Predicted structures of shRNA target sequences in CHIKV genomic RNA and anti-CHIKV shRNA sequences designed.

<p>(<b>A</b>) Region of shRNA E1 target site (location: 10614–10632), (<b>B</b>) Region of shRNA nsP1 target site (location: 694–712) and (<b>C</b>) Region of Capsid shRNA target site (location: 7743–7761). The exact target site in each region is indicated by black bold lines. (<b>D–F</b>) shRNA was expressed from the pSilencer vector as an oligonucleotide duplex construct (55-mer) that contains the antisense sequence which is complementary to its target in the CHIKV genome. Antisense sequences of (<b>D</b>) shRNA E1, (<b>E</b>) shRNA nsP1 and (<b>F</b>) shRNA Capsid shown here are not predicted to form considerable secondary structures. All structures are predicted using mfold web server <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0046396#pone.0046396-Zuker1" target="_blank">[29]</a>.