Part:BBa_K1677666:Design

HCV229E 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 genome flank either side of the pseudoknot region.

3' flanking sequence AACAGTTATTTAAACGAGTC

5' flanking sequence AGGCTGTAGTGCTGTTGCTA

The actual pseudoknot is:

CGGGGCUCUAGUGCCGCUCGACUAGAGCCCUGUAUUGGUACAGACAUAGAUUACUGUGUCCGUGCAUUUGACGUUUACAAUAAAGAUCCGUCUUUUAUCGGAAAAAAUCUGAAGACCAAUUGUGUGUGCUUCAAGAAUAUAGAUAAGGUUGACGGGUUCUAUAUUGUUAAACGUUGCAAUAAGUCAGUUAAGGACCACGAGCAGUCCUUG

((((((((((((...[[[[[))))))))))))(((((((((.(((((((....))))))).))))....(((((((((((((...(((((((((((((((((.....)))..............((((.........)))))))))))..)))))))....))))).)))))))).))))).......(((((((..]]]]].)))))))

Estimated free energy: -74.29 kcal/mol

Source

Hepatitis C virus 299E