Difference between revisions of "Part:BBa K3425031"

Revision as of 13:47, 14 October 2020

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.

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_B0032 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_B0032 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_B0032 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 [1]). Aligned spacing generally varies from 5 to 13 bases [1] and optimal distance varies for organisms. Final aligned spacing of BBa_K3425031 is 9 nucleotides when assembled using Type IIS iGEM Standard assembly.

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.