The triple helix DNA

Some research over a number of years has been devoted to the existence of triple helix DNA, which results from the interaction of native and single stranded DNA [9-11]. The triple helix complex formed between two strands of poly(uridylic acid) and one strand of poly(adenylic acid) was first described in 1957 by Felsenfeld [4]. Later in 1959, Hoogsteen [12] 

Triple-stranded DNA can be generated intermolecularly or intramolecu-larly and can only be formed if one strand of the original B-helix is all purines (A and G) and the corresponding region of the other strand is all pyrimidines. It is more stable at low pH and has a second polypyrimidine strand wound in the major grove of B-DNA where it forms Hoogsteen base-triples with a complementary polypurine strand. Fig. 3.2. Triple- 

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]. 

The identification of in vivo intramolecular triple helixes have been made by immunological techniques [20], the use of chemical probes [21] and by detection of uncoupled DNA chains sensitive to the action of nucleases [22]. 

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These interesting observations could be explained through the formation of triple helix DNA on the electrode surface. Side- and main-chain atoms may interact with a particular DNA base-pair of another chain or with more than one base-pair supporting each other in interwoven hydrogenbonding networks that stabilize the contacts between the bases, forming a triple helix on the DNA adsorbed to the electrode surface [9-11]. The triple helix DNA is formed by interaction of the ssDNA in the bulk... 

Examples of the various helical forms found in nature are the single helix (RNA), the double helix (DNA), the triple helix (collagen fibrils), and complex multiple helices (myosin, F-actin). Generally, these single and double helices are fairly readily soluble in dilute aqueous salt solution. The triple and complex helices are soluble only if the secondary bonds are broken. 

A novel approach to specific binding involves the use of triple-helix affinity capture [26,27]. Triple-helix DNA has proven to be a useful approach to... 

The importance of Gly at every third residue is seen when a mutation in the DNA leads to the incorporation of a different amino acid at just one position in the 1000 residue polypeptide chain. For example, if a mutation leads to the incorporation of Cys instead of Gly, the triple helix is disrupted as the -CH2-SH side-chain of Cys is too large to fit in the interior of the triple helix. This leads to a partly unfolded structure that is susceptible to excessive hydroxy-lation and glycosylation and is not efficiently secreted by the fibroblast cells. This, in turn, results in a defective collagen structure that can give rise to brittle bones and skeletal deformities. A whole spectrum of such mutations... 

Keiderling reported the VCD spectra of triple helices in ribonucleic acids by investigating the temperature dependent VCD features of a mixture of poly(rA) and poly(rU) [54]. The spectra of the triple helix are more complicated than those of a double strand, as expected. We have reported the VCD of a number of oligo deoxynu-cleotides with between four and twelve base pairs. These studies will be elaborated upon after a detailed discussion of the VCD features of polymeric DNA and RNA samples, for which the solution structures are well established. 

DNA supercoiling provides conformational potential energy for DNA tertiary structure formation such as the development of DNA cruciform structures (Figure 1.77). Supercoiling also leads to the creation of DNA triple helix (DNA triplex) structures, which form when an oligodeoxynucleotide chain, with an appropriately complementary deoxynucleotide residue... 

The non-natural pyrid[2,3-d] pyrimidine nucleoside (195) pairs preferentially with guanine and adenine in DNA but specifically recognises AT base pairs within the triple helix structure. It is thought that this sequence specificity may be caused by the ability of the nucleoside to adopt different tautomeric forms. 

A counterion polarization mechanism has been proposed to explain the electric induction of conformational changes in polyelectrolyte complexes such as the (U A U) triple helix. In accordance with this idea, the external electric field shifts the ionic atmosphere of the (U A U) complex and thereby induces a dipole moment. At the negative pole of the induced macrodipole, the screening by the ion cloud of the negative phosphate residues is reduced. This, in turn, causes repulsion between the ends of the polyanions and leads finally to the unwinding of the triple helix. It later came to our attention that a polarization mechanism had already been proposed for strand separation of DNA by Poliak and Rein. " ... 

By employing the triple helix catenation approach, more complex supramolecular plasmid DNA architectures proved to be accessible. Two different plasmids were catenated by a dumbbell-shaped ODN (Figure 35.8c) [52], an architecture that was realized by first winding an ss DNA loop with an adjacent stem structure around each of the two plasmids, making use of triple hehx formation. In a second step, the 5 sticky ends protruding from the two stems that were complementary to each other were first hybridized and then connected covalently with the help of T4 DNA ligase. In this way, a 130-mer DNA dumbbell interlocked two plasmids with sizes of 3050 and 4079bp, respectively. 

The triple helix is another type of superstructure of DNA [91]. A-T-T (A-T-U) and G-C-C base-trimers are formed by combination of Watson-Crick and Hoogsteen-type hydrogen bonding. Base-trimers are formed in the DNA-mimetic system at the air-water interface between the Watson-Crick-type monolayer and... 

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