Difference between revisions of "Part:BBa K3425033"

Revision as of 09:32, 14 October 2020

iGEM Type IIS pSB1K03-DY

This part (BBa_K3425025) is an RBS (<a href="https://parts.igem.org/wiki/index.php/Part:BBa_B0030">BBa_B0030</a>) 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_B0030 to keep the distance between the RBS and the ATG the same as when BioBrick assembly was used. 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_B0030 was characterized as strong, however due to the dependence on the sequence context the result is affected by the choice of the reporter. Therefore, the performance will differ fr expression of different genes.

Aligned spacing is the distance between the centre of Shine-Dalgarno sequence and ATG start codon (see https://parts.igem.org/Ribosome_Binding_Sites/Design or Ma et al. (2002)). Aligned spacing generally varies from 5 to 13 bases, with optimum for E. coli

Optimal distance between the RBS and the ATG start codon for E. coli (see https://parts.igem.org/Ribosome_Binding_Sites/Design for more general information). Whereas Biobrick assembly generates six-nucleotide scar, Type IIS iGEM Standard assembly generates only one-nucleotide scar between RBS and ATG.

Strength of an RBS is dependent on the sequence similarity of

Sequence and Features