Figure 9.

Strand displacement analysis by EMSA. Labeled LTR-III+IV (LTR-III+IV*) was annealed to 1.1-fold excess of LTR-III+IV complementary sequences (Compl) of different lengths (13 or 17 nucleotides) and incubated with increasing fold excess (0.5-4X) of NDI-PNA 6 or PNA 7 (PNA), as indicated, at 37°C, overnight. Reaction solutions were loaded onto 16% native polyacrylamide gel in 1X TBE buffer and KCl (1 × 10⁻¹ M). The gel was run overnight at 60 V and DNA molecules were visualized by phosphorimaging. Lane M: markers of 33 and 55 nt-long oligonucleotides. ‘Ss’ indicates the folded LTR-III+IV* oligonucleotide; ‘ss + compl’ indicates the LTR-III+IV* oligonucleotide complemented to the 13- or 17-nt long oligonucleotides; ‘ss + PNA’ indicates the complex between the LTR-III+IV* oligonucleotide and the indicated PNA derivative.