Phosphine derivatives of fluorescent compounds
A phosphine derivative of DyLight dyes modified with ethylene glycol or (poly)ethylene glycol groups. In one embodiment, the compounds are useful in chemoselective ligation reactions.
1. A compound of general formula III
where
each of R 1 , R 2 , R 5 , and R 6 is the same or different and is independently selected from the group consisting of an aliphatic, heteroaliphatic, sulfoalkyl group, heteroaliphatic with terminal SO 3 , a PEG group P-L 1 -Z where P is selected from an ethylene glycol group, a diethylene glycol group, and a polyethylene glycol group, where the polyethylene glycol group is (CH 2 CH 2 O) s , where s is an integer from 3-6 inclusive, a sulfonamide group -L 1 -SO 2 NH—P-L 1 -Z, and a caboxamide group -L 1 -CONH—P-L 1 -Z;
each of R 7 and R 8 is the same or different and is independently selected from either H, SO 3 , sulfoalkyl, heteroaliphatic, heteroaliphatic with terminal SO 3 , a PEG group P-L 1 -Z where P is selected from an ethylene glycol group, a diethylene glycol group, and a polyethylene glycol group, where the polyethylene glycol group is (CH 2 CH 2 O) s , where s is an integer from 3-6 inclusive, a sulfonamide group -L 1 -SO 2 NH—P-L 1 -Z, or a caboxamide group -L 1 -CONH—P-L 1 -Z;
each of R9 and R10 is the same or different and is independently selected from either aryl groups, substituted aryl groups, or cycloalkyl groups;
R11 is an electrophilic group selected from the group consisting of a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, and amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, and alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro;
L is a linking group selected from the group consisting of a divalent linear (—(CH 2 ) o —, o=1 to 15), crossed, cyclic, and combinations thereof alkylene group which can be substituted by at least one atom selected from the group consisting of oxygen, substituted nitrogen, and sulfur;
L 1 is selected from a divalent linear (—(CH 2 ) o —, o=0 to 15), branched, or cyclic alkane group that can be substituted by at least one atom selected from oxygen, substituted nitrogen, and/or sulfur;
Z is selected from H, CH 3 , an alkyl group, or a heteroalkyl group;
Kat is a number of Na + , K + , Ca 2+ , ammonia, or other cation(s) needed to compensate the negative charge brought by the cyanine;
m is an integer from 0 to 5 inclusive; o is an integer from 0 to 12 inclusive; and n is an integer from 1 to 3 inclusive;
with the proviso that at least one of R 1 , R 2 , R 5 , R 6 , R 7 , and R 8 contains a PEG group.
2. A compound of general formula IV
where
each of R 1 , R 2 , R 5 , and R 6 is the same or different and is independently selected from the group consisting of an aliphatic, heteroaliphatic, sulfoalkyl group, heteroaliphatic with terminal SO 3 , a PEG group P-L 1 -Z where P is selected from an ethylene glycol group, a diethylene glycol group, and a polyethylene glycol group, where the polyethylene glycol group is (CH 2 CH 2 O) s , where s is an integer from 3-6 inclusive, a sulfonamide group -L 1 -SO 2 NH—P-L 1 -Z, and a caboxamide group -L 1 -CONH—P-L 1 -Z;
each of R 7 and R 8 is the same or different and is independently selected from either H, SO 3 , sulfoalkyl, heteroaliphatic, heteroaliphatic with terminal SO 3 , a PEG group P-L 1 -Z where P is selected from an ethylene glycol group, a diethylene glycol group, and a polyethylene glycol group, where the polyethylene glycol group is (CH 2 CH 2 O) s , where s is an integer from 3-6 inclusive, a sulfonamide group -L 1 -SO 2 NH—P-L 1 -Z, and a caboxamide group -L 1 -CONH—P-L 1 -Z;
each of R9 and R10 is the same or different and is independently selected from either aryl groups, substituted aryl groups, or cycloalkyl groups;
R11 is an electrophilic group selected from the group consisting of a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, and amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, and alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro;
L is a linking group selected from the group consisting of a divalent linear (—(CH 2 ) o —, o=1 to 15), crossed, cyclic, and combinations thereof alkylene group which can be substituted by at least one atom selected from the group consisting of oxygen, substituted nitrogen, and sulfur;
L 1 is selected from a divalent linear (—(CH 2 ) o —, o=0 to 15), branched, or cyclic alkane group that can be substituted by at least one atom selected from oxygen, substituted nitrogen, and/or sulfur;
Z is selected from H, CH 3 , an alkyl group, or a heteroalkyl group
Kat is a number of Na + , K + , Ca 2+ , ammonia, or other cation(s) needed to compensate the negative charge brought by the cyanine;
m is an integer from 0 to 5 inclusive; p is an integer from 1 to 6 inclusive; and n is an integer from 1 to 3 inclusive;
with the proviso that at least one of R 1 , R 2 , R 5 , R 6 , R 7 , and R 8 contains a PEG group.
