Methods and compositions for synthesis of labelled oligonucleotides and analogs on solid-supports

• US 6,255,476 B1
• Filed: 02/22/1999
• Issued: 07/03/2001
• Est. Priority Date: 02/22/1999
• Status: Expired due to Term

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: PQ Corporation (Ecovyst, Inc.)
• Inventors: Lee, Linda G., Rosenblum, Barnett B., Mullah, Khairuzzaman B., Vinayak, Ravi S.
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/256,340
• Time in Patent Office: 862 Days
• Field of Search: 536/22.1, 536/23.1, 536/24.1, 536/24.3, 536/24.31, 536/24.32, 536/24.33, 536/25.3, 536/25.32, 435/6, 436/501
• US Class Current: 536/25.32
• CPC Class Codes: C07H 19/10 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 19/20 with the saccharide radical esterified by phosphoric or polyphosphoric acids
• CPC Class Codes: C07H 21/00 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 Class Codes: Y02P 20/55 Design of synthesis routes, e.g. reducing the use of auxiliary or protecting groups

Abstract

Methods and compositions to label oligonucleotides and analogs directly on a solid-support having the structure

where S is a solid-support, A is a cleavable linker, X is a moiety with three or more attachment sites, L is a label, Y is a nucleophile, i.e. O, NH, NR or S, and P₁ is an acid cleavable protecting group are provided. The labelled solid-support is reacted in a cyclical fashion to synthesize a labelled oligonucleotide on a solid-support in the 5′ to 3′ direction, having the structure:

Labelled oligonucleotides are also synthesized by reacting: (i) a label reagent bearing functionality consisting of carboxylic acid, sulfonic acid, phosphonic acid, or phosphoric acid, (ii) an oligonucleotide on solid support with nucleophilic functionality, and (iii) a coupling reagent, whereby an ester, amide, thioester, sulfonamide, sulfonate, phosphonate, phosphoramidate, phosphorothioate, or phosphate bond is formed. The labelling reaction may be conducted at label sites including the 5′ terminus, the 3′ terminus, a nucleobase, an internucleotide linkage, a sugar, amino, sulfide, hydroxyl, and carboxyl.

Claims

1. A method for 5′

to 3′

synthesis of 5′

labelled oligonucleotides comprising the steps of;

a) providing a labelled solid-support having the structure

where,

S is a solid-support;

A is a cleavable linker;

X is a moiety with three or more attachment sites;

L is a label;

Y is selected from the group consisting of oxygen, NH, NR where R is methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl, and sulfur; and

P₁ is an acid-cleavable protecting group;

b) reacting the labelled solid-support with acid to remove the acid-cleavable protecting group, P₁; and

c) adding a 5′

-phosphoramidite, 3′

protected nucleoside and an activator, thereby forming a bond between Y 5′

terminus of the and the nucleoside.

2. The method of claim 1 further comprising the steps of

d) capping any unreacted sites on the solid-support; and

e) adding an oxidizing reagent.

3. The method of claim 1 further comprising the steps of

d) capping any unreacted sites on the solid-support;

e) adding an oxidizing reagent; and

f) repeating steps (b) to (c) until the labelled oligonucleotide is completely synthesized.

4. The method of claim 3 further comprising the step of deprotecting the labelled oligonucleotide.

5. The method of claim 3 further comprising the steps of cleaving the labelled compound from the solid-support and deprotecting the labelled oligonucleotide.

6. The method of claim 1 wherein the solid-support S is selected from the group consisting of polystyrene, controlled-pore-glass, silica gel, silica, polyacrylamide, magnetic beads, polyacrylate, hydroxyethylmethacrylate, polyamide, polyethylene, polyethyleneoxy, and copolymers and grafts of such.

7. The method of claim 1 wherein the form of the solid support S is selected from the group consisting of small particles, beads, membranes, frits, slides, plates, micromachined chips, alkanethiol-gold layers, non-porous surfaces, addressable arrays, and polynucleotide-immobilizing media.

8. The method of claim 1 wherein the cleavable linker A is selected from the group consisting of:

9. The method of claim 1 wherein the linker X is selected from the group consisting of:

where n is 1 to 12.

10. The method of claim 1 wherein the label L is selected from the group consisting of hybridization-stabilizing moieties, fluorescent dyes, fluorescence quenchers, energy-transfer dye sets, chemiluminescent dyes, amino acids, proteins, peptides, enzymes, and affinity ligands.

