Figure 1.

H-DNA and its stable analog. (A) H-DNA formation by completely complementary double-stranded sequences. Homopurine strand in the acceptor part of the H-palindrome, which would become a central strand of H-DNA triplex, is shown in red; its complementary homopyrimidine strand is shown in blue; homopurine strand from the donor part of H-palindrome, which would be donated to a triplex is shown in orange; its Watson–Crick complement is shown in turquoise; flanking sequences are in black. The donor and acceptor parts of the H-palindrome could be separated by several base pairs of arbitrary sequence. In the process of H-DNA formation, the donor part of an H-palindrome unwinds and donates one of its strands to the triplex. Usually, the energy of triplex formation is not sufficient to compensate the melting of duplex regions required for triplex formation. Consequently, transition to H-DNA requires additional energetic input from negative supercoiling. (B) Stable H-DNA analog. Strands in the donor part of the H-palindrome (as well as in the middle, and a few nucleotides at the flank) are not complementary, eliminating the energetically unfavorable step of duplex melting from the triplex formation process. Consequently, H-DNA is exceptionally stable and its formation is practically irreversible.