Fluorescence quenching azo dyes, their methods of preparation and use

• US 9,540,515 B2
• Filed: 01/09/2013
• Issued: 01/10/2017
• Est. Priority Date: 11/14/2003
• Status: Active Grant

• Current Assignee: Integrated DNA Technologies, Inc. (Danaher Corporation)
• Original Assignee: Integrated DNA Technologies, Inc. (Danaher Corporation)
• Inventors: Laikhter, Andrei, Behlke, Mark Aaron, Walder, Joseph, Roberts, Kevin William, Yong, Yawfui
• Primary Examiner(s): Chu, Yong
• Assistant Examiner(s): WRIGHT, SONYA N
• Application Number:
  US13/736,999
• Publication Number:
  US 20130116415A1
• Time in Patent Office: 1,462 Days
• Field of Search: 534/727
• US Class Current: 1/1
• 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 making an oligonucleotide, comprising introducing the compound of Formula 1 to an automated oligonucleotide synthesizer to chemically incorporate a quencher compound into the oligonucleotide:

2. The method of claim 1, wherein the phosphoramidite group is a cyanoethylphosphoramidite.

3. The method of claim 2, wherein the quencher compound is coupled to the 3′

-terminus of the oligonucleotide.

4. The method of claim 3, wherein the quencher compound is coupled to the 5′

-terminus of the oligonucleotide.

5. The method of claim 1, wherein the synthesis step comprises linking the compound of Formula 1 to a solid support.

6. The method of claim 5, wherein the solid support is controlled pore glass.

7. The method of claim 1, wherein the compound of Formula 1 is the compound of Formula 13:

8. The method of claim 1, wherein the compound of Formula 1 is the compound of Formula 14:

9. The method of claim 1, wherein the oligonucleotide further comprises a fluorophore.