Displacement assay for detection of small molecules

Abstract

Complex of an anti-cocaine aptamer and the dye diethylthiotricarbocyanine behaves as a colorimetric sensor with attenuation in absorbance at 760 nm for cocaine in the concentration range of 2-5000 μM. Mechanistic studies indicate an intermolecular displacement of the dye as the mechanism of action of the sensor. As the dye is insoluble in buffer, cocaine binding can be detected as displaced dye precipitates and supernatant decolorizes.

We claim:  
     
         1 . A sensor for detecting the presence of a compound, which comprises an oligonucleotide receptor capable of binding to the compound, wherein the receptor comprises a dye attached to the receptor which is released when the receptor binds to the compound.  
     
     
         2 . The sensor of  claim 1 , wherein the compound is a small molecule.  
     
     
         3 . The sensor of  claim 1 , wherein the compound is a polypeptide.  
     
     
         4 . The sensor of  claim 1 , wherein the compound is a protein.  
     
     
         5 . The sensor of  claim 1 , wherein the compound is cocaine.  
     
     
         6 . The sensor of  claim 1 , wherein the receptor comprises DNA.  
     
     
         7 . The sensor of  claim 1 , wherein the receptor comprises RNA.  
     
     
         8 . The sensor of  claim 1 , wherein the receptor comprises a hydrophobic pocket which binds the compound.  
     
     
         9 . The sensor of  claim 8 , wherein the hydrophobic pocket comprises a noncanonical three-way junction.  
     
     
         10 . The sensor of  claim 1 , wherein the receptor comprises a plurality of stems, wherein one or more stems comprises complementary nucleotide base pairing.  
     
     
         11 . The sensor of  claim 1 , wherein the receptor comprises a plurality of stems, wherein the structive of one or more stems excludes complementary nucleotide base pairing.  
     
     
         12 . The sensor of  claim 1 , wherein the attachment of the dye to the receptor comprises a covalent bond.  
     
     
         13 . The sensor of  claim 1 , wherein the attachment of the dye to the receptor comprises a non-covalent bond.  
     
     
         14 . The sensor of  claim 1 , wherein a plurality of dye molecules are attached to the receptor.  
     
     
         15 . The sensor of  claim 1 , wherein the dye is a cyanine dye.  
     
     
         16 . The sensor of  claim 1 , wherein the dye is diethylthiotricarbocyanine iodide.  
     
     
         17 . The sensor of  claim 1 , wherein the absorbance of the dye is attenuated when the dye is released.  
     
     
         18 . The sensor of  claim 1 , wherein the absorbance of the dye is enhanced when the dye is released.  
     
     
         19 . The sensor of  claim 1 , wherein the wavelength of absorbance of the dye is modified when the dye is released.  
     
     
         20 . The sensor of  claim 1 , wherein the released dye is insoluble in solution.  
     
     
         21 . The sensor of  claim 1 , wherein the released dye is detected with a visual indicator.  
     
     
         22 . The sensor of  claim 1 , wherein the released dye precipitates and the supernatant decolorizes.  
     
     
         23 . The sensor of  claim 1 , wherein the dye has a fluorescence property which is changed when the dye is released.  
     
     
         24 . A method of detecting the presence of a compound in solution which comprises: 
 (a) providing an oligonucleotide receptor with an attached dye    (b) contacting the oligonucleotide receptor with the compound,    (c) releasing the dye from the oligonucleotide receptor, and    (d) detecting the presence of the released dye, 
 wherein the presence of the released dye indicates the presence of the compound in the solution.  
   
     
     
         25 . The method of  claim 24 , wherein the compound is a small molecule.  
     
     
         26 . The method of  claim 24 , wherein the compound is a polypeptide.  
     
     
         27 . The method of  claim 24 , wherein the compound is a protein.  
     
     
         28 . The method of  claim 24 , wherein the compound is cocaine.  
     
     
         29 . The method of  claim 24 , wherein the receptor comprises DNA.  
     
     
         30 . The method of  claim 24 , wherein the receptor comprises RNA.  
     
     
         31 . The method of  claim 24 , wherein the receptor comprises a hydrophobic pocket which binds the compound.  
     
     
         32 . The method of  claim 31 , wherein the hydrophobic pocket comprises a noncanonical three-way junction.  
     
