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

Anal Biochem. 2007 Jul 15;366(2):126-30. doi: 10.1016/j.ab.2007.03.006. Epub 2007 Mar 13.


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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Fluorescent Dyes / chemistry
  • Models, Biological
  • Molecular Structure
  • Nucleic Acid Conformation
  • Nucleic Acid Hybridization / methods*
  • Nucleic Acids / chemistry*
  • Nucleic Acids / genetics
  • Oligonucleotide Probes / chemical synthesis
  • Oligonucleotide Probes / chemistry*
  • Spectrometry, Fluorescence


  • Fluorescent Dyes
  • Nucleic Acids
  • Oligonucleotide Probes