Activity Base-pairing dynamics

We emphasize that the critical ion pair stilbene+, CA in the two photoactivation methodologies (i.e., charge-transfer activation as well as chloranil activation) is the same, and the different multiplicities of the ion pairs control only the timescale of reaction sequences.14 Moreover, based on the detailed kinetic analysis of the time-resolved absorption spectra and the effect of solvent polarity (and added salt) on photochemical efficiencies for the oxetane formation, it is readily concluded that the initially formed ion pair undergoes a slow coupling (kc - 108 s-1). Thus competition to form solvent-separated ion pairs as well as back electron transfer limits the quantum yields of oxetane production. Such ion-pair dynamics are readily modulated by choosing a solvent of low polarity for the efficient production of oxetane. Also note that a similar electron-transfer mechanism was demonstrated for the cycloaddition of a variety of diarylacetylenes with a quinone via the [D, A] complex56 (Scheme 12). 

The fluorescence of 2AP is strongly quenched by nucleic acid bases [17, 18, 24-29]. Time-correlated single-photon counting studies have shown that the interactions of 2AP with different nucleic acid bases significantly decrease the 2AP fluorescence hfetime [17, 24-29]. While the fluorescence lifetime of free 2AP in aqueous solution is about 10 ns, in double-stranded DNA the 2AP hfetimes are reduced to 30-50 ps. This effect has been used extensively to study the dynamics of mismatched base pairs [19, 21, 25, 30], local changes in dynamics of DNA molecules produced by their binding to the active sites of polymerases [26, 31-33], stacking interactions at abasic... 

Ligands that selectively bind to G-quadruplex structures may modulate telom-erase activity, alter telomere structure or repress the transcription of key oncogenes (for a review, see this book s chapters by M. Searle and J.F. Riou). The way ligands interact with quadruplexes also give clues on the dynamics of the G-quartets with the possible exception of a porphyrin derivative, true intercalation (between two quartets) is considered unfavourable or impossible. This indicates that, contrary to DNA base pairs, transient unstacking/opening of two G-quartets is an extremely rare or short event, incompatible with the incorporation of a planar chromophore. End stacking, which does not require the separation of two quartets nor the release of cation is therefore the most frequently observed mode of interaction. ... 

Hereupon, adding to the more static view of those system a more dynamic aspect, it was only a short step to look also for thermotropic behaviour of components, that display interaction activities with nucleic acid bases, so for instance among other base-pair analogues the stereoidal hormones (33,50-55,100-104). 

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