Duplex-triplex transition

Triple-helix formation by G-rich oligonncleotides is supported by Mg + but strongly inhibited by physiological concentrations of certain monovalent cations, especially K+, most likely dne to oligonncleotide self-association in competitive structures such as guanine-quadruplexes. " Variation of the cation enviromnent can differentially promote the assembly of multistranded nncleic acid structural alternatives. For example, by specifically counteracting the induction/stabilization of quadruplex structures by potassium ions, certain divalent ions (i.e. Mn +, Co +, and Ni + but not Mg +) at low millimolar concentrations allow triplex formation in the presence of 150mMK+. In contrast, certain mono- and divalent metal ions can promote the transition from Watson-Crick duplexes to G4 quadruplex structures relatively efficiently K" " > Ca + >... 

The rich coordination chemistry of transition metal ions has been used not only to create metal-ligand complexes that play the role of alternative nucleo-base pairs within nucleic acid duplexes, but also to influence the secondary structure adopted by the nucleic acid, for example, hairpin, duplex, or triplex, and to create connectors for such nucleic acid structures. In this context, oligonucleotides that contain terminal ligands can lead to structures distinct from those accessible by using centrally-modified oligonucleotides, such as cyclic structures or hairpins (Fig. 3). 

CD has been used extensively for following conformational transitions in DNA, such as denaturation and transitions from B A and B — Z DNA. In addition, the CD of DNA triplexes has features which are distinct from those of the duplex. Some of these important applications of CD to the study of DNA have been described by Gray et in this volume. 

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