     
         33 . The method of  claim 24 , wherein the receptor comprises a plurality of stems, wherein one or more stems comprises complementary nucleotide base pairing.  
     
     
         34 . The method of  claim 24 , wherein the receptor comprises a plurality of stems, wherein the structure of one or more stems excludes complementary nucleotide base pairing.  
     
     
         35 . The method of  claim 24 , wherein the attachment of the dye to the receptor comprises a covalent bond.  
     
     
         36 . The method of  claim 24 , wherein the attachment of the dye to the receptor comprises a non-covalent bond.  
     
     
         37 . The method of  claim 24 , wherein a plurality of dye molecules are attached to the receptor.  
     
     
         38 . The method of  claim 24 , wherein the dye is a cyanine dye.  
     
     
         39 . The method of  claim 24 , wherein the dye is diethylthiotricarbocyanine iodide.  
     
     
         40 . The method of  claim 24 , wherein the absorbance of the dye is attenuated when the dye is released.  
     
     
         41 . The method of  claim 24 , wherein the absorbance of the dye is enhanced when the dye is released.  
     
     
         42 . The method of  claim 24 , wherein the wavelength of absorbance of the dye is modified when the dye is released.  
     
     
         43 . The method of  claim 24 , wherein the released dye is insoluble in solution.  
     
     
         44 . The method of  claim 24 , wherein the released dye is detected with a visual indicator.  
     
     
         45 . The method of  claim 24 , wherein the released dye precipitates and the supernatant decolorizes.  
     
     
         46 . The method of  claim 24  wherein the dye has a fluorescence property which changes when the dye is released.  
     
     
         47 . A method of determining the concentration of a compound in solution which comprises: 
 (a) providing an oligonucleotide receptor with an attached dye    (b) contacting the oligonucleotide receptor with the compound,    (c) releasing the dye from the oligonucleotide receptor, and    (d) measuring a change in absorbance of the dye, 
 wherein the change in absorbance indicates the concentration of the compound in solution.  
   
     
     
         48 . The method of  claim 47 , wherein the compound is a small molecule.  
     
     
         49 . The method of  claim 47 , wherein the compound is a polypeptide.  
     
     
         50 . The method of  claim 47 , wherein the compound is a protein.  
     
     
         51 . The method of  claim 47 , wherein the compound is cocaine.  
     
     
         52 . The method of  claim 47 , wherein the receptor comprises DNA.  
     
     
         53 . The method of  claim 47 , wherein the receptor comprises RNA.  
     
     
         54 . The method of  claim 47 , wherein the receptor comprises a hydrophobic pocket which binds the compound.  
     
     
         55 . The method of  claim 54 , wherein the hydrophobic pocket comprises a noncanonical three-way junction.  
     
     
         56 . The method of  claim 47 , wherein the receptor comprises a plurality of stems, wherein one or more stems comprises complementary nucleotide base pairing.  
     
     
         57 . The method of  claim 47 , wherein the receptor comprises a plurality of stems, wherein the structure of one or more stems excludes complementary nucleotide base pairing.  
     
     
         58 . The method of  claim 47 , wherein the attachment of the dye to the receptor comprises a covalent bond.  
     
     
         59 . The method of  claim 47 , wherein the attachment of the dye to the receptor comprises a non-covalent bond.  
     
     
         60 . The method of  claim 47 , wherein a plurality of dye molecules are attached to the receptor.  
     
     
         61 . The method of  claim 47 , wherein the dye is a cyanine dye.  
     
     
         62 . The method of  claim 47 , wherein the dye is diethylthiotricarbocyanine iodide.  
     
     
         63 . The method of  claim 47 , wherein the absorbance of the dye is attenuated when the dye is released.  
     
     
         64 . The method of  claim 47 , wherein the absorbance of the dye is enhanced when the dye is released.  
     
     
         65 . The method of  claim 47 , wherein the wavelength of absorbance of the dye is modified when the dye is released.  
     
     
         66 . The method of  claim 47 , wherein the released dye is insoluble in solution.  
     
     
         67 . The method of  claim 47 , wherein the released dye is detected with a visual indicator.  
     
     
         68 . The method of  claim 47 , wherein the released dye precipitates and the supernatant decolorizes.  
     
     
         69 . The method of  claim 47 , wherein the dye has a fluorescence property which changes when the dye is released.