Multistep Energy Transfer in Single Molecular Photonic Wires

Abstract

A photonic wire is a molecular device that conveys excited-state energy from an input to an output unit. 1,2 In contrast to conductive nanowires, photonic wires are addressable at a distance without the need of physical contacts. In 1994, Lindsay and co-workers realized the first molecular photonic wire based on conjugated porphyrin arrays. 1 However, strongly coupling porphyrin arrays exhibit the disadvantage of forming so-called energy sinks due to different local interactions of the chromophores. 3 Furthermore, as molecular photonic wires have to operate at the single molecule level they have to be studied at this individual level as well. Therefore, the chromophores used have to exhibit special spectroscopic characteristics, such as high photostability and fluorescence quantum yield. The ideal photonic wire consists of a very regular arrangement of chromophores which allows for efficient energy transfer but prevents alterations of photophysical properties of the individual chromophores, resulting in the formation of energy sinks.In this communication, we report on the development of a molecular photonic wire based on (i) the use of conventional chromophores with high fluorescence quantum yield, (ii) an energy cascade as the driving force for the excited-state energy to ensure unidirectionality, and (iii) an arrangement of the chromophores such that strong electronic interactions promoting fluorescence quenching are prevented. Because of the unique molecular recognition properties and the scaffoldlike structure, double-stranded DNA constitutes an ideally suited building block on which to base the construction of nanoscale molecular devices. In addition, the use of DNA offers many well-developed labeling and post-labeling strategies to introduce a variety of different chromophores in a modular conception, i.e., short oligonucleotides carrying the desired chromophores can be selectively hybridized to a complementary template strand (Figure 1). The resulting wire is addressed by excitation of the primary donor, which transfers excited-state energy according to Förster theory 4 by weak dipole-dipole induced chromophore interactions through the transmitter chromophores to the final acceptor. The acceptor releases the transferred energy by emission of a fluorescence photon.To realize a unidirectional photonic wire based on multistep fluorescence resonance energy transfer, five different chromophores were attached covalently to single-stranded DNA fragments of various lengths (60 or 20 bases). Hybridization of the labeled DNA fragments results in a double-stranded 60 base pair (bp) DNA construct containing five chromophores at well-defined positions and distances. To ensure highly efficient fluorescence resonance energy transfer (FRET) without quenching electronic interactions, an interchromophore distance of 10 bp corresponding to 3.4 nm was used. 6 The overall spatial range covered by this photonic wire is 13.6 nm. The spectral range comprises more than 200 nm of the visible spectrum, starting from ∼488 to ∼700 nm...

Quantitative Förster resonance energy transfer efficiency measurements using simultaneous spectral unmixing of excitation and emission spectra

“…This could be useful, for example, when FRET is simultaneously taking place between different types of fluorophores, such as in three-color FRET where the acceptor for transfer from another fluorophore can act as a donor for transfer to a third fluorophore. [38][39][40][41][42][43] Unmixing of both the excitation and emission wavelengths would allow for robust analysis without making any assumptions about how each excitation wavelength excites each fluorophore type.…”

A practical guide to single-molecule FRET

“…A multi-color excitation scheme for further distinguishing different molecular species 83,84 has recently been extended to threecolor FRET 85 . Promise has also been shown for extending FRET further with several fluorophores on single DNA molecules 86 .…”

Generating highly ordered DNA nanostrand arrays

“…On the other hand, 1D nanostructures are of great interest for the construction of future devices (4)(5)(6). With its high aspect ratio, unique base-pairing ability, designable base sequence, and availability of various techniques for functionalization, DNA is a very attractive material for preparing 1D nanostructures for electronic, magnetic, photonic, and chemical sensing applications (7)(8)(9)(10)(11)(12)(13). The ability to position a large number of 1D nanostructures with well defined linear arrangements is a prerequisite for integrating them into functional devices.…”