Monoazo dyes with cyclic amine as fluorescence quenchers

Patent metadata

Field	Value
Publication number	US-2016289779-A1
Application number	US-201514672944-A
Country	US
Kind code	A1
Filing date	Mar 30, 2015
Priority date	Mar 30, 2015
Publication date	Oct 6, 2016
Grant date	—

Abstract

The present disclosure provides reactive quencher dyes that can be used in the detection and/or quantification of desirable target molecules, such as proteins, nucleic acids and various cellular organelles. These dyes are essentially non-fluorescent but are efficient quenchers of various fluorescent dyes. Also, provided are methods of using the dyes, bio-probes incorporating dyes and methods of using the bio-probes. The quencher dyes described herein are modified to provide beneficial properties.

First claim

What is claimed is:

1 . A compound of formula I:

wherein R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , and R 9 are each independently selected from H, F, Cl, Br, I, CN, nitro, azido, hydroxyl, amino, hydrazino, aryl, substituted aryl, aroxyl, substituted aroxyl, alkenyl, alkynyl, alkyl, alkoxy, alkylamino, dialkylamino, arylamino, diarylamino, alkyl(aryl)amino, alkanoylamino, alkylthio, alkylcarbonyl, aryl carbonyl, alkylthiocarbonyl, arylthiocarbonyl, alkyloxycarbonyl, aroxycarbonyl, alkylaminocarbonyl, arylaminocarbonyl, dialkylaminocarbonyl, diarylaminocarbonyl, alkyl(aryl)aminocarbonyl, arylcarboxamido, or Q, wherein the alkyl or alkoxy groups are saturated or unsaturated, linear or branched, unsubstituted or optionally substituted by F, Cl, Br, I, CN, OH, alkenyl, alkynyl, alkylcarbonyl, amide, thioamide, or Q, and the aryl group is optionally substituted by F, Cl, Br, I, CN, OH, alkenyl, alkynyl, alkylcarbonyl, amide, thioamide, or Q; or
one or more of R 1 in combination with R 2 , R 2 in combination with R 3 , R 3 in combination with R 4 , R 4 in combination with R 5 , R 6 in combination with R 7 , and R 8 in combination with R 9 , form a 5- to 10-member ring that is saturated or unsaturated, unsubstituted or optionally substituted with one or more of alkyl, aryl, alkenyl, alkynyl, alkoxy, aroxyl, hydroxyl, F, Cl, Br, I, CN, nitro, alkylsulfonyl, arylsulfonyl, alkylsulfinyl, arylsulfinyl, (thio)carbonyl, (thio)carboxylic acid, (thio)carboxylic acid ester, nitro, amino, (thio)amide, azido, hydrazino, or (thio)phosphonate, wherein the alkyl or alkoxy groups are saturated or unsaturated, linear or branched, substituted or unsubstituted, and the aryl group is optionally substituted with F, Cl, Br, I, CN, OH, alkyl, alkenyl, alkynyl, alkoxy, aryoxy, alkylthio, arylthio, nitro, azido, hydrazino, carboxyl, thiocarboxyl, carbonyl, thiocarbonyl, carboxylic acid ester, thiocarboxylic acid ester, unsubstituted or substituted amino, amide, thioamide, or Q;
Q is selected from a carboxyl group (CO 2 − ), a carbonate ester (COER 12 ), a sulfonate ester (SO 2 ER 12 ), a sulfoxide (SOR 12 ), a sulfone (SO 2 CR 12 R 13 R 14 ), a sulfonamide (SO 2 NR 12 R 13 ), a phosphate (PO 4 = ), a phosphate monoester (PO 3 − ER 12 ), a phosphate diester (PO 2 ER 12 ER 13 ), a phosphonate (PO 3 = ) a phosphonate monoester (PO 2 − ER 12 ) a phosphonate diester (POER 12 ER 13 ), a thiophosphate (PSO 3 = ), a thiophosphate monoester (PSO 2 − ER 12 ) a thiophosphate diester (PSOER 12 ER 13 ), a thiophosphonate (PSO 2 = ), a thiophosphonate monoester (PSO − ER 12 ) a thiophosphonate diester (PSER 12 ER 13 ), a phosphonamide (PONR 12 R 13 NR 15 R 16 ), its thioanalogue (PSNR 12 R 13 NR 15 R 16 ), a phosphoramide (PONR 12 R 13 NR 15 R 16 ), its thioanalogue (PSNR 12 R 13 NR 14 NR 15 R 16 ), a phosphoramidite (PO 2 R 15 NR 12 R 13 ) or its thioanalogue (POSR 15 NR 12 R 13 ), wherein E is independently O or S;
R 10 and R 11 are each independently selected from H, a saturated or unsaturated, linear or branched, unsubstituted or further substituted alkyl group, aryl group, alkylcarbonyl, aryl carbonyl, alkylthiocarbonyl, arylthiocarbonyl, alkoxycarbonyl, aroxycarbonyl, alkylaminocarbonyl, arylaminocarbonyl, dialkylaminocarbonyl, diarylaminocarbonyl, alkyl(aryl)aminocarbonyl, arylcarboxamido, or Q, the alkyl or alkoxy portions of which are, alkenyl, alkynyl, alkylcarbonyl, amide, thioamide, or Q, or the aryl portions of which are optionally substituted by F, Cl, Br, I, CN, OH, alkenyl, alkynyl, alkylcarbonyl, amide, thioamide, or Q; or
at least one of R 7 in combination with R 10 , or R 9 in combination with R 11 forms a 5- to 10-member saturated or unsaturated ring optionally further substituted with one or more saturated or unsaturated, linear or branched, substituted or unsubstituted alkyl, aryl, alkenyl, alkynyl, saturated or unsaturated, linear or branched, substituted or unsubstituted alkoxy, aroxyl, hydroxyl, F, Cl, Br, I, CN, nitro, alkylsulfonyl, arylsulfonyl, alkylsulfinyl, arylsulfinyl, (thio)carbonyl, (thio)carboxylic acid, (thio)carboxylic acid ester, nitro, amino, (thio)amide, azido, hydrazino, or (thio)phosphonate; wherein the aryl group is optionally substituted with one or more of F, Cl, Br, I, CN, OH, alkyl, alkenyl, alkynyl, alkoxy, aryoxy, alkylthio, arylthio, nitro, azido, hydrazino, carboxyl, thiocarboxyl, carbonyl, thiocarbonyl, carboxylic acid ester, thiocarboxylic acid ester, unsubstituted or substituted amino, amide, thioamide, or Q;
and wherein R 12 , R 13 , R 14 , R 15 and R 16 are independently selected from hydrogen, a halogen, an amino group, a saturated or unsaturated, linear or branched, substituted or unsubstituted alkyl group, a saturated or unsaturated, branched or linear, substituted or unsubstituted alkoxy group, a substituted or unsubstituted aryl group; or R 12 in combination with R 13 , R 14 in combination with R 16 , R 12 in combination with R 14 , R 12 in combination with R 15 , R 13 in combination with R 16 , and R 14 in combination with R 15 , one or more of which, form a 5- to 10-member ring.

