The oligonucleotides that invade duplex DNA and form triplexes are described as triplex forming oligonucleotides (TFOs). The TFO-DNA recognition also led to the development of an antigene strategy, so that the TFOs can be used to modulate gene activity in vivo, and therefore can be designed to form universal drugs or for targeted gene knockouts, both in plants and animals. Oligonucleotides with non-natural bases capable of binding duplex DNAs more strongly than the natural TEOs, can also be used as drugs. Similarly, PNAs with peptide-like backbone in place of sugar-phosphate backbone also form triplexes and can be used for a variety of purposes. For instance, PNAs form P-loops, while interacting with duplex DNA, forming triplexes. In this process, two PNA molecules form a triplex with one of the two DNA strands of duplex DNA leaving the other strand displaced in the form of P-loop.

The structure of triplexes may vary in any one of the following features :
(i) Triplexes may consist of two purine strands (TR*Y) or of two purine strands and one pyrimidine strand (TR*R).
(ii) Triplexes may be built from RNA or DNA or both.
(iii) Triplexes may be intramolecular or intermolecular.
(iv) Alternate strand triplexes may be formed due to strand-switch, when clustered purines and pyrimidines are found in different regions of the same strand.

Some triplex structures which are geometrically possible and have been studied areSimilarly, triads formed by the bases in YR*Y triplexes are shown in and those for YR*R triplexes are shown in Figure. It can be noted in that YR*Y and YR*R have the following common structural features:
(i) The duplex involved in triplex formation must have a homopurine sequence in one strand and
(ii) the orientation of two chemically homologous strands (two pyrimidine strands in the YR*Y triplex or two purine strands in YR*R triplex) is antiparallel.