title: Stem-loop probe with universal reporter for sensing unlabeled nucleic acids.
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.
authors.affiliation: Department of Chemistry, College of Science, University of Nevada, Reno, NV 89557, USA. tchang@unr.edu
authors.forename: Suk-Wah
authors.initials: SW
authors.lastname: Tam-Chang
authors.forename: Travis D
authors.initials: TD
authors.lastname: Carson
authors.forename: Liming
authors.initials: L
authors.lastname: Huang
authors.forename: Nelson G
authors.initials: NG
authors.lastname: Publicover
authors.forename: Kenneth W
authors.initials: KW
authors.lastname: Hunter
mesh_terms: D005456:Fluorescent Dyes / Q000737:chemistry; D008954:Models, Biological; D015394:Molecular Structure; D009690:Nucleic Acid Conformation; D009693:Nucleic Acid Hybridization / Q000379:methods*; D009696:Nucleic Acids / Q000737:chemistry* / Q000235:genetics; D015345:Oligonucleotide Probes / Q000138:chemical synthesis / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D005456:Fluorescent Dyes; D009696:Nucleic Acids; D015345:Oligonucleotide Probes