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US 2007/0179288 A1Published application
Triphosphate oligonucleotide modification reagents and uses thereof
AssigneeSolulink Biosciences, Inc.
InventorsDavid Schwartz, Richard Hogrefe
Life of this patent
Estimating the term…
Abstract
Hydrazino, oxyamino and carbonyl-based monomers and methods for incorporation into oligonucleotides during enzymatic synthesis are provided. Modified oligonucleotides are provided that incorporate the monomers provided herein. Immobilized oligonucleotides and oligonucleotide conjugates that contain covalent hydrazone or oxime linkages are provided. Methods for preparation of surface bound oligonucleotides are provided. Methods for the preparation of oligonucleotide conjugates are also provided
Claims46
A compound that has formula (I):
- P1—S1—B1-M-X
- or a derivative thereof, wherein:
- P1 is a triphosphate group;
- S1 is a ribose or a dideoxyribose;
- B1 is a nucleobase;
- X is a protected or unprotected hydrazino group, a protected or unprotected oxyamino group, or a carbonyl derivative;
- and
- M is a divalent group comprising any combination of any the following groups, which are combined in any order:
- arylene, heteroarylene, cycloalkylene, C(R1)2, —C(R1)═C(R1)—, >C═C(R2)(R3), >C(R2)(R3), —C≡C—, O, S(A)a, P(D)b(R1), P(D)b(ER1), N(R1), >N+(R2)(R3) and C(E);
- where a is 0, 1 or 2;
- b is 0, 1, 2 or 3;
- A is O or NR1;
- D is S or O;
- and E is S, O or NR1;
- each R1 is a monovalent group independently selected from hydrogen and M1-R4;
- each M1 is a divalent group each independently comprising anyu combination of the following groups, which groups are combined in any order:
- a direct link, arylene, heteroarylene, cycloalkylene, C(R5)2, —C(R5)═C(R5)—, >C═C(R2)(R3), >C(R2)(R3), —C≡C—, O, S(A)a, P(D)b(R5), P(D)b(ER5), N(R5), N(COR5), >N+(R2)(R3) and C(E);
- where a is 0, 1 or 2;
- b is 0, 1, 2 or 3;
- A is O or NR5;
- D is S or O;
- and E is S, O or NR5;
- R4 and R5 are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, SiR6R7R8, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and NR9R10;
- R9 and R10 are each independently selected from hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, aralkyl, heteroaryl, heteroaralkyl and heterocyclyl;
- R2 and R3 are selected from (i) or (ii) as follows:
- (i) R2 and R3 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl and heteroaryl;
- or
- (ii) R2 and R3 together form alkylene, alkenylene or cycloalkylene;
- R6, R7 and R8 are each independently a monovalent group selected from hydrogen, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and NR9R10;
- and
- each R1, R1, R2, R3. R4. R5, R6, R7, R8, R9 and R10 is unsubstituted or substituted with one or more substituents each independently selected from Z, wherein Z is selected from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, hydroxy, S(O)hR20, NR20R21, COOR20, COR20, CONR20R21, OC(O)NR20R21, N(R20)C(O)R21, alkoxy, aryloxy, heteroaryl, heterocyclyl, heteroaryloxy, heterocyclyloxy, aralkyl, aralkenyl, aralkynyl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, aralkoxy, heteroaralkoxy, alkoxycarbonyl, carbamoyl, thiocarbamoyl, alkoxycarbonyl, carboxyaryl, halo, pseudohalo, haloalkyl and carboxamido;
- h is 0, 1 or 2;
- and R20 and R21 are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, trialkylsilyl, dialkylarylsilyl, alkyldiarylsilyl, triarylsilyl, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy, amino, amido, alkylamino, dialkylamino, alkylarylamino, diarylamino and arylamino.
30 more elements
A compound that has formula (II):
- or a derivative thereof, wherein:
- O1 and O2 are each independently an oligonucleotide or an analogs thereof;
- P2 is a phosphodiester group;
- S1 is a ribose, a deoxyribose or a dideoxyribose;
- B1 is a nucleobase;
- X is a protected or unprotected hydrazino group, a protected or unprotected oxyamino group, or a carbonyl derivative;
- and
- M is a divalent group having any combination of the following groups, which can be combined in any order:
- arylene, heteroarylene, cycloalkylene, C(R1)2, —C(R1)═C(R1)—, >C═C(R2)(R3), >C(R2)(R3), —C≡C—, O, S(A)a, P(D)b(R1), P(D)b(ER1), N(R1), >N+(R2)(R3) and C(E);
- where a is 0, 1 or 2;
- b is 0, 1, 2 or 3;
- A is O or NR1;
- D is S or O;
- and E is S, O or NR1;
- each R1 is a monovalent group independently selected from hydrogen and M1-R4;
- each M1 is a divalent group independently having any combination of the following groups, which groups can be combined in any order:
- a direct link, arylene, heteroarylene, cycloalkylene, C(R5)2, —C(R5)═C(R5)—, >C═C(R2)(R3), >C(R2)(R3), —C≡C—, O, S(A)a, P(D)b(R5), P(D)b(ER5), N(R5), N(COR5), >N+(R2)(R3) and C(E);
- where a is 0, 1 or 2;
- b is 0, 1, 2 or 3;
- A is O or NR5;
- D is S or O;
- and E is S, O or NR5;
- R4 and R5 are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, SiR6R7R8, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and NR9R10;
- R9 and R10 are each independently selected from hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, aralkyl, heteroaryl, heteroaralkyl and heterocyclyl;
- R2 and R3 are selected from (i) or (ii) as follows:
- (i) R2 and R3 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl and heteroaryl;
- or
- (ii) R2 and R3 together form alkylene, alkenylene or cycloalkylene;
- R6, R7 and R8 are each independently a monovalent group selected from hydrogen, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and NR9R10;
- and
- R1, R2, R3, R4, R5, R6, R7, R8, R9 and R10 are unsubstituted or substituted with one or more substituents each independently selected from Z, wherein Z is selected from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, hydroxy, S(O)hR20, NR20R21, COOR20, COR20, CONR20R21, OC(O)NR20R21, N(R20)C(O)R21, alkoxy, aryloxy, heteroaryl, heterocyclyl, heteroaryloxy, heterocyclyloxy, aralkyl, aralkenyl, aralkynyl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, aralkoxy, heteroaralkoxy, alkoxycarbonyl, carbamoyl, thiocarbamoyl, alkoxycarbonyl, carboxyaryl, halo, pseudohalo, haloalkyl and carboxamido;
- h is 0, 1 or 2;
- and R20 and R21 are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, trialkylsilyl, dialkylarylsilyl, alkyldiarylsilyl, triarylsilyl, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy, amino, amido, alkylamino, dialkylamino, alkylarylamino, diarylamino and arylamino.
