Difference between revisions of "Part:BBa K1677369:Design"

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===Design Notes===
 
===Design Notes===
−
All start codons had to be removed from the pseudoknot.
+
All start codons had to be removed from the pseudoknot. <br>
−
20 base pairs from the viral DNA flank either side of the pseudoknot region.  
+
20 base pairs from the viral DNA flank either side of the pseudoknot region. <br>
−
3' flanking sequence AAATTCAAAAAACTTGTAAA
+
3' flanking sequence AAATTCAAAAAACTTGTAAA <br>
−
5' flanking sequence AAAGGTAAGGACTCAGGATT
+
5' flanking sequence AAAGGTAAGGACTCAGGATT <br>
  
−
The actual pseudoknot is:
+
The actual pseudoknot is: <br>
−
GGGGCAGUCCCCUAGCCCCACUCAAAAGGGGGAU  
+
GGGGCAGUCCCCUAGCCCCACUCAAAAGGGGGAU <br>
−
(((((.[[[[[[[.)))))........]]]]]]]  
+
(((((.[[[[[[[.)))))........]]]]]]] <br>
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Estimated free energy: -25.93 kcal/mol
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Estimated free energy: -25.93 kcal/mol <br>
  
 
===Source===
 
===Source===
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===References===
 
===References===
 
Staple, D. W., Butcher, S. E., Pseudoknots: RNA structures with diverse functions. PLoS biology 2005, 3, e213. <br>
 
Staple, D. W., Butcher, S. E., Pseudoknots: RNA structures with diverse functions. PLoS biology 2005, 3, e213. <br>
 +
Sperschneider, J., Datta, A., DotKnot: pseudoknot prediction using the probability dot plot under a refined energy model. Nucleic acids research 2010, 38, e103. <br>

Latest revision as of 07:23, 25 August 2015


MMTV Pseudoknot


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Unknown
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Unknown
  • 23
    INCOMPATIBLE WITH RFC[23]
    Unknown
  • 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.