Triple Helices of Optimally Capped Duplex DNA (σ-DNA) with Homopyrimidine DNA and RNA at Neutral pH

An optimally capped duplex DNA (σ-DNA) was synthesized in which the cytosines in the homopyrimidine strand of σ-DNA 1 were replaced by 5-methylcytosine leading to σ-DNA 2. Although only involving 13 base pairs, this modification resulted in very high melting temperatures above 90°. In addition, σ-DNA 2 was able to form triple helices with the corresponding homopyrimidine DNA or RNA even at neutral pH. This opens up the possibility to use σ-DNA in a triple-helix approach to modulate gene expressions on the level of the translation process.