RNA

Part:BBa_K1677369:Design

Designed by: Isabelle Capell-Hattam   Group: iGEM15_BABS_UNSW_Australia   (2015-08-25)
Revision as of 07:23, 25 August 2015 by I.capellhattam (Talk | contribs) (→‎References)

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MMTV Pseudoknot


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]


Design Notes

All start codons had to be removed from the pseudoknot.
20 base pairs from the viral DNA flank either side of the pseudoknot region.
3' flanking sequence AAATTCAAAAAACTTGTAAA
5' flanking sequence AAAGGTAAGGACTCAGGATT

The actual pseudoknot is:
GGGGCAGUCCCCUAGCCCCACUCAAAAGGGGGAU
(((((.[[[[[[[.)))))........]]]]]]]
Estimated free energy: -25.93 kcal/mol

Source

It is extracted from the Mouse mammary tumor virus.

References

Staple, D. W., Butcher, S. E., Pseudoknots: RNA structures with diverse functions. PLoS biology 2005, 3, e213.
Sperschneider, J., Datta, A., DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model. Nucleic acids research 2010, 38, e103.