The triplexes are most stable at low pH, and are readily formed within long sequences containing only purines in a given strand. Tetraplex structures may also form in DNA sequences with a very high proportion of guanosine residues.

Another DNA structure called H- DNA is found in a polypyrimidine or polypurine tract that also incorporates a mirror repeat. Two of the three strands in H- DNA triplex helix contain pyrimidines and the third contains purines.

Solution of native DNA is highly viscous at pH 7.0 and room temperature (25°C). When such a solution is subjected to extremes of pH or temperature above 80°C its viscosity decreases sharply due to disruption of hydrogen bonds and base stacking leading to unwinding of DNA double helix to form two single strands.

Due to base interaction the DNA shows decreased UV absorption relative to that of a solution with same concentration of free nucleotides. This is called as hypochromic effect. Denaturation produces opposite effect leading to an increase in absorption called as hyperchromic effect.

Incubation of DNA at low pH (≈3) causes selective removal of the purine bases, resulting in a derivative called apurinic acid which is highly unstable.