Fluorescence quenching azo dyes, their methods of preparation and use

• US 8,377,641 B2
• Filed: 11/17/2011
• Issued: 02/19/2013
• 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
• Primary Examiner(s): POWERS, FIONA
• Application Number:
  US13/298,479
• Publication Number:
  US 20120064633A1
• Time in Patent Office: 460 Days
• Field of Search: None
• US Class Current: 435/6.11
• 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 attached thereto a fluorescent quencher of Formula 1: