Compositions and methods for biodetection by nucleic acid-templated chemistry

1. An improved in vitro method for detecting a target analyte having two or more binding sites via nucleic acid-templated chemistry, wherein the improvement comprises:

a) detecting the target analyte by producing a hemicyanine dye having the chemical formula:

via an aldol condensation between an aldehyde having the chemical formula:

and an active hydrogen component having the chemical formula:

in an aqueous condition at room temperature in the presence of an organocatalyst

wherein:

Z′ is O, S, Se, P, NH 2 , N(alkyl), or C(CH 3 ) 2 ;

n is 0, 1, or 2;

R is H or alkyl;

R′ is phenyl, N-heterocycle, H, alkyl, —SO 3 H, —OH, —CN, Cl, Br, —NO 2 , —NH 2 , —N(alkyl) 2 ,

or —O-alkyl;

R″ is a linked nucleic acid;

R′″ is a linked nucleic acid; and

the organocatalyst is a secondary amine, a primary amine, or a bifunctional amine-acid catalyst, and

b) detecting the hemicyanine dye, wherein production of the hemicyanine dye is indicative of the presence of the target analyte.

2. The method of claim 1 , wherein the organocatalyst is a pyrrolidine, a piperidine, a nornicotine, or an analog thereof.

3. The method of claim 1 , wherein the organocatalyst is a valine or a peptide having fewer than 3 amino acid units.

4. The method of claim 1 , wherein the organocatalyst is pyrrolidine/AcOH.

5. The method of claim 1 , wherein the organocatalyst is pyrrolidnylmethyl-pyrrolidine, aminomethylpyrrolidine, dimethylethane-1,2-diamine, propane-1,2-diamine, 1-(2-aminoethyl)-piperidine, or diethylethylene-1,2-diamine.

6. The method of claim 1 , wherein Z′ is C(CH 3 ) 2 .

7. The method of claim 1 , wherein the aldehyde has the following formula:

wherein:

n 1 is 1 or 2;

n 2 is 0 to 16;

R 1 is H or alkyl; and

R 2 is phenyl, N-heterocycle, H, alkyl, —SO 3 H, OH, CN, Cl, Br, —NO 2 , —NH 2 , —N(alkyl) 2 , or —O-alkyl, and the aldehyde produces the hemicyanine dye via the aldol condensation between the aldehyde and the active hydrogen component.

8. The method of claim 1 , wherein the active hydrogen component has the following formula:

wherein:

Z 1 is O, S, Se, P, NH 2 , N(alkyl), or C(CH 3 ) 2 ;

Z 2 is benzene or an N-heterocycle;

n is 0 to 16; and

R is any substituted benzyl or higher fused benzyl rings, H, alkyl, —SO 3 H, —OH, CN, Cl, Br, —NO 2 , —NH 2 , —N(alkyl) 2 , or —O-alkyl.

9. The method of claim 7 , wherein the active hydrogen component has the following formula:

wherein:

Z 1 is O, S, Se, P, NH 2 , N(alkyl), or C(CH 3 ) 2 ;

Z 2 is benzene or an N-heterocycle;

n is 0 to 16; and

R is any substituted benzyl or higher fused benzyl rings, H, alkyl, —SO 3 H, —OH, CN, Cl, Br, —NO 2 , —NH 2 , —N(alkyl) 2 , or —O-alkyl.

10. The method of claim 1 , wherein the nucleic acid of R″ hybridizes to a portion of the nucleic acid of R′″ and the aldehyde reacts with the active hydrogen component to produce a hemicyanine dye.

11. The method of claim 1 , wherein the nucleic acid of R″ is hybridized to a portion of a zip-code oligonucleotide bearing a target binding moiety; and the nucleic acid of R′″ is hybridized to a portion of a zip-code oligonucleotide bearing a target binding moiety.

12. The method of claim 1 , wherein the target analyte is a protein.

13. The method of claim 1 , wherein the target analyte is a nucleic acid.