Quencher compositions comprising anthraquinone moieties

• US 20050227254A1
• Filed: 11/19/2004
• Published: 10/13/2005
• Est. Priority Date: 11/20/2003
• Status: Active Grant

• Current Assignee: Qiagen GmbH (Qiagen NV)
• Original Assignee: Exiqon A/S (Qiagen NV)
• Inventors: Pfundheller, Henrik M., Lomholt, Christian, Meldgaard, Michael
• Granted Patent: US 7,504,495 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids

Abstract

The present invention provides novel quencher composition comprising anthraquinone quencher moieties. The anthraquinone quencher moieties are useful as quencher labels when attached to biomolecules such as natural or modified polynucleotides, oligonucleotides, nucleosides, nucleotides, carbohydrates and peptides. For example, polynucleotides can be labeled at the 3′ terminus with fluorescence quencher solid support compositions, and polynucleotides can be labeled at internally or at the 5′ terminus. The detectable probes may have a format like molecular beacons, scorpion probes, sunrise probes, conformationally assisted probes and TaqMan probes.

Claims

1. A quencher compositions of the formula (III):

6. The quencher composition according to any one of claims 1 and 5, wherein Q is selected from 1,4-bis-(3-hydroxy-propylamino)-anthraquinone (1), 1,5-bis-(3-hydroxy-propylamino)-anthraquinone (4), 1,4-bis-(4-(2-hydroxyethyl)phenylamino)-anthraquinone (7), and 1,8-bis-(3-hydroxy-propylamino)-anthraquinone.

7. The quencher composition according to any one of claims 1 and 5, wherein Q is selected from 1,4-bis(3-hydroxypropylamino)-6-methylanthraquinone (11), 1,4-bis(4-(2-hydroethyl)phenylamino)-6-methyl-anthraquinone (15), 1,4-bis(4-methyl-phenylamino)-6-(N-(6,7-dihydroxy-4-oxo-heptane-1-yl))carboxamido-anthraquinone, 1,4-bis(4-methyl-phenylamino)-6-(N-(7-dimethoxytrityloxy-6-hydroxy-4-oxo-heptane-1-yl))carboxamido-anthraquinone (18), 1,4-bis(propylamino)-6-(N-(6,7-dihydroxy-4-oxo-heptane-1-yl))carboxamido-anthraquinone, 1,5-bis(4-(2-hydroethyl)phenylamino)-anthraquinone (20), 1,8-bis(3-hydroxypropylamino)-anthraquinone (23), and 1,8-bis(4-(2-hydroethyl)phenylamino)-anthraquinone (26).

8. A quencher composition according to claim 1, wherein X is a polynucleotide comprising a fluorescent dye, wherein the polynucleotide comprises one or more of 2′

-4′

or 3′

-4′

bicyclic sugar modifications.

9. A quencher composition according to claim 1, wherein

Z is a structure of the formula (V):

wherein A is a cleavable linker selected from the structures (Va-Vf);

wherein R¹⁴ is C_1-12 alkyl or C_1-12 alkoxy;

R¹⁵ is alkyl, aryl, arylalkyl or alkoxy;

L⁴ and L⁵ are independently selected from a bond and a linker, said linker being selected from C₁-C₁₂-alkyldiyl, C₁-C₁₂-alkoxydiyl, C₁-C₁₂-alkylaminodiyl, C₁-C₁₂-alkylamidediyl, aryldiyl and 1-20 ethyleneoxy units;

G is a bond, a nucleotide, a substituted nucleotide, a polynucleotide, a substituted polynucleotide or a hybridization-stabilizing moiety; and

B is a solid support.

2. A quencher composition of the formula (II):

3. The quencher composition according to claim 2, wherein Q is selected from 1,4-bis-(3-hydroxy-propylamino)-anthraquinone (1), 1-(3-(4,4′

-dimethoxy-trityloxy)propylamino)-4-(3-hydroxypropylamino)-anthraquinone (2), 1,5-bis-(3-hydroxy-propylamino)-anthraquinone (4), 1-(3-hydroxypropylamino)-5-(3-(4,4-dimethoxy-trityloxy)propylamino)-anthraquinone (5), 1,4-bis-(4-(2-hydroxyethyl)phenylamino)-anthraquinone (7), 1-(4-(2-(4,4′

-dimethoxy-trityloxy)ethyl)phenylamino)-4-(4-(2-hydroethyl)phenylamino)-anthraquinone (8), and 1,8-bis-(3-hydroxy-propylamino)-anthraquinone.

4. The quencher composition according to claim 2, wherein Q is selected from 1,4-bis(3-hydroxypropylamino)-6-methylanthraquinone (11), 1-(3-(4,4-dimethoxy-trityloxy)-propylamino)-4-(3-hydroxypropylamino)-6(7)-methyl-anthraquinone (12), 1,4-bis(4-(2-hydroethyl)phenylamino)-6-methyl-anthraquinone (15), 1,4-bis(4-methyl-phenylamino)-6-carboxy-anthraquinone (17), 1,4-bis(4-methyl-phenylamino)-6-(N-(6,7-dihydroxy-4-oxo-heptane-1-yl))carboxamido-anthraquinone, 1,4-bis(4-methyl-phenylamino)-6-(N-(7-dimethoxytrityloxy-6-hydroxy-4-oxo-heptane-1-yl))carboxamido-anthraquinone (18), 1,4-bis(propylamino)-6-carboxy-anthraquinone, 1,4-bis(propylamino)-6-(N-(6,7-dihydroxy-4-oxo-heptane-1-yl))carboxamido-anthraquinone, 1,4-bis(propylamino)-6-(N-(7-dimethoxytrityloxy-6-hydroxy-4-oxo-heptane-1-yl))carboxamido-anthraquinone, 1,5-bis(4-(2-hydroethyl)phenylamino)-anthraquinone (20), 1-(4-(2-hydroethyl)phenylamino)-5-(4-(2-(4,4′

-dimethoxy-trityloxy)ethyl)phenylamino)-anthraquinone (21), 1,8-bis(3-hydroxypropylamino)-anthraquinone (23), 1-(3-hydroxypropylamino)-8-(3-(4,4′

-dimethoxy-trityloxy)propylamino)-anthraquinone (24), 1,8-bis(4-(2-hydroethyl)phenylamino)-anthraquinone (26), and 1-(4-(2-hydroethyl)phenylamino)-8-(4-(2-(4,4′

-dimethoxy-trityloxy)ethyl)phenylamino)-anthraquinone (27).

10. A quencher composition according to any one of claims 2 and 5, wherein X is a 4,4′

-dimethoxytrityl, and Z is a phosphoramidite.

5. A quencher compositions of the formula (III):