title: Aptamer beacons for the direct detection of proteins.
abstract: 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.
authors.affiliation: Rosenstiel Basic Medical Sciences Research Center MS-029, Brandeis University, Waltham, Massachusetts 02454, USA.
authors.forename: N
authors.initials: N
authors.lastname: Hamaguchi
authors.forename: A
authors.initials: A
authors.lastname: Ellington
authors.forename: M
authors.initials: M
authors.lastname: Stanton
mesh_terms: D002942:Circular Dichroism; D005456:Fluorescent Dyes / Q000378:metabolism; D008024:Ligands; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry / Q000378:metabolism*; D011485:Protein Binding; D013050:Spectrometry, Fluorescence / Q000379:methods; D013917:Thrombin / Q000737:chemistry / Q000378:metabolism
chemical_list: D005456:Fluorescent Dyes; D008024:Ligands; D009841:Oligonucleotides; D013917:Thrombin