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US 2009/0275142 A1Published application
Compositions and methods for biodetection by nucleic acid-templated chemistry
AssigneeEnsemble Therapeutics Corporation
InventorsYumei Huang, James M. Coull
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Abstract
The invention provides compositions and methods for the detection of biological targets, (e.g. nucleic acids and proteins) by nucleic acid-templated chemistry, for example, by generating fluorescent polymethine dyes.
Claims20
An improved method for detecting a target analyte, wherein the improvement comprises producing a polymethine dye via an aldol condensation between an aldehyde and an active hydrogen component in an aqueous condition in the presence of an organocatalyst, wherein the aldol condensation reaction comprises:
- wherein:
- Z′ is O, S, Se, P, NH2, N(alkyl), or C(CH3)2;
- n is 0, 1, or 2;
- R is H or alkyl;
- R′ is phenyl, N-heterocycle, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- R″ is H, alkyl, an alkyl carboxylic acid, or a linked nucleic acid;
- R′″ is CH3 or a linked nucleic acid;
- and
- the organocatalyst is a secondary amine, a primary amine, or a bifunctional amine-acid catalyst, wherein production of the polymethine dye is indicative of the presence of the target analyte.
6 more elements
(canceled)
7-27. (canceled)
A hemicyanine dye of formulae I-V, wherein formula I is represented by:
- wherein:
- Z′ is O, S, Se, P, NH2, N(alkyl), or C(CH3)2;
- n is 0, 1, or 2;
- R is H or alkyl;
- R′ is phenyl, N-heterocycle, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- and
- R″ is H, alkyl, or an alkyl carboxylic acid;
- wherein formula II is represented by:
- wherein:
- Z′ is O, S, Se, P, NH2, N(alkyl), or C(CH3)2;
- n is 0, 1, or 2;
- R is H or alkyl;
- R′ is phenyl, N-heterocycle, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- R″ is a linked nucleic acid;
- and
- R′″ is a linked nucleic acid;
- wherein formula III is represented by:
- wherein:
- n1 is 1, 2, 3, 4, or 5;
- n2 and n3 are 0 to 16;
- Z1 is O, S, Se, P, NH2, N(alkyl), or C(CH3)2;
- Z2 is benzene or an N-heterocycle;
- R1 is H or alkyl;
- R2 is phenyl, N-heterocycle, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- and
- R3 is any substituted benzyl or higher fused benzyl rings, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- wherein formula IV is represented by:
- wherein:
- n1 is 1, 2, 3, 4, or 5;
- n2 and n3 are 0 to 16;
- R1 is alkyl;
- R2 is phenyl, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- and
- R3 is phenyl, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- and
- wherein formula V is represented by:
- wherein:
- n1 is 1, 2, 3, 4, or 5;
- n2 and n3 are 0 to 16;
- R1 is alkyl;
- R2 is phenyl, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- and
- R3 is phenyl, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl.
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A compound of formulae VI-XIII, wherein formula VI is represented by:
- wherein:
- n is 0, 1, or 2;
- R is H or alkyl;
- R′ is phenyl, N-heterocycle, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- R″ is H, alkyl, an alkyl carboxylic acid, or a linked nucleic acid;
- wherein formula VII is represented by:
- wherein:
- Z′ is O, S, Se, P, NH2, N(alkyl), or C(CH3)2;
- n is 0, 1, or 2;
- R′″ is CH3 or a linked nucleic acid;
- wherein formula VIII is represented by:
- wherein:
- Z1 is O, S, Se, P, NH2, N(alkyl), or C(CH3)2;
- Z2 is benzene or an N-heterocycle;
- R is a substituted benzyl or higher fused benzyl rings, H, alkyl, —SO3H, —OH, CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- and
- n is 0 to 16;
- wherein formula IX is represented by:
- wherein:
- n1 is 1, 2, 3, 4, or 5;
- n2 is 0 to 16;
- R1 is H or alkyl;
- and
- R2 is phenyl, N-heterocycle, H, alkyl, —SO3H, OH, CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- wherein formula X is represented by:
- wherein:
- n1 is 1, 2, 3, 4, or 5;
- n2 is 0 to 16;
- R1 is alkyl;
- and
- R2 is phenyl, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- wherein formula XI is represented by:
- wherein:
- n1 is 1, 2, 3, 4, or 5;
- n2 is 0 to 16;
- R1 is alkyl;
- and
- R2 is phenyl, H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- wherein formula XII is represented by:
- wherein:
- n is 0 to 16;
- and
- R is H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl;
- and
- wherein formula XIII is represented by:
- wherein:
- n is 0 to 16;
- and
- R is H, alkyl, —SO3H, —OH, —CN, Cl, Br, —NO2, —NH2, —N(alkyl)2, or —O-alkyl.
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Dependencies are inferred from the claim text.