Difference between revisions of "Part:BBa K3425033"
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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 the same as if BioBrick assembly were used. However, note that the nucleotides are different.
 
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 the same as if BioBrick assembly were used. However, note that the nucleotides are different.
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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 results were influenced by the choice of the reporter. In line with that, previous characterizations report different relative strength of BBa_B0030 and other members of [<a href="https://parts.igem.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Community_Collection">RBS Community Collection</a>]. Aligned spacing is the distance between the centre of Shine-Dalgarno sequence and ATG start codon (see <a href="https://parts.igem.org/Ribosome_Binding_Sites/Design">here</a> or refer to Ma <i>et al.</i> (2002)). Aligned spacing generally varies from 5 to 13 bases Ma <i>et al.</i> (2002).
 
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 results were influenced by the choice of the reporter. In line with that, previous characterizations report different relative strength of BBa_B0030 and other members of [<a href="https://parts.igem.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Community_Collection">RBS Community Collection</a>]. Aligned spacing is the distance between the centre of Shine-Dalgarno sequence and ATG start codon (see <a href="https://parts.igem.org/Ribosome_Binding_Sites/Design">here</a> or refer to Ma <i>et al.</i> (2002)). Aligned spacing generally varies from 5 to 13 bases Ma <i>et al.</i> (2002).

Revision as of 10:01, 14 October 2020


iGEM Type IIS pSB1K03-DY

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 the same as if BioBrick assembly were 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 results were influenced by the choice of the reporter. In line with that, previous characterizations report different relative strength of BBa_B0030 and other members of [<a href="https://parts.igem.org/Ribosome_Binding_Sites/Prokaryotic/Constitutive/Community_Collection">RBS Community Collection</a>]. Aligned spacing is the distance between the centre of Shine-Dalgarno sequence and ATG start codon (see <a href="https://parts.igem.org/Ribosome_Binding_Sites/Design">here</a> or refer to Ma et al. (2002)). Aligned spacing generally varies from 5 to 13 bases Ma et al. (2002).

In conclusion, the performance of BBa_K3425025 can be only approximated by the characterization available for BBa_B0030 and it will always differ for expression of different genes.

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]