Formylpyrrole-based heterocycles for nucleic acid attachment to supports

Patent metadata

Field	Value
Publication number	US-9475831-B2
Application number	US-201615002258-A
Country	US
Kind code	B2
Filing date	Jan 20, 2016
Priority date	Jan 19, 2011
Publication date	Oct 25, 2016
Grant date	Oct 25, 2016

Abstract

A compound has Formula I:

A, B, C, D, W, X, Y, and Z are independently selected from hydrogen, optionally substituted C 1 -C 6 alkyl, optionally substituted C 1 -C 6 alkoxy, aryl, aldehyde, protected aldehyde, CH, N, O, S, null, and bond; Q is selected from aldehyde, protected aldehyde, and null, at least one of A, B, C, D, W, X, Y, Z, or Q is an aldehyde or protected aldehyde; the bonds between each of A-B, B-C, C-D, W-X, X-Y, and Y-Z are selected from single bond, double bond, triple bond, and no bond; L is a linker selected from a C 1 -C 12 alkyl, aralkyl, and aryl, any of which is optionally substituted; one or more methylene unit (CH 2 ) of the C 1 -C 12 alkyl is optionally replaced by any combination of oxygen, carbonyl(C═O), and NH; and R 1 and R 2 are independently selected from —NR 3 R 4 , halogen, C 1 -C 8 alkoxy, aralkoxy, alkenyloxy, alkynyloxy, and OCH 2 CH 2 CN; R 3 and R 4 are independently a C 1 -C 4 , straight chain or branched alkyl group.

First claim

What is claimed is:

1. A compound of Formula III:

wherein,
W, X, Y, and Z comprise a fused ring system selected from the group consisting of a furan, a thiophene, a pyridazine, a pyrazine, and a pyrimidine;
A is selected from the group consisting of aryl, hydrogen, hydroxyl, hydroxyalkyl, a C 1 -C 4 straight chain or branched alkyl and alkoxy;
Q is an aldehyde or protected aldehyde;
L is a linker selected from a C 1 -C 12 alkyl, aralkyl, and aryl, any of which is optionally substituted; wherein one or more methylene unit (CH 2 ) unit of said C 1 -C 12 alkyl is optionally replaced by any combination of oxygen, carbonyl (C═O), and NH; and
R 1 and R 2 are independently selected from the group consisting of —NR 3 R 4 , halogen, C 1 -C 8 alkoxy, aralkoxy, alkenyloxy, alkynyloxy, and OCH 2 CH 2 CN;
wherein R 3 and R 4 are independently a C 1 -C 4 , straight chain or branched alkyl group.

2. The compound of claim 1 , wherein the protected aldehyde is selected from the group consisting of an acetal, an aminal, a dithioacetal, a protected hemiaminal, an alkene, and a protected hemithioacetal.

3. The compound of claim 1 , wherein A is hydrogen or methyl, Q is a protected aldehyde, R 1 is N-iPr 2 , and R 2 is OCH 2 CH 2 CN.

4. The compound of claim 1 , wherein A is a hydroxyl, alkoxy or hydroxyalkyl, Q is a protected aldehyde, R 1 is N-iPr 2 , and R 2 is OCH 2 CH 2 CN.

5. A compound of Formula IV:

wherein,
W, X, Y, and Z comprise a fused ring system selected from the group consisting of a furan, a thiophene, a pyridazine, a pyrazine, and a pyrimidine;
A is selected from the group consisting of aryl, hydrogen, hydroxyl, alkoxy hydroxyalkyl, and a C 1 -C 4 straight chain or branched alkyl;
Q is an aldehyde or protected aldehyde;
L is a linker selected from a C 1 -C 12 alkyl, aralkyl, and aryl, any of which is optionally substituted; wherein one or more methylene unit (CH 2 ) of said C 1 -C 12 alkyl is optionally replaced by any combination of oxygen, carbonyl (C═O), and NH; and
Nu is a nucleic acid.

6. The compound of claim 5 , wherein the protected aldehyde is selected from the group consisting of an acetal, an aminal, a dithioacetal, a protected hemiaminal, an alkene, and a protected hemithioacetal.

7. The compound of claim 5 , wherein A is hydrogen or methyl, Q is a protected aldehyde, Nu is selected from the group consisting of a 3′-phosphate-linked nucleic acid, a 3′-thiophosphate-linked nucleic acid, and a 3′-phosphate linked modified nucleic acid.

8. The compound of claim 5 , wherein A is hydrogen or methyl, Q is a protected aldehyde, Nu is selected from the group consisting of a 5′-phosphate-linked nucleic acid, a 5′-thiophosphate-linked nucleic acid, and a 5′-phosphate linked modified nucleic acid.

9. The compound of claim 5 , wherein A is hydroxyl, alkoxy, or hydroxyalkyl, Q is a protected aldehyde, and Nu is selected from the group consisting of a 3′-phosphate-linked nucleic acid, a 3′-thiophosphate-linked nucleic acid, and a 3′-phosphate linked modified nucleic acid.

