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Anal Biochem. 2007 Jul 15;366(2):126-30. Epub 2007 Mar 13.

Stem-loop probe with universal reporter for sensing unlabeled nucleic acids.

Author information

1
Department of Chemistry, College of Science, University of Nevada, Reno, NV 89557, USA. tchang@unr.edu

Abstract

In this article, we present the design principles and application of a motif composed of a stem-loop probe (SP) hybridized to a fluorescently labeled universal reporter (UR) for sensing unlabeled nucleic acids. At room temperature, SP-UR is in the hairpin-closed form in which the fluorophore of UR is in proximity to the G bases of the hairpin, where consequently the fluorescent emission is quenched significantly. On hybridization with target, SP-UR is trapped in the hairpin-opened configuration in which the fluorophore and the G quenchers are apart. This turns off quenching, increases emission intensity, and signals the presence of target. Compared with the common approach that employs an oligonucleotide probe with a covalently linked fluorophore, the use of a fluorescently labeled universal reporter strand hybridized to an unlabeled stem-loop probe provides a more efficient approach to the fabrication of nucleic acid sensors and microarrays potentially useful for real-time analysis.

PMID:
17509514
DOI:
10.1016/j.ab.2007.03.006
[Indexed for MEDLINE]

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