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Unsymmetrical cyanine dimer compounds and their application

a technology of cyanine dimer and compound, applied in the field of unsymmetrical cyanine dimer compound, can solve the problems of inconvenient synthetic method, no fluorescent dye capable of detecting rna, and many steps

Inactive Publication Date: 2005-04-07
MOLECULAR PROBES
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

Embodiments of the present invention provide nucleic acid reporter molecules that are dimers of unsymmetrical cyanine dyes covalently attached by a linker that contains at least one aromatic, heteroaromatic, cyclic or heterocyclic moiety. The linker comprises 3-20 non-hydrogen atoms selected from the group consisting of O, N, S, P and C. The linkers may be flexible, rigid or some degree thereof. The present nucleic acid reporter molecules find utility in detecting nucleic acid polymers wherein the dimer compounds complex with nucleic acid and provide a detectable signal. These nucleic acid polymers are single, double, triple or quadruple stranded DNA or RNA. Typically the DNA is single or double stranded and the RNA is single stranded. In one aspect of the present invention, the nucleic acid reporter molecules detect RNA in the presence of DNA by producing a fluorescent intensity signal that is greater on RNA than on DNA.

Problems solved by technology

However, there still remains no fluorescent dye that is capable of detecting RNA in the presence of DNA for easy and direct detection of RNA.
However, this method is synthetically inconvenient and requires many steps to accomplish the desired results.

Method used

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  • Unsymmetrical cyanine dimer compounds and their application
  • Unsymmetrical cyanine dimer compounds and their application
  • Unsymmetrical cyanine dimer compounds and their application

Examples

Experimental program
Comparison scheme
Effect test

example 1

Preparation of Compound 1

To 52 mg of 2-chloro-4-(2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene-1-phenylquinolinium iodide in 5 mL of methylene chloride, 19 mg of 1,9-nonanedithiol is added followed by 20 μL of triethylamine. The mixture is stirred at room temperature overnight and 3.5 mL of ethyl acetate is then added to precipitate out Compound 1.

example 2

Preparation of Compound 2

A mixture of 150 mg of 2-chloro-4-(2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene-1-phenylquinolinium chloride, 32 mg of 4,7,10-trioxa-1,13-tridecanediamine, and 48 μL of triethylamine is heated in 10 mL of dichloroethane at 40-50 C for 4 hours. The solvent is evaporated and the residue is dissolved in 2 mL of DMF and added to 0.43 g of sodium iodide in 10 mL of water. Compound 2 is collected by filtration.

example 3

Preparation of Compound 3

A mixture of 26 mg 2-(3-succinimidyloxycarbonylethylthio)-4-(2,3-dihydro-3-methyl-(benzo-1,3-thiazol-2-yl)-methylidene-1-phenylquinolinium iodide, 2.7 mg of 3,3′-diamino-n-methyldipropylamine, and 7 μL of triethylamine is stirred in 1 mL of DMF at room temperature for 30 minutes. At the end of the period, 2 mL of ethyl acetate is added to precipitate Compound 3.

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Abstract

Embodiments of the present invention provide methods and nucleic acid reporter molecules for the detection of nucleic acid in a sample. The nucleic acid reporter molecule comprises two unsymmetrical cyanine monomer moieties, which may be the same or different, that are covalently attached by a linker comprising at least one aromatic, heteroaromatic, cyclic or heterocyclic moiety comprising 3-20 non-hydrogen atoms selected from the group consisting of O, N, S, P and C. The linker may be rigid, relatively flexible or some degree thereof. The unsymmetrical cyanine monomer moieties comprise a substituted or unsubstituted benzazolium moiety and a substituted or unsubstituted pyridinium or quinolinium moiety that is connected by a methine bridge that is monomethine, trimethine or pentamethine. The linkers form the cyanine dimer compounds by attaching to the pyridinium or quinolinium moiety of the monomer moieties. The present nucleic acid reporter molecules find utility in forming a nucleic acid-reporter molecule complex and detecting the nucleic acid. In particular, present nucleic acid reporter molecules with a rigid linker and monomer moieties with a monomethine bridge find utility in detecting RNA in the presence of DNA.

Description

FIELD OF THE INVENTION The present invention relates to unsymmetrical cyanine dimer compounds that provide a detectable fluorescent signal when complexed with nucleic acid polymers. The invention has applications in fields such as molecular biology, cell biology and fluorescence based assays. BACKGROUND OF THE INVENTION The detection of nucleic acid is used in a wide variety of assay formats to obtain both qualitative and quantitative information about the nucleic acid content of a sample. Fluorescent dyes that complex with DNA and in turn produce a detectable signal have increased the sensitivity and quality of information gained from such experiments. However, there still remains no fluorescent dye that is capable of detecting RNA in the presence of DNA for easy and direct detection of RNA. Currently there exists fluorescent hybridization methods for detection of RNA in the presence of DNA wherein a dye is covalently attached to a nucleic acid hybridization probe (Micklefield, ...

Claims

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Application Information

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IPC IPC(8): C07D215/18C07H21/02C09B23/02C12Q1/68
CPCC12Q1/6816C12Q2563/173C09B23/04C09B23/06Y10S436/80C09B23/0016C09B23/0066C09B55/006
Inventor YUE, STEPHENCHEUNG, CHING-YING
Owner MOLECULAR PROBES
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