Topology of triple helical DNA.

From the stereochemical modeling of a triple helix, the third poly(dT) strand can bind in anti-parallel direction to the poly(dA) strand from the major groove of the poly(dA)-poly(dT) double helix. We designed a single strand 46mer DNA named AP46 which may form an anti-parallel triple helix containing only ATT base triplet by folding back in the strand. The UV melting profile of AP46 showed an increase of absorbance at 260 nm as temperature was raised, but no obvious double transition points were observed. We examined the type of a triple helix by using 3'-5' exonuclease activity of T4 DNA polymerase. The digestion experiment indicates that an anti-parallel triple helix is not so stable even if it exists. This enzymatic method is useful for probing the secondary structure of DNA strand.