3. A compound of the formula
where
each of R 1 , R 2 , R 5 , and R 6 is the same or different and is independently selected from the group consisting of an aliphatic, heteroaliphatic, sulfoalkyl group, heteroaliphatic with terminal SO 3 , a PEG group P-L 1 -Z where P is selected from an ethylene glycol group, a diethylene glycol group, and a polyethylene glycol group, where the polyethylene glycol group is (CH 2 CH 2 O) s , where s is an integer from 3-6 inclusive, a sulfonamide group -L 1 -SO 2 NH—P-L 1 -Z, and a caboxamide group -L 1 -CONH—P-L 1 -Z;
each of R is the same or different and is independently selected from either H, SO 3 , sulfoalkyl, heteroaliphatic, heteroaliphatic with terminal SO 3 , a PEG group P-L 1 -Z where P is selected from an ethylene glycol group, a diethylene glycol group, and a polyethylene glycol group, where the polyethylene glycol group is (CH 2 CH 2 O) s , where s is an integer from 3-6 inclusive, a sulfonamide group -L 1 -SO 2 NH—P-L 1 -Z, or a caboxamide group -L 1 -CONH—P-L 1 -Z;
each of R9 and R10 is the same or different and is independently selected from either aryl groups, substituted aryl groups, or cycloalkyl groups;
R11 is an electrophilic group selected from the group consisting of a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, and amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, and alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro;
L is a linking group selected from the group consisting of a divalent linear (—(CH 2 ) o —, o=1 to 15), crossed, cyclic, and combinations thereof alkylene group which can be substituted by at least one atom selected from the group consisting of oxygen, substituted nitrogen, and sulfur;
L 1 is selected from a divalent linear (—(CH 2 ) o —, o=0 to 15), branched, or cyclic alkane group that can be substituted by at least one atom selected from oxygen, substituted nitrogen, and/or sulfur;
Z is selected from H, CH 3 , an alkyl group, or a heteroalkyl group;
Kat is a number of Na + , K + , Ca 2+ , ammonia, or other cation(s) needed to compensate the negative charge brought by the cyanine;
m is an integer from 0 to 5 inclusive; o is an integer from 0 to 12 inclusive; and n is an integer from 1 to 3 inclusive.
4. A compound of the formula
where each of R 1 , R 2 , R 5 , and R 6 is the same or different and is independently selected from the group consisting of an aliphatic, heteroaliphatic, sulfoalkyl group, heteroaliphatic with terminal SO 3 , a PEG group P-L 1 -Z where P is selected from an ethylene glycol group, a diethylene glycol group, and a polyethylene glycol group, where the polyethylene glycol group is (CH 2 CH 2 O) s , where s is an integer from 3-6 inclusive, a sulfonamide group -L 1 -SO 2 NH—P-L 1 -Z, and a caboxamide group -L 1 -CONH—P-L 1 -Z;
each R is the same or different and is independently selected from either H, SO 3 , sulfoalkyl, heteroaliphatic, heteroaliphatic with terminal SO 3 , a PEG group P-L 1 -Z where P is selected from an ethylene glycol group, a diethylene glycol group, and a polyethylene glycol group, where the polyethylene glycol group is (CH 2 CH 2 O) s , where s is an integer from 3-6 inclusive, a sulfonamide group -L 1 -SO 2 NH—P-L 1 -Z, and a caboxamide group -L 1 -CONH—P-L 1 -Z;
each of R9 and R10 is the same or different and is independently selected from either aryl groups, substituted aryl groups, or cycloalkyl groups;
R11 is an electrophilic group selected from the group consisting of a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, and amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, and alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro;
L is a linking group selected from the group consisting of a divalent linear (—(CH 2 ) o —, o=1 to 15), crossed, cyclic, and combinations thereof alkylene group which can be substituted by at least one atom selected from the group consisting of oxygen, substituted nitrogen, and sulfur;
L 1 is selected from a divalent linear (—(CH 2 ) o —, o=0 to 15), branched, or cyclic alkane group that can be substituted by at least one atom selected from oxygen, substituted nitrogen, and/or sulfur;
Z is selected from H, CH 3 , an alkyl group, or a heteroalkyl group
Kat is a number of Na + , K + , Ca 2+ , ammonia, or other cation(s) needed to compensate the negative charge brought by the cyanine;
m is an integer from 0 to 5 inclusive; p is an integer from 1 to 6 inclusive; and n is an integer from 1 to 3 inclusive.
