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US 7,956,169 B1Granted
Synthesis of novel azo-dyes and their use in oligonucleotide synthesis
AssigneeChemGenes Corporation
InventorsAndrei Laikhter, Suresh C. Srivastava, Naveen P. Srivastava
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Abstract
The invention provides a novel group of azo quencher compositions that are useful as quenchers of fluorescence and to methods for making and using them. The quenchers contain an azo bond and 1,3,3-trimethyl-2-methyleneindoline ring system. The quenchers can be derivatized to facilitate their conjugation to a variety of biologically relevant compounds, including lipids, nucleic acids, peptides, proteins, and the like.
Claims24
A compound represented by Formula 4:
- wherein:
- each of R1, R2, R3 and R4 is independently hydrogen, halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- or
- R1 and R2 together or R3 and R4 together form a five- or six-membered ring, wherein said five- or six-membered ring is optionally substituted with halogen, NO2, SO3R, SO2N(R)2, CN, CNS, keto, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- R is H or C1-C10 alkyl;
- X is a C1-C100 straight or branched alkyl linking group, wherein one or more carbon atoms is optionally replaced with a nitrogen, oxygen or sulfur atom, or a combination thereof;
- and
- Y is controlled pore glass (CPG), polystyrene or
- wherein each of Ra and Rb is straight or branched C1-C10 alkyl;
- and Rc is straight or branched C1-C10 alkyl or cyanoethyl.
7 more elements
A compound represented by formula 6:
- wherein:
- each of R1, R2, R3 and R4 is independently hydrogen, halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- or
- R1 and R2 together or R3 and R4 together form a five- or six-membered ring, wherein said five- or six-membered ring is optionally substituted with halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- R is H or C1-C10 alkyl;
- each of R6 and R7 is independently hydrogen, methyl, or methoxy;
- X is a C1-C100 straight or branched alkyl linking group, wherein one or more carbon atoms are optionally replaced with nitrogen, oxygen or sulfur, or a combination thereof;
- and
- Y is controlled pore glass (CPG), polystyrene or
- wherein each of Ra and Rb is straight or branched C1-C10 alkyl;
- and Rc is straight or branched C1-C10 alkyl or cyanoethyl.
8 more elements
A compound represented by formula 7:
- wherein:
- A− is an anion selected from Cl−, Br−, I−, ClO4−, BF4− or CH3COO−;
- each of R1, R2, R3 and R4 is independently hydrogen, halogen, NO2, SO3R, SO2N(R)2, CN, CNS, C1-C10 alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- or
- R1 and R2 together or R3 and R4 together form a five- or six-membered ring, wherein said five- or six-membered ring is optionally substituted with halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- X is a C1-C100 straight or branched alkyl linking group, wherein one or more carbon atoms are optionally replaced with nitrogen, oxygen or sulfur, or a combination thereof;
- and
- Y is controlled pore glass (CPG), polystyrene or
- wherein each of Ra and Rb is straight or branched C1-C10 alkyl;
- and Rc is straight or branched C1-C10 alkyl or cyanoethyl.
7 more elements
A method for synthesizing an oligonucleotide containing a fluorescent quenching compound comprising:
- a) treating a composition containing a derivatized aromatic ring with NaNO2 to form a diazonium salt;
- b) reacting the diazonium salt with a composition comprising a 1,3,3-trimethyl-2-methyleneindoline to form a product comprising an azo group;
- and
- c) covalently attaching the product into an oligonucleotide, thereby forming the oligonucleotide containing a fluorescent quenching compound.
1 more element
A compound represented by Formula 8:
- wherein:
- each of R1, R2, R3 and R4 is independently hydrogen, halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- or
- R1 and R2 together or R3 and R4 together form a five- or six-membered ring, wherein said five- or six-membered ring is optionally substituted with halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- and
- R is H or C1-C10 alkyl.
3 more elements
A compound represented by formula 9:
- wherein:
- each of R1, R2, R3 and R4 is independently hydrogen, halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- or
- R1 and R2 together or R3 and R4 together form a five- or six-membered ring, wherein said five- or six-membered ring is optionally substituted with halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- R is H or C1-C10 alkyl;
- and
- each of R6 and R7 is independently hydrogen, methyl, or methoxy.
4 more elements
A compound represented by formula 10:
- wherein:
- A− is an anion selected from Cl−, Br−, I−, ClO4−, BF4− or CH3COO−;
- each of R1, R2, R3 and R4 is independently hydrogen, halogen, NO2, SO3R, SO2N(R)2, CN, CNS, C1-C10 alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- or
- R1 and R2 together or R3 and R4 together form a five- or six-membered ring, wherein said five- or six-membered ring is optionally substituted with halogen, NO2, SO3R, SO2N(R)2, CN, CNS, (C1-C10)alkoxy, C1-C10 alkyl, aryl, or heteroaryl;
- and
- R is H or C1-C10 alkyl.
4 more elements
Dependencies are inferred from the claim text.