Process for preparing polynucleotides

• US 4,458,066 A
• Filed: 03/24/1981
• Issued: 07/03/1984
• Est. Priority Date: 02/29/1980
• Status: Expired due to Term

• Current Assignee: University Patents, Inc.
• Original Assignee: University Patents, Inc.
• Inventors: Caruthers, Marvin H., Matteucci, Mark D.
• Primary Examiner(s): Hazel, Blondel
• Application Number:
  US06/247,144
• Time in Patent Office: 1,197 Days
• Field of Search: 536/26, 536/27, 536/28, 536/29, 556/404, 556/400, 556/425, 556/439
• US Class Current: 536/25.34
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00389 Feeding through valves
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/0068 Means for controlling the apparatus of the process
• CPC Class Codes: B01J 2219/00686 Automatic
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C07H 19/04 Heterocyclic radicals containing only nitrogen atoms as ring hetero atom
• 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: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 for creating libraries
• CPC Class Codes: Y02P 20/582 Recycling of unreacted starting or intermediate materials

Abstract

New and useful intermediate nucleotides bound to an inorganic polymer support, including the preparation thereof, and processes for the conversion to oligonucleotides which are especially useful for the synthesis of polynucleotides, particularly ribonucleic (RNA) and deoxyribonucleic acids (DNA).

Claims

1. A modified inorganic polymer represented by the formula:

##STR5## wherein P is an inorganic polymer linked to the 3'"'"' or 5'"'"' --O-- of the nucleoside through a base hydrolyzable covalent bond;

R is H or a blocking group;

R₁ is a hydrocarbyl radical containing up to 10 carbons;

each B is a nucleoside or deoxynucleoside base; and

each A is H or OR.

2. The modified polymer according to claim 1 wherein R₁ is lower alkyl.

3. The modified polymer according to claim 1 wherein the polymer is a silica gel.

4. The modified polymer according to claim 3 wherein free silanol hydroxy groups on the silica gel are blocked.

5. The modified polymer according to claim 3 wherein the 5'"'"' --O-- blocking group is a trityl group.

6. The modified polymer according to claim 3 wherein the silica gel is macroporous and of a particle size ranging from about 5 to about 1,000 m.

7. A modified inorganic polymer represented by the formula:

##STR6## wherein P is an inorganic polymer linked to the 3'"'"' --O through an ester linkage;

R is H or a blocking group;

R₁ is a hydrocarbyl radical containing up to 10 carbons, each B is a nucleoside or deoxynucleoside base and each A is H or OR.

8. The modified polymer according to claim 7 wherein the polymer is a silica gel and A is H.

9. The modified polymer according to claim 8 wherein free silanol hydroxy groups of the silica gel are blocked.

10. The modified polymer according to claim 8 wherein the 5'"'"' --O-- blocking group is a trityl group.

11. The modified polymer according to claim 10 wherein the trityl group is dimethoxytrityl or monomethoxytrityl.

12. The modified polymer according to claim 8 wherein B is at least one of adenine, guanine, cytosine, uracil and thymine.

15. The modified polymer according to claim 12 wherein the free silanol hydroxy groups on the silica gel are blocked.

16. The modified polymer according to claim 12 wherein the 5'"'"' --O-- blocking group is a trityl group.

13. A modified inorganic polymer comprising an oligonucleotide or deoxyoligonucleotide covalently bound to said polymer through an ester linkage formed through the 3'"'"' --OH of the initial nucleoside moiety, wherein the terminal nucleoside is attached through a phosphite or phosphate triester linkage to the oligonucleotide chain and the 5'"'"' --O-- substituent is H or a blocking group.

14. The modified polymer according to claim 13 wherein the polymer is a silica gel.

17. The modified polymer according to claim 14 wherein the oligonucleotide or deoxyoligonucleotide is attached to said silica gel through the 3'"'"' --O-- linkage, --Si--Z--NHCO--Z--₁ --CO-- wherein each of Z and Z₁ is a hydrocarbyl radical containing up to 10 carbons.