5. A compound of the formula
where
each of R 1 , R 2 , R 5 , and R 6 is the same or different and is independently selected from the group consisting of an aliphatic, heteroaliphatic, sulfoalkyl group, or heteroaliphatic with terminal SO 3 ;
each of R is the same or different and is independently selected from either H, SO 3 , sulfoalkyl, heteroaliphatic, or heteroaliphatic with terminal SO 3 ;
each of R9 and R10 is the same or different and is independently selected from either aryl groups, substituted aryl groups, or cycloalkyl groups;
R11 is an electrophilic group selected from the group consisting of a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, and amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, and alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro;
L is a linking group selected from the group consisting of a divalent linear (—(CH 2 ) o , o=1 to 15), crossed, cyclic, and combinations thereof alkylene group which can be substituted by at least one atom selected from the group consisting of oxygen, substituted nitrogen, and sulfur;
Kat is a number of Na + , K + , Ca 2+ , ammonia, or other cation(s) needed to compensate the negative charge brought by the cyanine;
m is an integer from 0 to 5 inclusive; o is an integer from 0 to 12 inclusive; and n is an integer from 1 to 3 inclusive.
6. A compound of the formula
where
each of R 1 , R 2 , R 5 , and R 6 is the same or different and is independently selected from the group consisting of an aliphatic, heteroaliphatic, sulfoalkyl group, or heteroaliphatic with terminal SO 3 ;
each of R is the same or different and is independently selected from either H, SO 3 , sulfoalkyl, heteroaliphatic, or heteroaliphatic with terminal SO 3 ;
each of R9 and R10 is the same or different and is independently selected from either aryl groups, substituted aryl groups, or cycloalkyl groups;
R11 is an electrophilic group selected from the group consisting of a carboxylic acid, an alkyl ester, an aryl ester, a substituted aryl ester, an aldehyde, and amide, an aryl amide, an alkyl halide, a thioester, a sulfonyl ester, and alkyl ketone, an aryl ketone, a substituted aryl ketone, a halosulfonyl, a nitrile, and a nitro;
L is a linking group selected from the group consisting of a divalent linear (—(CH 2 ) o —, o=1 to 15), crossed, cyclic, and combinations thereof alkylene group which can be substituted by at least one atom selected from the group consisting of oxygen, substituted nitrogen, and sulfur;
Kat is a number of Na + , K + , Ca 2+ , ammonia, or other cation(s) needed to compensate the negative charge brought by the cyanine;
m is an integer from 0 to 5 inclusive; p is an integer from 1 to 6 inclusive; and n is an integer from 1 to 3 inclusive.
7. A compound of claim 1 selected from the group consisting of
8. A compound of claim 2 selected from the group consisting of
9. A compound of claim 3 selected from the group consisting of
10. The compound of claim 4 selected from the group consisting of
11. The compound of claim 5 selected from the group consisting of
12. The compound of claim 6 selected from the group consisting of
13. A method using the compound of claim 1 in a chemoselective ligation reaction with an azido compound.
14. A method of labeling at least one biomolecule, the method comprising providing a composition comprising at least one excipient and the compound of claim 1 in an effective concentration to the biomolecule under conditions sufficient for specifically binding the compound to the biomolecule, in the absence of non-specific binding, resulting in labeling of the biomolecule.
15. The method of claim 14 further comprising reacting a linking moiety with the at least one biomolecule to result in an at least one biomolecule-linking moiety conjugate, and reacting the compound with the at least one biomolecule-linking moiety conjugate to result in an at least one biomolecule-linking moiety-compound conjugate.
16. The method of claim 15 where the linking moiety is a heterobifunctional linking moiety having a first terminal group reactive with an amine group and a second terminal azide.
17. The method of claim 16 where the linking moiety comprises a polyethylene glycol (PEG) group between the first and the second functional termini.
18. A method of detecting at least one biomolecule, the method comprising providing a composition comprising at least one excipient and the compound of claim 1 in an effective concentration to at least one biomolecule under conditions sufficient for binding the compound to the biomolecule, and detecting the biomolecule-bound compound.
19. A kit comprising a compound of claim 1 and instructions for performing a chemoselective ligation reaction using the compound with an azido compound.