New hairpin-structured DNA probes: alternatives to classical molecular beacons

Achim Friedrich; Gregor Habl; Markus Sauer; Jürgen Wolfrum; Jörg Hoheisel; Nicole Marmé; Jens-Peter Knemeyer

doi:10.1117/12.700346

14 February 2007 New hairpin-structured DNA probes: alternatives to classical molecular beacons

Achim Friedrich, Gregor Habl, Markus Sauer, Jürgen Wolfrum, Jörg Hoheisel, Nicole Marmé, Jens-Peter Knemeyer

Proceedings Volume 6444, Ultrasensitive and Single-Molecule Detection Technologies II; 64440M (2007) https://doi.org/10.1117/12.700346
Event: SPIE BiOS, 2007, San Jose, California, United States

Abstract

In this article we report on two different classes of self-quenching hairpin-structured DNA probes that can be used as alternatives to Molecular Beacons. Compared to other hairpin-structured DNA probes, the so-called smart probes are labeled with only one extrinsic dye. The fluorescence of this dye is efficiently quenched by intrinsic guanine bases via a photo-induced electron transfer reaction in the closed hairpin. After hybridization to a target DNA, the distance between dye and the guanines is enlarged and the fluorescence is restored. The working mechanism of the second class of hairpin DNA probes is similar, but the probe oligonucleotide is labeled at both ends with an identical chromophore and thus the fluorescence of the closed hairpin is reduced due to formation of non-fluorescent dye dimers. Both types of probes are appropriate for the identification of single nucleotide polymorphisms and in combination with confocal single-molecule spectroscopy sensitivities in the picomolar range can be achieved.

Citation Download Citation

Achim Friedrich, Gregor Habl, Markus Sauer, Jürgen Wolfrum, Jörg Hoheisel, Nicole Marmé, and Jens-Peter Knemeyer "New hairpin-structured DNA probes: alternatives to classical molecular beacons", Proc. SPIE 6444, Ultrasensitive and Single-Molecule Detection Technologies II, 64440M (14 February 2007); https://doi.org/10.1117/12.700346

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