An unusual form of three-stranded structure, called triplex DNA, can arise in vitro when a single-stranded region of DNA pairs with a paired duplex DNA helix through additional hydrogen bonding between the bases of all three strands.
Based upon your knowledge of the structure of helical DNA, where would you predict that a short DNA strand would ‘sit’ within this structure for such an interaction to occur?
Within the major groove, where several potential hydrogen bonding sites are available, as shown in Figure 9c.
The formation of these hydrogen bonds arises because of what are termed Hoogsteen bonds, which form between bases in the incoming single-stranded DNA and the already paired bases in the duplex, as shown in Figure 15. The various combinations of bonds, C–G·C, T–A·T, T–A·A and C–G·G (where the dash denotes Watson-Crick base pairing and the dot denotes Hoogsteen pairing), have varying degrees of stability, with bonds between the purines being most stable. Whilst many in vitro studies have examined the possible structures of these triplex DNAs, their role in vivo remains unclear. Their significance lies in the observation that triplex structures in vitro have been shown to inhibit transcription. Thus formation of these structures in vivo, for example between a duplex region and single-stranded DNAs or between two duplex regions (as shown in Figure 15b), could play a role in gene regulation.