The photochemical properties of various alkynylpyrene derivatives have been investigated in detail with a view to developing a new class of pyrene-based biomolecular probes. The absorption maxima of the alkynylpyrenes were seen to be shifted to longer wavelengths compared with those of the unsubstituted parent pyrene. Fluorescence quantum yields of the alkynylpyrenes dramatically increased up to 0.99 in ethanol, and only slight quenching of the fluorescence occurred even under aerated conditions. The alkynylpyrenes have been successfully introduced into representative biomolecules such as peptides, proteins, and DNAs. The detectabilities of the labeled biomolecules were significantly improved, with the unique photochemical characteristics of the pyrene nucleus being maintained.

The Sonogashira coupling of γ-CD-encapsulated alkynylpyrenes with terphenyl-type stopper molecules gave a doubly alkynylpyrene-threaded [4]rotaxane. The rotaxane showed only excimer emission, with a high fluorescence quantum yield of Φf =0.37, arising from the spatially restricted excimer within the cavity of the γ-CD. The excimer emission suffered little from self-quenching up to a concentration of 1.5×10(-5)  M and was circularly polarized with a high glum  value of -1.5×10(-2) . The strong circularly polarized luminescence may result from the two stacked pyrenes existing in the rotaxane in an asymmetrically twisted manner.

Conformational transitions of biopolymers are well-known to be affected by noncovalent interactions with small molecules. We found that synthetic polymers, poly- and oligo(meta-ethynylpyridine)s, are guided to helical structures by uncharged hydrogen-bonding interactions with saccharides enclosed in the inner sphere of the polymers. Circular dichroism (CD) studies revealed that chirality of saccharide was transferred to the helical sense of the polymers. Among the n-octyl pyranosides of naturally important hexoses, beta-glucoside induced CDs most effectively. Size-regulated 18-mer and longer oligomers also showed the induced CDs similar to those for the polymers. Furthermore, native monosaccharides were extracted into less polar organic solvent with the help of the polymers, inducing similar CD signals.

A new class of molecular beacons were developed in which pyrene fluorophores were connected both at 3' and 5' ends of a single-stranded oligonucleotide. The two pyrene-based fluorophores were synthesized from the same starting material, so that the preparation of the beacons was simplified. The detection strategy of the beacons for target DNAs is based on "excimer-monomer emission switching" of the pyrene fluorophores: excimer emission of the pyrene moieties changed to monomer one when the beacons hybridized with the targets. This type of two-state mode of fluorescence allows unambiguous detection of the target DNAs because strict 1:1 correlation between the nonhybridized and the hybridized beacons can be monitored by the presence of isoemissive points of the fluorescence changes. The beacons can detect target 19-mer DNAs and can discriminate the targets from their single-nucleotide mismatches at 1 nM concentration. Advantages of the excimer-monomer switching molecular beacons were discussed in comparison with conventional ones.

Establishing a reliable genotyping protocol is a critical matter in postsequence genetics. In this article, we describe a highly sensitive electrochemical detection of complementary DNAs (up to 43-mer) based on hole transport with molecular-scale, ''wire-like'' DNA probes. The presence of a single-base mismatch in the DNA duplexes caused a dramatic decrease in the electrochemical response. We applied this method to detect all of the possible transition and transversion SNPs and achieved ''on-off''-type discrimination of fully complementary DNAs from their SNPs. Furthermore, naturally occurring polymorphisms, ''hot spots'' from the p53 gene, could clearly be distinguished from wild type by using our methodology.electrochemistry ͉ hole transport ͉ ferrocene ͉ gold electrode

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Co-oligomers involving (1H)-4-pyridone and 4-alkoxypyridine rings were studied, and it was found that their supramolecular transformation was caused by saccharide recognition. In the co-oligomers, pyridone and pyridine rings are alternately linked at their 2,6-position with an acetylene bond. The pyridine rings behave as a hydrogen bonding acceptor, and the pyridone rings and tautomerized 4-pyridinol work as a donor. Pyridine-pyridone-pyridine 3-mer was found to self-dimerize on the basis of vapor pressure osmometry in CHCl(3), and the association constant was obtained as 2.3 x 10(3) M(-1) by (1)H NMR titration. Longer 5-, 7-, 9-, and 11-mer oligomers showed considerable broadening and anisotropy in the (1)H NMR spectra due to self-association. These longer oligomers recognized octyl beta-D-glucopyranoside and changed their form into a chiral helical complex, showing characteristic circular dichroism.

Novel ferrocene-modified artificial nucleobase receptors were designed and synthesized. The nucleobase receptors possess hydrogen-bonding and pi-stacking interaction sites that act simultaneously for binding to 1-butylthymine utilizing the pivot character of the ferrocene skeleton. Diamidopyridine was chosen for the hydrogen-bonding moiety, and various polynuclear aromatics were used for pi-stacking one. The two components were tethered to the cyclopentadienyl rings via ethynediyl and oxymethylene spacers. The binding affinity of the receptors to 1-butylthymine was found to be dependent on the aromatic structures. Thus, the association constants for perylene-linked receptors were approximately doubled compared to those of aromatic-free ones, an energy difference of approximately 0.5 kcal/mol. Detailed comparisons between the 10 receptors clarified the value of the pivot character of the ferrocene for construction of the intermolecular interaction site.