User:Bcanton/Dedicated RBSs

Family Description

Dedicated ribosome binding sites (dRBSs) are designed to not be recognized by E. coli ribosomes. Instead they are designed to be recognized by orthogonal or dedicated ribosomes Brink, Rackham. This specificity is achieved by mutating the Shine-Dalgarno (SD) sequence of E. coli RBSs.

dRBSs for BrinkBrink ribosomes

dRBSs for RackhamRackham ribosomes

Design notes for mRNA-A derivatives

B0072	caccactactag	atg
B0073	tcacaccactactag	atg
B0074	tcacaccaccctactag	atg

BBa_B0072

This dRBS is the mutated portion of the Shine-Dalgarno (SD) sequence. By defining the RBS as just this sequence, the spacing between the SD sequence and the start codon in a BioBricks construction is the same as that used by Rackham et al. B0072 forms a hairpin with a ∆G of -2-.8kCal/mol at the start of the BBa_E70201transcript.

BBa_B0073

This dRBS is identical to BBa_B0072 except 3 bases are added upstream. This was done in case these upstream bases also interact with the dedicated ribosomes and are necessary for efficient translation initiation. BBa_B0073forms a hairpin with a ∆G of -4.2kCal/mol at the start of the BBa_E70202 transcript.

BBa_B0074

This dRBS is identical to BBa_B0073 except 2 bases are added downstream. This was done in case these downstream bases also interact with the dedicated ribosomes and are necessary for efficient translation initiation. The downside to this is that when assembling this dRBS with a coding region using BioBricks standard assembly, the spacing between the SD and the start codon is not the same as in the published work.BBa_B0074forms a hairpin with a ∆G of -1.8kCal/mol at the start of the BBa_E70203 transcript.

Design notes for mRNA-C derivatives

BBa_B0076

This dRBS is the mutated portion of the Shine-Dalgarno (SD) sequence. By defining the RBS as just this sequence, the spacing between the SD sequence and the start codon in a BioBricks construction is the same as that used by Rackham et al.

BBa_B0077

This dRBS is identical to BBa_B0076 except 3 bases are added upstream. This was done in case these upstream bases also interact with the dedicated ribosomes and are necessary for efficient translation initiation.

BBa_B0078

This dRBS is identical to BBa_B0077 except 2 bases are added downstream. This was done in case these downstream bases also interact with the dedicated ribosomes and are necessary for efficient translation initiation. The downside to this is that when assembling this dRBS with a coding region using BioBricks standard assembly, the spacing between the SD and the start codon is not the same as in the published work.

References

Rackham pmid=16408021
Brink pmid=7758959

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