I am looking for a tool or methods which can help me to choose the stretch of sequence from my target miRNAs which can be used to design siRNA in order to inhibits its expression in cultured cells.
You can use miRNA Inhibitors to inhibit the level of that particular miRNA in your cells. For that better prefer to Pre-made miRNA oligos (from any one of them: Thermo/Dharmacon/Eurogentec/Qiagen), they mostly comes with LNA tech. which help them to avoid non-specific binding.