Figure 2. Binding affinity of PNA_PBS-MTD peptide conjugates to their target sequences.

The gel mobility shift assay was performed to assess the binding affinity of the PNA_PBS-MTD peptide conjugates in comparison to that of unconjugated naked PNA_PBS control. PNA_PBS-Penetratin, PNA_PBS-Tat, and unconjugated naked PNA_PBS were incubated at varying concentrations with 10 nM of internally ³²P-labeled U5-PBS RNA transcript in the binding buffer for 30 min at room temperature. The incubated samples were then loaded on a pre-run 8% native polyacrylamide gel. The RNA: PNA complex was resolved and separated from free RNA by running at 150 V for 3 h. Lane 1 represents U5-PBS RNA alone; lanes 2 to 7 represent increasing amounts of PNA_PBS or its MTD conjugates, ranging through 2.5, 5.0, 7.5, 10, 15, and 20 nM. (A) PNA_PBS alone; (B) PNA_PBS-Penetratin; (C) PNA_PBS-Tat.