Fluorescent dyes and related methods

Patent metadata

Field	Value
Publication number	US-9702870-B2
Application number	US-201615203607-A
Country	US
Kind code	B2
Filing date	Jul 6, 2016
Priority date	Aug 7, 2012
Publication date	Jul 11, 2017
Grant date	Jul 11, 2017

Abstract

Fluorescent dyes with affinity for nucleic acids and related methods are provided. Dielectric or semiconducting films including fluorescent dyes with affinity for nucleic acids and related methods are also provided. Coumarin-based surfactants conjugated to the fluorescent dyes with affinity for nucleic acids and related methods are provided.

First claim

The invention claimed is:

1. A method of staining a cell, the method comprising:
combining a compound and the cell comprising a nucleic acid molecule to form a complex including the compound and the nucleic acid molecule, thereby staining the cell; and
detecting the complex including the compound and the nucleic acid molecule,
wherein the compound has the genera formula (I):

wherein
each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,
or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
each of R 3A , R 3B , R 3C , R 3D , R 3E , R 3F , R 4A , R 4B , R 4C , and R 4D are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;
and salts and isomers thereof;

or the general formula (II):

wherein
each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,
or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl;
each of R 3A , R 3B , R 3C , R 3D , R 3E , R 3F , R 4A , R 4B , R 4C , and R 4D are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;
R 5 is selected from the group consisting of a halide, —CN, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;
and salts and isomers thereof.

2. The method of claim 1 , further comprising detecting the complex including the compound and the nucleic acid molecule.

3. The method of claim 1 , wherein
the compound has the genera formula (I), wherein
each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,
or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
each of R 3A , R 3B , R 3C , R 3D , R 3E and R 3F are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;
R 4A , R 4D are hydrogen;
each of R 4B and R 4C are independently hydrogen or —CN;
and salts and isomers thereof;

or the general formula (II):
wherein
each of R 1 and R 2 are independently selected from the group consisting of hydrogen, substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl,
or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl or substituted or unsubstituted heteroaryl;
each of R 3A , R 3B , R 3C , R 3D , R 3E and R 3F are independently selected from the group consisting of hydrogen, a halide, —OH, —NH 2 , —CN, —SH, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;
R 4A , R 4D are hydrogen;
each of R 4B and R 4C are independently hydrogen or —CN;
R 5 is selected from the group consisting of a halide, —CN, —NO 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted acyl, substituted or unsubstituted alkoxy, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, and substituted or unsubstituted heteroaryl;
and salts and isomers thereof;

provided that
when R 4A , R 4B , R 4C and R 4D are hydrogen, R 1 and R 2 are not phenyl.

4. The method of claim 1 , wherein each of R 1 and R 2 are independently selected from substituted or unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, unsubstituted acyl, substituted or unsubstituted alkoxy, unsubstituted heteroalkyl, unsubstituted cycloalkyl, unsubstituted heterocycloalkyl, unsubstituted aryl, substituted or unsubstituted aryl, and unsubstituted heteroaryl.

5. The method of claim 1 , wherein each of R 1 and R 2 are unsubstituted methyl, ethyl, propyl, isopropyl, isobutyl, sec-butyl, tert-butyl, pentyl, isopentyl, hexyl, heptyl, octyl, nonyl, decyl, substituted butyl, or wherein R 1 and R 2 are joined together to form a substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl.

6. The method of claim 1 , wherein R 5 is fluorinated alkyl, fluorinated heteroalkyl, fluorinated acyl, fluorinated alkoxy, fluorinated cycloalkyl, fluorinated heterocycloalkyl, fluorinated aryl, or fluorinated heteroaryl.

Assignees

• Univ Washington Through Its Center For Commercialization

Inventors

• Johnson Lewis E
• Cattolico Rose Ann
• Robinson Bruce H
• Latimer Luke N
• Watanabe-Gastel Zachary H
• Hardin William Robert

Classifications

• G01N33/582

  with fluorescent label · CPC title

• C12Q1/6806

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• C07D213/89

  with hetero atoms directly attached to the ring nitrogen atom · CPC title

• G01N2001/302

  Stain compositions · CPC title

• C09B57/00 Primary

  Other synthetic dyes of known constitution · CPC title