Difference between revisions of "Part:BBa K3425031"

Revision as of 10:24, 14 October 2020

iGEM Type IIS pSB3C11-DY

BBa_K3425025 is an RBS (<ahref="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 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 <ahref="https://parts.igem.org/wiki/index.php/Part:BBa_B0030">BBa_B0030</a> 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 strength of <ahref="https://parts.igem.org/wiki/index.php/Part:BBa_B0030">BBa_B0030</a> 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) and optimal distance varies for organisms. Final aligned spacing of BBa_K3425025 when Type IIS iGEM Standard assembly is used is 10 nucleotides.

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]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K3425027 short</partinfo>
-This part (BBa_K3425027) is a weak RBS (BBa_B0032) modified for Type IIS iGEM Standard assembly (RFC 1000) by adding five nucleotides (TACTA) to the end of the sequence.
+BBa_K3425025 is an RBS (<ahref="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.
-Five to six nucleotides is the optimal distance between the RBS and the ATG start codon for <i>E. coli</i> (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. To keep the distance optimal, five nucleotides were added to the BBa_B0032 for its use in Type IIS assembly.
+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 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 <ahref="https://parts.igem.org/wiki/index.php/Part:BBa_B0030">BBa_B0030</a> 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 strength of <ahref="https://parts.igem.org/wiki/index.php/Part:BBa_B0030">BBa_B0030</a> 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) and optimal distance varies for organisms. Final aligned spacing of BBa_K3425025 when Type IIS iGEM Standard assembly is used is 10 nucleotides.
+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.
 <!-- Add more about the biology of this part here