context described above, the results are necessarily affected by the choice of the reporter.
In line with that, previous characterizations report different relative strengths of
BBa_B0032
and other members of
RBS Community Collection.
In conclusion, the performance of BBa_K3425031 can be only approximated by the characterization available for BBa_B0032 and it will always vary when used for expression of different genes.
Refereces
[1] Ma, J., Campbell, A., and Karlin, S. (2002) Correlations between Shine-Dalgarno Sequences and Gene Features Such as Predicted Expression Levels and Operon Structures. J. Bacteriol. 184, 5733–5745
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
//collections
//collections/typeiis/uppsala
//direction/forward
//rbs/prokaryote/constitutive/community
//rbs/prokaryote/constitutive/constitutive
//regulation/constitutive
chassis | E. coli |
direction | forward |
function | protein expression regulation |
rbs | constitutive |