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Proceedings Paper

New hairpin-structured DNA probes: alternatives to classical molecular beacons
Author(s): Achim Friedrich; Gregor Habl; Markus Sauer; Jürgen Wolfrum; Jörg Hoheisel; Nicole Marmé; Jens-Peter Knemeyer
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Paper 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.

Paper Details

Date Published: 14 February 2007
PDF: 7 pages
Proc. SPIE 6444, Ultrasensitive and Single-Molecule Detection Technologies II, 64440M (14 February 2007); doi: 10.1117/12.700346
Show Author Affiliations
Achim Friedrich, German Cancer Research Ctr. (Germany)
Gregor Habl, Univ. of Heidelberg (Germany)
Markus Sauer, Univ. of Bielefeld (Germany)
Jürgen Wolfrum, Univ. of Heidelberg (Germany)
Jörg Hoheisel, German Cancer Research Ctr. (Germany)
Nicole Marmé, Univ. of Heidelberg (Germany)
Jens-Peter Knemeyer, German Cancer Research Ctr. (Germany)

Published in SPIE Proceedings Vol. 6444:
Ultrasensitive and Single-Molecule Detection Technologies II
Jorg Enderlein; Zygmunt K. Gryczynski, Editor(s)

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