Difference between revisions of "Part:BBa K1323008"

Revision as of 20:43, 17 October 2014

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: a region complementary to the target mRNA (target binding site) and MicC scaffold region for recruitment of Hfq BBa_K1323004, a protein which enhances the hybridization between the sRNA and target mRNA (Yoo et al., 2013). The MicC RNA sequence is the best scaffold sequence as shown by previous studies done by the same research 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.

This part was DNA-synthesized by Bio Basic.

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 138
23
COMPATIBLE WITH RFC[23]
25
COMPATIBLE WITH RFC[25]
1000
COMPATIBLE WITH RFC[1000]

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.

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 <partinfo>BBa_K1323008 short</partinfo>
-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 [https://parts.igem.org/Part:BBa_K1323019 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).
+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: a region complementary to the target mRNA (target binding site) and MicC scaffold region for recruitment of Hfq [https://parts.igem.org/Part:BBa_K1323004 BBa_K1323004], a protein which enhances the hybridization between the sRNA and target mRNA (Yoo et al., 2013). The MicC RNA sequence is the best scaffold sequence as shown by previous studies done by the same research 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.
-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 by Bio Basic.
-This part was DNA-Synthesized.