11. The method of claim 10 where the fluorescent dyes and fluorescence quenchers are selected from the group consisting of FAM, TET, HEX JOE, TAMRA, d-TAMRA, JODA, ROX, VIC, NED, dJON, dR139, DABCYL, DABSYL, malachite green, 4,7-dichloro-fluoresceins, 4,7-dichloro-rhodamines, NTB, and cyanines.

12. The method of claim 10 where the hybridization-stabilizing moieties are selected from the group consisting of Hoechst 33258, CDPI_1-3, MGB1, netropsin, and distamycin.

13. The method of claim 1 wherein the acid-cleavable protecting group P₁ is selected from the group consisting of DMT, MMT, trityl, substituted trityl, pixyl, and trialkylsilyl.

14. The method of claim 1 wherein the 5′

-phosphoramidite, 3′

protected nucleoside monomer has the structure;

where,

R is selected from the group consisting of cyanoethyl, methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl;

R₁ and R₂ are individually selected from the group consisting of isopropyl, morpholino, methyl, ethyl, lower alkyl, cycloalkyl, and aryl;

P₂ is an exocyclic nitrogen protecting group selected from the group consisting of benzoyl, isobutyryl, acetyl, phenoxyacetyl, aryloxyacetyl, dimethylformamidine, dialkylformamidine, and dialkylacetamidine; and

P₃ is an acid-labile protecting group selected from the group consisting of DMT, MMT, pixyl, trityl, and trialkylsilyl.

15. The method of claim 3 wherein the oligonucleotide comprises one or more DNA, RNA, and nucleic acid analog monomer units wherein the nucleic acid analog is selected from the group consisting of nucleobase analogs, sugar analogs, and internucleotide analogs.

16. The method of claim 15 wherein nucleobase analogs are selected from the group consisting of C-5-alkyl pyrimidine, 2,6-diaminopurine, 2-thiopyrimidine, C-5-propyne pyrimidine, phenoxazine, 7-deazapurine, isocytidine, pseudo-isocytidine, isoguanosine, hypoxanthine, 8-oxopurine, and universal base.

17. The method of claim 15 wherein sugar analogs are selected from the group consisting of 2′

-O-alkyl-ribonucleotides, 2′

-O-methyl-ribonucleotides, 2′

-O-allyl-ribonucleotides, 2′

-allyl-ribonucleotides, 2′

-halo-ribonucleotides, 2′

-O-methoxyethyl-ribonucleotides, 2′

-branching group-ribonucleotides, 2′

-O-branching group-ribonucleotides, 4′

-α

-anomeric nucleotides, and 1′

-α

-anomeric nucleotides.

18. The method of claim 15 wherein internucleotide analogs are selected from the group consisting of 2-aminoethylglycine (PNA), 2′

-5′

-linkage, inverted 3′

-3′

linkage, inverted 5′

-5′

linkage, phosphorothioate, methyl phosphonate, non-bridging N-substituted phosphoramidate, alkylated phosphotriester branched structure, and 3′

-N-phosphoramidate.

19. The method of claim 1 wherein the labelled solid-support comprises a compound of the formula

where S is polystyrene or controlled-pore-glass;

and

L is a label.

20. A solid-support comprising a compound of the formula

where,

S is a solid-support;

A is a cleavable linker;

X is a moiety with three or more attachment sites;

L is a label;

Y is selected from the group consisting of O, NH, NR, and S;

R is selected from the group consisting of cyanoethyl, methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl;

P₂ is an exocyclic nitrogen protecting group selected from the group consisting of benzoyl, isobutyryl, acetyl, phenoxyacetyl, aryloxyacetyl, dimethylformamidine, dialkylformamidine, and dialkylacetamidine; and

P₃ is acid-labile protecting group selected from the group consisting of DMT, MMT, trityl, substituted trityl, pixyl, and trialkylsilyl.

21. A solid-support comprising a compound of the formula

where n is an interger from 0 to 100;

S is a solid-support;

A is a cleavable linker;

X is a moiety with three or more attachment sites;

L is a label;

Y is selected from the group consisting of O, NH, NR, and S;

R is cyanoethyl, methyl, lower alkyl, substituted alkyl, phenyl, aryl, and substituted aryl;

P₂ is an exocyclic nitrogen protecting group selected from the group consisting of benzoyl, isobutyryl, acetyl, phenoxyacetyl, aryloxyacetyl, dimethylformamidine, dialkylformamidine, and dialkylacetamidine.

