Figure 2.

DNA substrates used in transcription experiments. (A) General scheme of a transcription template containing a perfect YR*R triplex. It consists of the promoter-containing fragment (thin black lines) ligated to a triplex-forming construct pre-assembled from synthetic DNA oligonucleotides (the color-coding is the same as in Figure 1). Modifications of the third strand within the triplex are shown in gray underneath. A sequence with three T-to-C point substitutions is called ‘mismatched’, a sequence with seven point substitutions, which efficiently prevents duplex or triplex formation, is referred to as ‘bulged’. (B) Various triplex- and duplex-forming constructs studied. T-to-C substitutions in mismatched substrates are shown as gray squares; highly mismatched sequences in ‘bulge’ substrates are shown in yellow-gray.