10. The compound of claim 5 , wherein A is hydroxyl, alkoxy or hydroxyalkyl, Q is a protected aldehyde, and Nu is selected from a group consisting of a 5′-phosphate-linked nucleic acid, a 5′-thiophosphate-linked nucleic acid, and a 5′-phosphate linked modified nucleic acid.

11. A support-bound nucleic acid of Formula V:

wherein,
W, X, Y, and Z comprise a fused ring system selected from the group consisting of a furan, a thiophene, a pyridazine, a pyrazine, and a pyrimidine;
A is selected from the group consisting of aryl, hydrogen, hydroxyl, alkoxy hydroxyalkyl, and a C 1 -C 4 straight chain or branched alkyl;
L is a linker selected from a C 1 -C 12 alkyl, aralkyl, and aryl, any of which is optionally substituted; wherein one or more methylene unit (CH 2 ) of said C 1 -C 12 alkyl is optionally replaced by any combination of oxygen, carbonyl (C═O), and NH;
Nu is a nucleic acid;
Su is a support material; and
B is a single or double bond, such that when B is a single bond, R is hydrogen and when B is a double bond R is null.

12. The support-bound nucleic acid of claim 11 , wherein A is hydrogen or methyl, Nu is selected from the group consisting of a 3′-phosphate-linked nucleic acid, a 3′-thiophosphate-linked nucleic acid, and a 3′-phosphate linked modified nucleic acid.

13. The support-bound nucleic acid of claim 11 , wherein A is hydrogen or methyl, Nu is selected from the group consisting of a 5′-phosphate-linked nucleic acid, a 5′-thiophosphate-linked nucleic acid, and a 5′-phosphate linked modified nucleic acid.

14. The support-bound nucleic acid of claim 11 , wherein A is hydroxyl, alkoxy, or hydroxyalkyl, and Nu is selected from the group consisting of a 3′-phosphate-linked nucleic acid, a 3′-thiophosphate-linked nucleic acid, and a 3′-phosphate linked modified nucleic acid.

15. The support-bound nucleic acid of claim 11 , wherein A is hydroxyl, alkoxy or hydroxyalkyl, and Nu is selected from the group consisting of a 5′-phosphate-linked nucleic acid, a 5′-thiophosphate-linked nucleic acid, and a 5′-phosphate linked modified nucleic acid.

16. The support-bound nucleic acid of claim 11 , wherein the support material is selected from the group consisting of a silica bead, CPG glass, a polymer bead, a microfluidic cell, and a 96 well plate.

17. The support-bound nucleic acid of claim 16 , wherein said polymer bead comprises a polymer selected from the group consisting of polystyrene, agarose, polyacrylate, and polyacrylamide.

18. A method of immobilizing a nucleic acid comprising forming a Schiff-base product by reaction of a compound of Formula IV:

wherein,
W, X, Y, and Z comprise a fused ring system selected from the group consisting of a furan, a thiophene, a pyridazine, a pyrazine, and a pyrimidine;
A is selected from the group consisting of aryl, hydrogen, hydroxyl, alkoxy hydroxyalkyl, and a C 1 -C 4 straight chain or branched alkyl;
Q is an aldehyde (alkene) or protected aldehyde;
L is a linker selected from a C 1 -C 12 alkyl, aralkyl, and aryl, any of which is optionally substituted; wherein one or more methylene unit (CH 2 ) of said C 1 -C 12 alkyl is optionally replaced by any combination of oxygen, carbonyl (C═O), and NH; and
Nu is a nucleic acid;

with a support material displaying an amino or masked amino functional group.

19. The method of claim 18 , wherein A is hydrogen or methyl, Q is a protected aldehyde, Nu is selected from the group consisting of a 3′-phosphate-linked nucleic acid, a 3′-thiophosphate-linked nucleic acid, and a 3′-phosphate linked modified nucleic acid.

20. The method of claim 18 , wherein A is hydrogen or methyl, Q is a protected aldehyde, Nu is selected from the group consisting of a 5′-phosphate-linked nucleic acid, a 5′-thiophosphate-linked nucleic acid, and a 5′-phosphate linked modified nucleic acid.

21. The method of claim 18 , wherein A is hydroxyl, alkoxy, or hydroxyalkyl, Q is a protected aldehyde, and Nu is selected from the group consisting of a 3′-phosphate-linked nucleic acid, a 3′-thiophosphate-lin

Assignees

• Illumina Inc

Inventors

• Smith Ryan Christopher
• Smith Randall
• Zhao Xiaodong

Classifications

• C07H21/00

  Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids · CPC title

• C07F9/65031

  having the nitrogen atoms in the positions 1 and 2 · CPC title

• A61K31/675

  having nitrogen as a ring hetero atom, e.g. pyridoxal phosphate · CPC title

• C07F9/6506

  having the nitrogen atoms in positions 1 and 3 · CPC title

• C07F9/5728 Primary

  condensed with carbocyclic rings or carbocyclic ring systems · CPC title