30 more elements
A compound that has formula:
- F*-M-X,
- or a derivative thereof, wherein:
- F* is a fluorophore;
- X is a protected or unprotected hydrazino group, a protected or unprotected oxyamino group or a carbonyl group;
- and
- M is a divalent group having any combination of the following groups, which can be combined in any order:
- arylene, heteroarylene, cycloalkylene, C(R1)2, —C(R1)═C(R1)—, >C═C(R2)(R3), >C(R2)(R3), —C≡C—, O, S(A)a, P(D)b(R1), P(D)b(ER1), N(R1), >N+(R2)(R3) and C(E);
- where a is 0, 1 or 2;
- b is 0, 1, 2 or 3;
- A is O or NR1;
- D is S or O;
- and E is S, O or NR1;
- each R1 is a monovalent group independently selected from hydrogen and M1-R4;
- each M1 is a divalent group independently having any combination of the following groups, which groups can be combined in any order:
- a direct link, arylene, heteroarylene, cycloalkylene, C(R5)2, —C(R5)═C(R5)—, >C═C(R2)(R3), >C(R2)(R3), —C≡C—, O, S(A)a, P(D)b(R5), P(D)b(ER5), N(R5), N(COR5), >N+(R2)(R3) and C(E);
- where a is 0, 1 or 2;
- b is 0, 1, 2 or 3;
- A is O or NR5;
- D is S or O;
- and E is S, O or NR5;
- R4 and R5 are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, SiR6R7R8, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and NR9R10;
- R9 and R10 are each independently selected from hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl, aralkyl, heteroaryl, heteroaralkyl and heterocyclyl;
- R2 and R3 are selected from (i) or (ii) as follows:
- (i) R2 and R3 are independently selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, aryl and heteroaryl;
- or
- (ii) R2 and R3 together form alkylene, alkenylene or cycloalkylene;
- R6, R7 and R8 are each independently a monovalent group selected from hydrogen, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy and NR9R10;
- and
- R1, R2, R3, R4, R5, R6, R7, R8, R9 and R10 are unsubstituted or substituted with one or more substituents each independently selected from Z, wherein Z is selected from alkyl, alkenyl, alkynyl, aryl, cycloalkyl, cycloalkenyl, hydroxy, S(O)hR2, NR20R21. COOR20, COR20, CONR20R21, OC(O)NR20R21, N(R20)C(O)R21, alkoxy, aryloxy, heteroaryl, heterocyclyl, heteroaryloxy, heterocyclyloxy, aralkyl, aralkenyl, aralkynyl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, aralkoxy, heteroaralkoxy, alkoxycarbonyl, carbamoyl, thiocarbamoyl, alkoxycarbonyl, carboxyaryl, halo, pseudohalo, haloalkyl and carboxamido;
- h is 0, 1 or 2;
- and R20 and R21 are each independently selected from the group consisting of hydrogen, halo, pseudohalo, cyano, azido, nitro, trialkylsilyl, dialkylarylsilyl, alkyldiarylsilyl, triarylsilyl, alkyl, alkenyl, alkynyl, haloalkyl, haloalkoxy, aryl, aralkyl, aralkenyl, aralkynyl, heteroaryl, heteroaralkyl, heteroaralkenyl, heteroaralkynyl, heterocyclyl, heterocyclylalkyl, heterocyclylalkenyl, heterocyclylalkynyl, hydroxy, alkoxy, aryloxy, aralkoxy, heteroaralkoxy, amino, amido, alkylamino, dialkylamino, alkylarylamino, diarylamino and arylamino.
28 more elements
A method of preparation of a hydrazino, oxyamino or carbonyl modified nucleoside triphosphate, comprising the steps of:
- (i) derivatizing a carboxylic acid selected from an ω-carbonyl, an ω-protected hydrazino, and an ω-protected oxyamino substituted carboxylic acid as the corresponding active ester;
- (ii) reacting the resulting active ester with an amino substituted nucleoside triphosphate;
- and
- (iii) deprotecting the hydrazino or oxyamino group, if present.
1 more element
Dependencies are inferred from the claim text.