22. A method to synthesize a labelled oligonucleotide comprising:

synthesizing an oligonucleotide on a solid support wherein the oligonucleotide includes nucleophilic functionality consisting of alcohol, amine, or thiol, and

coupling a label reagent with functionality consisting of carboxylic acid, sulfonic acid, phosphonic acid, or phosphoric acid;

to the oligonucleotide

bound to the solid support with a coupling reagent;

wherein the coupling reagent is HATU, HBTU, TBTU, BOP, PyBOP, EEDQ, DCC, DIPCDI, HOBt, MSNT, triisopropylbenzenesulfonyl chloride, or an aryl sulfonyl halide;

whereby an ester, amide, thioester, sulfonamide, sulfonate, phosphonate, phosphoramidate, phosphorothioate, or phosphate bond is formed.

23. The method of claim 22 wherein the label reagents are selected from the group consisting of hybridization-stabilizing moieties, fluorescent dyes, fluorescence quenchers, energy-transfer dye sets, chemiluminescent dyes, amino acids, proteins, peptides, enzymes, and affinity ligands.

24. The method of claim 23 where the fluorescent dyes and fluorescence quenchers are selected from the group consisting of FAM, TET, HEX, JOE, TAMPA, d-TAMRA, JODA, ROX, VIC, NED, dJON, dR139, DABCYL, DABSYL, malachite green, 4,7-dichloro-fluoresceins, 4,7-dichloro-rhodamines, NTB, and cyanines.

25. The method of claim 23 where the hybridization-stabilizing moieties are selected from the group consisting of Hoechst 33258, CDPI_1-3, MGB1, netropsin, and distamycin.

26. The method of claim 22 wherein the labels are attached to the oligonucleotide at label sites consisting of the 5′

terminus, the 3′

terminus, a nucleobase, an internucleotide linkage, a sugar, amino, sulfide, hydroxyl, and carboxyl.

27. The method of claim 22 wherein the solid-support is selected from the group consisting of polystyrene, controlled-pore-glass, silica gel, silica, polyacrylamide, magnetic beads, polyacrylate, hydroxethylmethacrylate, polyamide, polyethylene, polyethyleneoxy, and copolymers or grafts of such.

28. The method of claim 27 wherein the form of the solid support is selected from the group consisting of small particles, beads, membranes, frits, non-porous surfaces, slides, plates, micromachined chips, alkanethiol-gold layers, addressable arrays, or polynucleotide-immobilizing media.

29. The method of claim 22 wherein the oligonucleotide comprises one or more DNA, RNA, PNA and nucleic acid analog monomer units wherein the nucleic acid analog is selected from the group consisting of nucleobase analogs, sugar analogs, and internucleotide analogs.

30. The method of claim 29 wherein nucleobase analogs are selected from the group consisting of C-5-alkyl pyrimidine, 2,6-diaminopurine, 2-thiopyrimidine, C-5-propyne pyrimidine, phenoxazine, 7-deazapurine, isocytidine, pseudo-isocytidine, isoguanosine, hypoxanthine, 8-oxopurine, and universal base.

31. The method of claim 29 wherein sugar analogs are selected from the group consisting of 2′

-O-alkyl-ribonucleotides, 2′

-O-methyl-ribonucleotides, 2′

-O-allyl-ribonucleotides, 2′

-allyl ribonucleotides, 2′

-halo-ribonucleotides, 2′

-O-methoxyethyl-ribonucleotides, 2′

-branching group-ribonucleotides, 2′

-O-branching group-ribonucleotides, 4′

-α

-anomeric nucleotides, and 1′

-α

-anomeric nucleotides.

32. The method of claim 29 wherein internucleotide analogs are selected from the group consisting of 2-aminoethylglycine (PNA), 2′

-5′

-linkage, inverted 3′

-3′

linkage, inverted 5′

-5′

linkage, phosphorothioate, methyl phosphonate, non-bridging N-substituted phosphoramidate, alkylated phosphotriester branched structure, and 3′

-N- phosphoramidate.

33. The method of claim 22, wherein the direction of oligonucleotide synthesis is 5′

to 3′

.

34. The method of claim 22, wherein the direction of oligonucleotide synthesis is 3′

to 5′

.