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This study developed an adenosine-based molecular beacon (MB) for selective and sensitive detection of heparin at room temperature based on the fact that electrostatic attraction between heparin and coralyne is much stronger than coordination between the stem of MB and coralyne in the presence of high concentration of NaCl.The designed MB (A12-MB-A12) contains a 22-mer loop and a stem of a pair of 12-mer adenosine (A) bases,a carboxyfluorescein (FAM) unit at the 5-end,and a 4-([4-(dimethylamino)phenoyl]azo)- benzoic acid (DABCYL) unit at the 3-end.Through the A2-coralyne-A2 coordination,coralyne causes conformation change of A12-MB-A12 from a random coil to a hairpin structure.A hairpin-shaped MB places FAM and DABCYL in proximity to each other,resulting in the collisional quenching of fluorescence between two organic dyes.When a hairpin-shaped MB encounters heparin,the formed complex of coralyne and heparin forces the stem apart.Such as conformational change in MB leads to the restoration of FAM fluorescence.Under the optimal conditions (10 nM A12-MB-A12,4 μM coralyne,and 150 mM NaCl),the selectivity of this probe is more than 100-fold for heparin over hyaluronic acid and chondroitin sulfate; the limit of detection at a signal-to-noise ratio of 3 for heparin was determined to be 60 ng/mL (~3 nM).To the best of our knowledge,this is first example for the quantification of heparin using an adenosine-based molecular beacon.The practicality of using coralyne- A12-MB-A12 complex to determination of heparin in serum is also validated.