Intramolecular triplex

In 1985, Lyamichev et al. [15] called H-DNA to the intramolecular triplex of sequence PyPuPy in order to indicate the high H+ concentration of the media where this triplex exists. This requires protonation of one cytosine in each base-triplet and the two pyrimidine strands must run antiparallel. These form has undergone much research recently [16, 17], as it is very important to understand what is the role of triplex DNA in the nucleic acid characteristics and biotechnological applications may be of great relevance. 

On the other hand, the formation of intramolecular triplexes of PyPuPu sequence is favoured by the presence in neutral media of multivalent cations that stabilize the triple helix [18, 19]. 

Two types of single-stranded, intramolecular triple helices of the type shown in Figure 12(d) are possible by double-hairpin formation [37]. This was demonstrated for the R RY motif by the design of suitable 18-mer sequences containing two G tracts to fold in an antiparallel fashion. The salient features of this intramolecular triplex motif are that (1) Mg2+ is not essential, (2) compared to the intermolecular version, a shorter triplex stem can be formed in a much lower DNA concentration, and (3) acidic conditions are not required as it is the R-RY motif. The evidence for triplex existence came from the observation that duplex-hairpin intercalator binders such as actinomycin D, chromomycin Aj and ethidium bromide bind poorly. 

Figure 13 An example of pH-dependent intramolecular triplex formation. Reproduced by permission from J. Mol. Biol., 230, 1278 (1993)...

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... 

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.

In addition to intermolecular triplexes, intramolecular triplexes or H-DNA (Fig. 2e) can be formed under certain conditions (see Section 4.4.3). 

Always two isomeric forms of H-DNA are possible, which are designated as H-y3, H-y5, H -r3 and H-r5, depending on which kind of triplex is formed and which half of the insert forms the triplex (see Fig. 2e). H-DNA may be considered as an intramolecular triplex (it is often referred to in this way). Its formation under physiological ambient conditions occurs only under superhelical stress. 

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... 

Figure 2. Phase diagram (7 , vs. pH) of an intramolecular triplex in 100 mM [Na ] Adapted from Reference [39],...

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