Part:BBa_K3893000

Shine Dalgarno for E coli

This sequence is part of the Modular Platform for dsRNA production in the proyect AgroBactory 593.

The Shine-Dalgarno (SD) is a sequence located 4 to 10 bases upstream of start codons and it is often 4 to 6 nucleotides long (most common: 5' AAGAG 3').

Usage and Biology

During translation, the SD sequence join to the 3' end of the 16S rRNA by base pairing with the anti-SD sequence (ASD); this mating helps the ribosomes to reach the right position of the start codon and therefore, translation can begin [1]. In synthetic biology, the SD sequence has been used to increase translation rate and as well as the yield of protein production. On the other hand, for interference RNA (RNAi) assays, studies has shown that the SD sequence provides stability to the dsRNA molecules, preventing its degration [2]. For this reason, we decided to attach the SD sequence to our parts.

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]

References

[1] A. Yurovsky, M. R. Amin, J. Gardin, Y. Chen, S. Skiena, y B. Futcher, “Prokaryotic coding regions have little if any specific depletion of Shine-Dalgarno motifs”, PLOS ONE, vol. 13, núm. 8, p. e0202768, ago. 2018, doi: 10.1371/journal.pone.0202768.

[2] Chen, H., Bjerknes, M., Kumar, R., & Jay, E. (1994). Determination of the optimal aligned spacing between the Shine–Dalgarno sequence and the translation initiation codon of Escherichia coli m RNAs. Nucleic acids research, 22(23), 4953-4957.