Aptamer beacons for the direct detection of proteins

Anal Biochem. 2001 Jul 15;294(2):126-31. doi: 10.1006/abio.2001.5169.


We have designed a new class of molecules, which we term aptamer beacons, for detecting a wide range of ligands. Similar to molecular beacons, aptamer beacons can adopt two or more conformations, one of which allows ligand binding. A fluorescence-quenching pair is used to report changes in conformation induced by ligand binding. An anti-thrombin aptamer was engineered into an aptamer beacon by adding nucleotides to the 5'-end which are complementary to nucleotides at the 3'-end of the aptamer. In the absence of thrombin, the added nucleotides will form a duplex with the 3'-end, forcing the aptamer beacon into a stem-loop structure. In the presence of thrombin, the aptamer beacon forms the ligand-binding structure. This conformational change causes a change in the distance between a fluorophore attached to the 5'-end and a quencher attached to the 3'-end. Aptamer beacon can be a sensitive tool for detecting proteins and other chemical compounds.

Publication types

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

MeSH terms

  • Circular Dichroism
  • Fluorescent Dyes / metabolism
  • Ligands
  • Nucleic Acid Conformation*
  • Oligonucleotides / chemistry
  • Oligonucleotides / metabolism*
  • Protein Binding
  • Spectrometry, Fluorescence / methods
  • Thrombin / chemistry
  • Thrombin / metabolism


  • Fluorescent Dyes
  • Ligands
  • Oligonucleotides
  • Thrombin