Watson-Crick pairing triplex structures

The formation of three-stranded nucleic acid complexes was first demonstrated over five decades ago [56] but the possible biological role of an extended triplex was expanded by the discovery of the H-DNA structure in natural DNA samples [57-59]. H-DNA is an intermolecular triplex that is generally of the pyrimidine-purine x pyrimidine type ( dot -Watson-Crick pairing and cross Hoogsteen base paring) and can be formed at mirror repeat sequences in supercoiled plasmids [59]. 

Fig. 2. Hydrogen-bonding patterns in polynucleotides, including Watson-Crick pairing characteristic of duplex DNA and RNA (top) Hoogsteen pairing formed in triplex structures (bottom left) and wobble pairing often found in RNA (bottom right).

Figure 5-34 (A) Two conformations of a segment of the yeast phenylalanine tRNA gene. The segment shown codes for the 3 end of the tRNA molecule shown in Fig. 5-30, including the T /C loop. (B) Formation of H-DNA (Fig. 5-24) proposed for a sequence in plasmid pGG32. The major element of the structure is the triplex, which is formed from the Watson-Crick duplex ( ) associated with the homopyrimidine loop through Hoogsteen base pairing (o, +). One of the two possible "isomeric" forms is shown. See Mirkin et al.378...

Figure 2 Most common DNA/RNA binding modes. Left Strand invasion of homopyrimidine PNA into duplex DNA yields a PNA2-DNA triplex. Right Hybridization of mixed sequence PNA with complementary DNA or RNA produces Watson-Crick base-paired duplex structures.

The regular double-helix structure of DNA, typically called B-DNA, in which two complementary strands are held together by Watson-Crick base pairs, is well recognized. Recently it has been found that under certain conditions DNA can form non-canonical structures, such as Z-DNA, A-motif, G-quadru-plex, i-motif, triplex, hairpin, and erueiform. These structures are particularly seen in the human genome with repeat DNA sequences, which account for more than 50% of the total genomie DNA, while simple sequence repeats account for approximately 3% of the total DNA. Although some of these unusual DNA structures have not been directly detected in vivo, they have been... 

FIGURE 1.7 Base pairing schemes of Watson-Crick and non-Watson-Crick types. Among the non-Watson-Crick base pairs, wobble pairs are formed by H-bonds between tautomeric forms of hydroxyl (OH) and imino (NH) groups. Non-Watson-Crick base pairs also comprise Hoogsteen base pairs and reverse Watson-Crick base pairs which form the basal structural units in triplex DNA and In parallel-stranded DNA (psDNA), respectively. 

---