Parallel tetraplex structure

Base triads do, of course, occur in nucleic acid triplexes. However, tetraplex structures may also contain triads and in RNA structures triads often play a crucial role. Triplexes are formed by the interaction of a third strand in the major groove of a double helix. The duplex has to be composed of a homopurine-homopyrimidine sequence (piuine - R, pyrimidine - Y). The third strand can bind in a parallel or antiparallel orientation to one of the duplex strands. In parallel orientation, a homopyrimidine third strand binds to the homopurine strand of the duplex (YRY). This leads to the two canonical triads TAT and C+GC. Protonation of C (C+) at N3 is required for the formation of two H-bonds between C and G. Therefore, parallel triplexes are pH dependent. These structures have two canonical base triads TAT and C+GC. For an antiparallel orientation of the third strand relative to the binding duplex strand, a homopruine sequence is required that binds to the homopurine strand of the duplex (RRY). This results in the canonical triads GGC, AAT and TAT, where however the TAT triad is different to the corresponding triad in parallel triplexes. In addition to these standard triads, triplexes can also accommodate non-canonical base triads. Fig. 3 shows the two canonical triads C+GC and TAT in an intra-molecular triplex consisting of a DNA duplex and... 

In other nanosecond MD simulations on parallel and antiparallel G-tetrads the effect of coordinated cations on structure, flexibility and stability has been studied. A further MD study has started with G-tetraplex structure without any ions in the initial structure. The tetraplex structure is not disrupted but undergoes small structural changes, which allow the Na ions to move into the empty central ion channel. Even though not all potential ion binding sites were occupied during the time of simulation the structure remained stable. 

G. Laughlan et al., The high-resolution crystal structure of a parallel-stranded guanine tetraplex. Science 265, 520-524 (1994)... 

Tetraplex (= quadruplex) DNA (Fig. 4.9 and 4.12) has also been a target for detection by photophysical probes. The fluorescence of the dye DODC (see above) was found to be quenched by hairpin tetraplex DNA but not single-stranded DNA, duplex DNA, or parallel-stranded tetraplexes [326]. However, a later study found that triplex DNA competed very well with tetraplex DNA for DODC binding [322], The nature of the binding of DODC to these nucleic acid structures has not been clarified [322, 326]. 

Figure 4.12. Crystal structure of the parallel stranded tetraplex of 5 -TGGGGT-3, downloaded fixxn the Protein Data Bank (ID 244D) and visualized in RasMol [74].

Fig. 6. Parallel-stranded DNA tetraplex formed from the Tetrahymena telomeric sequence d(TTGGGGT) solved by NMR spectroscopy (PDB code 139d). The structure contains four stacked G-tetrads in e center and additional T-tetrads. The latter ones are underdefined, however. The G-tetrads have a cyclic topology IV.2(24).

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