Part:BBa_K1323008
sRNA control for S. epidermidis: targets the non-coding region
Small RNAs (sRNAs) are small double-stranded transcripts capable of silencing mRNAs of complementary sequence (Yoo et al., 2013). The sRNA sequence was designed with two functional parts: the part that is complementary to the target mRNA (target binding site) and MicC scaffold region for recruitment of Hfq (BBa_K1323019), a protein which enhances the sRNA to target mRNA hybridization (Yoo et al., 2013). The MicC RNA sequence is the best scaffold sequence as shown by previous studies done by the same group (Na et al., 2013).
This is a control sRNA that targets a non-coding region in the genome of S.epidermidis (2314773-2314796) which is a intergenic region that is downstream of two genes on two different strands. It contains binding energy of only -7.8kcal/mol to YFP gene as determined using DINAMelt software (http://mfold.rna.albany.edu/?q=DINAMelt/Two-state-melting). For effective binding, sRNA must have binding energy between -30kcal/mol to -40kcal/mol (Yoo et al., 2013). This shows that control sRNA cannot effectively bind YFP and it serves as a control which allows us to determine if production of sRNA places a metabolic load on the organism (Dokyun et al., 2013).
This part was DNA-Synthesized.
References
Dokyun Na, S. M. (2013). Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nature Biotechnology, 170-174.
Na, D. et al (2013). Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nature Biotechnology 31, 170–174.
Yoo, S, M., Na, D., Lee, S. Y. (2013). Design and use of synthetic regulatory small RNAs to control gene expression in Escherichia coli. Nature protocol 8(9), 1694-1707.
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21INCOMPATIBLE WITH RFC[21]Illegal XhoI site found at 138
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]
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