2 . The compound of claim 1 , wherein at least one of R 1 , R 2 , R 3 , R 4 , R 5 , R 6 , R 7 , R 8 , R 9 , R 10 , R 11 , R 12 , R 13 , R 14 , R 15 , and R 16 further comprises one or more reactive groups Z.

3 . The compound of claim 2 , wherein the reactive group comprises a nucleophilic reactive group, an electrophilic reactive group, a terminal alkene, a terminal alkyne, a coordinate group or an alkylating agent.

4 . The compound of claim 3 , wherein the nucleophilic reactive group is selected from thiol, amine or hydroxyl group.

5 . The compound of claim 3 , wherein the electrophilic reactive group is selected from isocyanate, isothiocyanate, monochlorotriazine, dichlorotriazine, 4,6-dichloro-1,3,5-triazines, mono- or di-halogen substituted pyridine, mono- or di-halogen substituted diazine, maleimide, haloacetamide, aziridine, sulfonyl halide, acid halide, hydroxysuccinimide ester, hydroxysulfosuccinimide ester, imido ester, hydrazine, azidonitrophenol, imido ester, hydrazine, azide, 3-(2-pyridyl dithio)-propionamide, glyoxal and aldehyde.

6 . The dye of claim 1 , which is linked to a target molecule.

7 . The dye of claim 6 , wherein the target molecule is selected from a nucleoside, a nucleotide, an oligonucleotide, a polynucleotide, a peptide nucleic acid, a protein, a peptide, an enzyme, an antigen, an antibody, a hormone, a hormone receptor, a cellular receptor, a lymphokine, a cytokine, a hapten, a lectin, avidin, strepavidin, digoxygenin, a carbohydrate, an oligosaccharide, a polysaccharide, a lipid, liposomes, a glycolipid, a viral particle, a viral component, a bacterial cell, a bacterial component, a eukaryotic cell, a eukaryotic cell component, a natural drug, a synthetic drug, a glass particle, a glass surface, natural polymers, synthetic polymers, a plastic particle, a plastic surface, a silicaceous particle, a silicaceous surface, an organic molecule, a dye or a derivative thereof.

8 . The dye of claim 7 , wherein the nucleoside, nucleotide, oligonucleotide or polynucleotide comprises one or more ribonucleoside moieties, ribonucleotide moieties, deoxyribonucleoside moieties, deoxyribonucleotide moieties, modified ribonucleosides, modified ribonucleotides, modified deoxyribonucleosides, modified deoxyribonucleotides, ribonucleotide analogues, deoxyribonucleotide analogues, and a combination thereof.

9 . The dye of claim 6 , wherein the dye is linked to the target molecule through a linker arm.

10 . The dye of claim 9

Assignees

• Enzo Biochem Inc

Inventors

• Li Zaiguo
• Pande Praveen
• Raju Natarajan

Classifications

• C12Q1/6876

  Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes · CPC title

• C09B56/005

  Azo-nitro dyes · CPC title

• C12Q1/708 Primary

  for papilloma · CPC title

• C12Q1/6818

  involving interaction of two or more labels, e.g. resonant energy transfer · CPC title

• C12Q1/6846

  Common amplification features · CPC title