Part:BBa_K3425032

iGEM Type IIS pSB1K04-DY

BBa_K3425026 is an RBS (BBa_B0034) modified for Type IIS iGEM Standard assembly (RFC1000) by adding a five-nucleotide spacer (TAGTA) to the end of the sequence.

The distance between an RBS and the ATG start codon is an important factor affecting the strength of an RBS. Whereas BioBrick assembly generates six-nucleotide scar between the RBS and the ATG, Type IIS iGEM Standard assembly generates only one-nucleotide scar. Therefore, five nucleotides were added to the BBa_B0034 for its use in Type IIS assembly. However, note that the nucleotides are different.

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. Ancestral RBS BBa_B0034 was characterized as strong, however due to the dependence on the sequence context, the results are necessarily affected by the choice of the reporter. In line with that, previous characterizations report different relative strengths of BBa_B0034 and other members of RBS Community Collection. Aligned spacing is the distance between the centre of Shine-Dalgarno sequence and ATG start codon (see iGEM resourcesor refer to Ma et al. (2002)). Aligned spacing generally varies from 5 to 13 bases Ma et al. (2002) and optimal distance varies for organisms. Final aligned spacing of BBa_K3425025 is 10 nucleotides when assembled usingType IIS iGEM Standard assembly.

In conclusion, the performance of BBa_K3425025 can be only approximated by the characterization available for BBa_B0034 and it will always vary when used for expression of different genes.

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

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  COMPATIBLE WITH RFC[21]
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]