Hoogsteen-Watson-Crick triplexes

Hoogsteen/Watson-Crick triplex base pairs... 

Figure 1.79 Illustration of triplex base pairs that enable triplex DNA to form, (a) Pyrimidine Purine Pyrimidine (Py Pu Py) Hoogsteen/Watson-Crick triplex base pairs that form between the indicated deoxynucleoside residues (see Figs. 1.68 1.67) (b) Purine Purine Pyrimidine (Pu Pu Py) Reverse...

Fig. 9.2 Part of a quantitative- /NN HNN-COSY spectrum of a 1.5 mM uniformly 13C/15N-labeled intramolecular DNA triplex. This triplex consists of five Hoogsteen-Watson-Crick T A-T and three Hoogsteen C+ G-C base triplets. The spectral region corresponds to the 10 imino resonances of the Hoogsteen-Watson-Crick T A-T triplets. The data matrix consisted of 250 (q) X1024 (i2) data points (where n refers to complex points) with acquisition times of 45 ms (tn) and 85 ms...

Fig. 4.3 Triplex invasion by homopyrimidine PNA oligomers. One PNA strand binds via Watson-Crick base pairing (preferably in the antiparallel orientation), while the other binds via Hoogsteen base pairing (preferably in the parallel orientation). It is usually advanta-...

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]. 

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...

The extra hydrogen-bonding sites can, however, also form further base pairs, as observed for poly(A) poly(U). In the Watson-Crick A-U pair, one of the adenine N(6)-H donors and the N(7) acceptor are still free and can form another A-U pair of the Hoogsteen type (Fig. 16.16). This is in fact observed if the Watson-Crick duplex poly(A) poly(U) is exposed to high salt conditions, it disproportionates to form a triplex poly(A)-2poly(U) and a single strand poly(A) [539] ... 

The central strand of the triplex must be purine rich since a pyrimidine does not have two hydrogen bonding surfaces with more than one hydrogen bond. Thus triple-stranded DNA requires a homopurine homopyrimidine region of DNA. If the third strand is purine rich, it forms reverse Hoogsteen hydrogen bonds in an antiparallel orientation with the purine strand of the Watson-Crick helix. If the third strand is pyrimidine rich, it forms Hoogsteen bonds in a parallel orientation with the Watson-Crick paired purine strand. 

Figure 3.1 Hydrogen bond formation in G-tetrad, parallel triplexes consisting of T X a-T and C x g-C triads, A-motif, and i-motif (Watson-Crick basepairing is shown with dashed bonds, and Hoogsteen or reversed Hoogsteen base-pairing is shown with hashed bonds).

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