Biological Background on Triplex Formation
Nucleic acid triplex formation - biochemistry and binding rules
Triplex-formation requires a double-stranded nucleotide in Watson-Crick
configuration (duplex) and a single-stranded nucleotide
sequence that is acting as the third strand:
The third strand binds in the major groove of the duplex forming Hoogsteen and
reverse Hoogsteen hydrogen bonds with the purines of the duplex, respectively.
This also determines the orientation of the third strand with respect to the
purines in the duplex:
There are six nucleotide triads that allow the formation of two hydrogen bonds
between the purines in the duplex and the nucleotides binding in the major groove.
These nucleotide triads are used in the canonical ruleset for triplex formation, i.e.
- the pyrimidine motif, [TC] - where thymines and cytosines bind parallel
- the purine motif, [GA] - where guanines and adenines bind anti-parallel
- the purine-pyrimidine motif, [GT] - where guanines and thymines bind either parallel or anti-parallel with respect to the purines in the duplex
For additional information we refer to our review
on nucleic acid triplex formation published in RNA biology (Landes Bioscience - open access article).