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The DNA three-way junction serves as a scaffold for the molecular organization of non-nucleosidic alkynylpyrene and perylenediimide chromophores located at the branch point of the structure. Depending on the composition of the tripartite assembly, the constructs possess distinct spectroscopic properties, ranging from monomer or excimer fluorescence to completely quenched tripartite aggregates.

The electronic absorption, fluorescence, and excitation spectra of furo[3,4-c]furanone (1) have been measured in different solvents at different concentrations. We observed a complex dependence of absorption and excitation spectra as a function of the concentration in CH(2)Cl(2) and THF due to aggregate formation. Interestingly, the fluorescence spectra were not affected. Resolving the puzzle was made possible by the fact that 1 fits perfectly into the channels of zeolite L (ZL) microcrystals to form 1-ZL guest-host composites. The geometry of the ZL channel system ensures a well-defined orientation of the embedded dye molecules, thereby leading to a preferred orientation of their electronic transition dipole moment (ETDM) and thus to objects with pronounced optical anisotropy properties. This enabled us to understand that in solution the monomers that are present at low concentration form an aggregate in which the molecules sit on top of each other and arrange into a J-type aggregate configuration at higher concentrations. The signature of the latter is observed in the 1-ZL composites. This seems to be the first example in which the insertion of molecules into a nanochannel microcrystal has helped in understanding the weak intermolecular interactions that take place in solution.

The photophysics of free pyrenedicarboxamide (Py-DCA) in solution as well as of single-stranded and double-stranded oligonucleotides (ss and ds ONs) containing 1-7 pyrene building blocks per strand were studied by steady-state and time-resolved fluorescence spectroscopy. It was found that the fluorescence quantum yield Phi(F) of free Py-DCA chromophore in solution is rather high (Phi(F) = 0.44). However, after incorporation of the chromophore into a ss ON the monomeric chromophore fluorescence is quenched more than 40-fold due to electron-transfer reactions with ON bases. An increase of the number n of neighboring pyrenes in an ON results in Phi(F) growth up to 0.25 at n = 6. Starting from n = 2, all fluorescence belongs mainly to excimer formed by pyrene chromophores. Sections composed of multiple pyrenes may be considered as robust functional entities that may serve as independent modules in DNA-based, functional nano-architectures.

The self-organization of oligopyrene foldamers is described. Bi- and tri-segmental oligomers composed of nucleotides and non-nucleosidic, achiral pyrene monomers form double-stranded helical structures, as shown by absorbance, fluorescence, and CD spectroscopy. The mixed nature of alternating aromatic and phosphate groups ensures water solubility which, in turn, favors folding of the aromatic units. Pyrene molecules also assemble though interstrand stacking interactions. Structural organization of the pyrene units is an intrinsic property of the oligoaryl part and takes place independently from the sequence of the attached DNA. Chirality transfer from DNA to the pyrene segment leads to formation of a double helix, in which neighboring pyrene units are, in the present case, twisted in a right-handed manner. Pyrene helicity is most pronounced in a bi-segmental chimera, in which a DNA stem is present only at one end of the pyrene section.

Synthesis of 1,6- and 1,8-triazolylpyrenes and their incorporation into oligonucleotides is described. In hybrids, triazolylpyrenes adopt interstrand stacking interactions. Exciton coupling is observed for the duplex containing a pair of the 1,6-isomer indicating a well-defined helical arrangement of the triazolylpyrene building blocks. Triazole substitution results in pronounced red-shifts of monomer as well as excimer fluorescence. Furthermore, quantum yields of the formed excimers are remarkably high.

The construction of natural product-like, tricyclic compounds is reported. Starting from a D-(-)-ribose-derived dihydrofurane, the tricyclic scaffold is prepared via an intramolecular hetero-Diels-Alder reaction. The reaction proceeds with very high diastereoselectivity through an endo transition state, as established on the basis of X-ray structural analysis of the products. Further modification and derivatization of the obtained products is described.