FLUORESCENCE QUENCHING AZO DYES, THEIR METHODS OF PREPARATION AND USE

• US 20120064633A1
• Filed: 11/17/2011
• Published: 03/15/2012
• Est. Priority Date: 11/14/2003
• Status: Active Grant

• Current Assignee: Integrated DNA Technologies (Danaher Corporation)
• Original Assignee: Integrated DNA Technologies (Danaher Corporation)
• Inventors: Laikhter, Andrei, Behlke, Mark Aaron, Walder, Joseph, Roberts, Kevin William, Yong, Yawfui
• Granted Patent: US 8,377,641 B2
• Time in Patent Office: Days
• US Class Current: 436/94
• CPC Class Codes: C07C 245/10 with nitrogen atoms of azo groups bound to carbon atoms of six-membered aromatic rings being part of condensed ring systems
• CPC Class Codes: C07F 9/091 with hydroxyalkyl compounds with further substituents on alkyl
• CPC Class Codes: C07F 9/2408 of hydroxyalkyl compounds
• CPC Class Codes: C07H 21/04 with deoxyribosyl as saccharide radical
• CPC Class Codes: C09B 29/00 Monoazo dyes prepared by diazotising and coupling
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

Disclosed is a group of azo quencher compositions useful as fluorescence quenchers having the general structure of formula 1, methods of making or using the compositions, and kits comprising the composition.

Claims

1. A method for detecting hybridization of nucleic acid polymers comprising:

a) incubating a first nucleic acid polymer complimentary to a second nucleic acid polymer having, attached thereto, a quencher compound of Formula 1;

2. The method of claim 1 further comprising altering the spatial relationship between the fluorophore and quencher.

3. The method of claim 2 wherein the altering of the spatial relationship between the fluorophore and quencher is a result of the hybridization of the first and second nucleic acid polymers.

4. The method of claim 1 wherein the fluorophore and quencher composition are linked to a single nucleic acid polymer.

5. The method of claim 1 further comprising, when the first and second nucleic acid polymers are hybridized to each other, releasing the fluorophore or quencher composition from the hybridized structure.

6. A method for synthesizing an oligonucleotide having a fluorescent quencher of Formula 1, comprising:

obtaining a first compound having a nitro group and a primary amino group;

treating the primary amino group of the first compound in the presence of NaNO2, followed by LiBF4, to form an diazonium salt;

reacting the diazonium salt with a second compound having a substituted aryl ring to form a product having an azo group;

covalently incorporating the product into an oligonucleotide.