A highly organized helical pi-stacked arrangement of 1-ethynylpyrene moieties along the major groove of duplex DNA can only be achieved if more than three chromophores have been synthetically incorporated adjacent to each other.

Ultrafast structural dynamics concomitant to excitation energy transfer in DNA has been studied using a pair of pyrene-labeled DNA bases. The temporal evolution of the femtosecond pump-probe spectra reveals the existence of two electronic coupling pathways, through-base stack and through-space, which lead to excitation energy transfer and excimer formation even when the labeled DNA bases are separated by one AT base pair. The electronic coupling which mediates through-base stack energy transfer is so strong that a new absorption band arises in the excited-state absorption spectrum within 300 fs. From the analysis of time-dependent spectral shifts due to through-space excimer formation, the local structural dynamics and flexibility of DNA are characterized on the picosecond and nanosecond time scale.

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The synthetic incorporation of indole as an artificial DNA base into oligonucleotides by two different structural approaches is described. For both types of modification, the indole moiety is attached through the C-3 position to the oligonucleotides. As a mimic of natural nucleosides, the indole nucleoside of β-2Ј-deoxyribofuranoside (In) was synthesized. The corresponding In-modified duplexes were compared with duplexes that contained the indole group connected through (S)-3-amino-1,2-propanediol as an acyclic linker between the phosphodiester bridges of the oligonucleotides. This linker was tethered to the C-3 position of the indole heterocycle either directly (InЈЈ) or by a carbamate function (InЈ). The melting temperatures of the corresponding indole-modi-