Intramolecular triplex structures

DNA is prone to structural polymorphism its structure can differ markedly from the classical double helix. For example, under superhelical stress, circular closed DNA can adopt an unusual structure, denoted ff-DNA, in which homopurine-homopyrimidine tracts unwind and utilize the pyrimidine-rich strand to form an intramolecular triplex with another homopurine-homopyrimidine tract the remaining purine single strand is left unpaired. The formation of ff-DNA requires the presence of metal ions such as Mg + or... 

Fig. 3. Canonical base triads TAT and C+GC in an intramolecular DNA triplex structure solved by NMR spectroscopy (PDB code ld3x). The triplex is linked by hexakis ethylene glycol units (EG) and has the sequence d(AGAGAGAA-(EG)6-TTCTCTCTt-(EG)6-TCTCTCTT). The triads have a non-cyclic topology III.l(2il2). In this and the following Figures the dotted lines indicate H-bonds.

Figure 2. Various DNA structures, (a) B-DNA (b) Z-DNA (c) intennolecular triplex (d) cruciform (e) H-DNA (intramolecular triplex) (f) G-quadruplex and its various foldings.

Intramolecular triplexes, or H-DNA, have been observed in supercoiled DNA at low pH in which half of the pyrimidine strand of the oligopurine oligopyrimidine forms the third strand of a triplex structure (Lyamichev et al., 1986). Thus the pyrimidine strand forms a kind of hairpin structure, while half of the purine strand is left formally single-stranded. Sequence variation showed the requirement for an oligopurine sequence with a mirror repeat (Hanvey et al, 1988 Mirkin et al., 1987), as expected for the H-structure. 

Macaya RP, Gilbert DE, Malek S, Sinsheimer JS, Feigon J (1991) Structure and stability of X G C mismatches in the third strand of intramolecular triplexes. Science 254 270-273... 

Fig. 24.15 Above-. Thymidine calix[4]nucleosides [42, 43]. Possible triplex fomiatirai patterns with hairpin structures (a) natural type, (b) hairpin moiety replaced by calixnucleoside 35, (c) hairpin moiety replaced by calixnucleoside 37 or 38 [42]. Possible intra- and intermolecular structures adopted by calixnucleotides (d) Hairpin structure intramolecular base pairing (e) bulged duplex intermolecular base pairing (f) V-shaped aggregate intermolecular base pairing [43]...

UV-monitored thermal denaturation experiments and CD spectra. Further experimental data obtained from melting curves point out that intermolecular base pairing is more favorable than intramolecular H-bond formation. Possible triplex formation patterns and structures with intra- and intermolecular base pairing are illustrated in Fig. 24.15. In this context the hybrid compotmds may serve as versatile building blocks for the construction of oligonucleotide nanostructures [42, 43]. 

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