However, the arrest site lacks the four G-rich repeats that are a hallmark of previously described intramolecular tetraplexes and contains a number of noncanonical bases that would be expected to greatly destabilize such a structure. A DNA triplex is formed when pyrimidine or purine bases occupy the major groove of the DNA double Helix forming Hoogsteen pairs with purines of the Watson-Crick basepairs. We have addressed structural aspects of this novel alignment. This prototype aptamer of thrombin has a unique double G-tetrad structure capable of inhibiting thrombin at nanomolar concentrations. Telomeres are structures at the ends of eukaryotic chromosomes, the DNA of which contains stretches of tandemly repeated sequences with G clusters along one strand.
Additional copies favor folded-back structures that associate to form an antiparallel dimer.
Intermolecular association of short telomeric sequences reported here provides a possible model for chromosomal pairing. The sequences G3T2A 3G3 and T2AG34 assume an antiparallel G quartet structure by intramolecular folding, while the sequence G3T2AG3 also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide G3T2AG3 forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes.