Part:BBa_K1323006

sRNA (2): YFP-targeting molecule

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). Since the target mRNA is YFP, the target binding sequence of this sRNA is complementary to the S. epidermidis codon optimized YFP (BBa_K1323010).

sRNA2 targets 5’UTR directly downstream of Shine Dalgarno sequence of the YFP construct. This 28 bp sequence has binding energy of -31.6 kcal/mol as determined using DINAMelt software (http://mfold.rna.albany.edu/?q=DINAMelt/Two-state-melting). For effective binding, sRNA should have binding energy between -30kcal/mol to -40kcal/mol (Yoo et al., 2013). We aligned sRNA2 sequence with other constructs and ATCC 12228 genome to determine the highest binding energy for non-specific RNA binding, which is -16.78 kcal/mol. This shows that sRNA2 binds more specifically to YFP and should not interfere with other gene expressions in our system.

Sequence and Features

Assembly Compatibility:

• 10
  COMPATIBLE WITH RFC[10]
• 12
  COMPATIBLE WITH RFC[12]
• 21
  INCOMPATIBLE WITH RFC[21]

  Illegal XhoI site found at 142
  
• 23
  COMPATIBLE WITH RFC[23]
• 25
  COMPATIBLE WITH RFC[25]
• 1000
  COMPATIBLE WITH RFC[1000]