When performing antisense experiments capping the 5' and 3' ends with phosphorothioate bonds is very common. For a negative control we actually recommend that you use your sequence in the reverse order (not it's complement) without phosphorothioate bonds.
For example, if your antisense oligo (phosphorothioate bonds are indicated by *) is:
5' A*T*C*G*A*TCGGATC*G*A*T*C*G 3'
Then the negative control would be:
5' GCTAGCTAGGCTAGCTA 3'
For phosphorothioated oligos we highly recommend HPLC purification and Sodium Salt Exchange to remove excess thioate residues that can be toxic to cell lines.