Consideration of end effects of DNA hybridization in selection of fluorescent dyes for development of optical biosensors

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Abstract

Intercalating fluorescent dyes are in widespread use to detect the presence of double-stranded DNA. Applications include the development of biosensors that rely on the attachment ("tethering") of a dye molecule by a short hydrocarbon chain to the terminus of a strand of DNA so that dye is continuously available and the biosensor is fully reversible. Double strands of DNA have end effects that limit the stability of hybridization and dye intercalation near the termini of the duplexes. Therefore, the selection of the dye must be based on consideration of spectroscopic properties and also issues associated with tether length and the stoichiometry of the binding of the dye with double- and single-stranded DNA. Ethidium bromide (EB) has been used extensively to detect hybridization of DNA in applications such as electrophoresis, gene chips, and biosensors. A number of dyes with greater quantum efficiency than EB for detection of hybridization have been reported. Furthermore, other practical spectroscopic advantages can be gained in terms of improved S/N by use of dyes that have excitation that is red shifted relative to EB. Pyrilium iodide has been disclosed as an intercalator of high quantum efficiency and long excitation wavelength. This work investigates pyrilium iodide in comparison to EB as a candidate for preparation of a tethered dye for detection of hybridization of DNA 20-mers.Key words: biosensors, DNA, hybridization, fluorescence, end effects.

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