18. A process for production of oligonucleotides which comprises the step of condensing the 3'"'"' --OH or 5'"'"' --OH group of a nucleoside or oligonucleotide covalently linked to an inorganic polymer by a coupling agent through the 5'"'"' --O-- or 3'"'"' --O--, respectively, of said nucleoside or oligonucleotide with a phosphite compound of the formula:

##STR7## wherein R is a blocking group;

B is a nucleoside or deoxynucleoside base;

A is H or OR;

R₁ is lower alkyl; and

X is Cl or Br, or a secondary amino group.

19. The process according to claim 18 wherein the phosphite compound is of the formula:

##STR8## wherein substituents R,R₁, X, A and B are as previously defined and said condensation occurs through the 5'"'"' --OH of said nucleoside or oligonucleotide.

20. The process according to claim 19 wherein R₁ is lower alkyl.

21. The process according to claim 19 wherein the inorganic polymer is a silica gel.

22. The process according to claim 21 wherein A is H and R is a trityl blocking group.

23. The process according to claim 22 wherein the free silanol hydroxy groups on the silica gel are blocked prior to the condensation reaction.

24. The process according to claim 22 wherein the trityl group is dimethoxytrityl.

25. The process according to claim 21 wherein the silica gel is covalently linked to said nucleoside or oligonucleotide through an ester linkage.

26. The process according to claim 21 including the further step of oxidizing the resulting phosphite triester to a phosphate triester.

27. The process according to claim 26 wherein I₂ is the oxidizing agent.

28. The process according to claim 26 wherein the 5'"'"' --O-- blocking group of the product thus obtained is removed and the product is then condensed with a further nucleoside phosphite compound of the said formula.

29. The process according to claim 28 wherein

(1) the product thus obtained is oxidized to obtain the corresponding phosphate triester;

(2) the 5'"'"' --O-- blocking group is removed; and

(3) the product is condensed with a further nucleoside or oligonucleoside phosphite of the said formula.

30. The process according to claim 29 wherein the 5'"'"' --O-- blocking group is a trityl group and the said group is removed by reaction with a Lewis acid.

31. The process according to claim 30 wherein the 5'"'"' --O-- blocking group is a dimethoxytrityl group and said Lewis acid is zinc bromide.

32. The process according to claim 29 wherein each of steps 1, 2 and 3 is repeated to successively add nucleosides to the oligonucleotide chain.

33. The process according to claim 32 wherein the oligonucleotide chain comprises from about 10 to about 30 nucleotides attached through the 5'"'"' --O and 3'"'"' --O positions.

34. A process for production of oligonucleotides which comprises the step of condensing a compound of the formula:

##STR9## wherein B is a nucleoside or deoxynucleoside base, A is H, OH or OR; and

P is silica covalently bound to the nucleoside by the group --Z₁ NHCOZCO-- wherein Z and Z₁ are each alkylene of up to 5 carbon atoms, with a nucleoside phosphite compound of the formula;

##STR10## wherein A and B are as previously defined;

R₁ is lower alkyl;

R is a blocking group; and

X is Cl or Br, or a secondary amino.

35. The process according to claim 34 including the further step of oxidizing the phosphite triester to a phosphate triester.

36. The process according to claim 35 wherein I₂ is the oxidizing agent.

37. The process according to claim 35 wherein the 5'"'"' --O-- blocking group of the product thus obtained is removed and the product is then condensed with a further nucleoside phosphite compound of the said formula.

38. The process according to claim 37 wherein

(1) the product thus obtained is oxidized to obtain the corresponding phosphate triester;

(2) the 5'"'"' --O blocking group is removed; and

(3) the product is condensed with a further nucleoside phosphite of the said formula.

39. The process according to claim 38 wherein each of steps 1, 2 and 3 are repeated to successively add nucleosides to the oligonucleotide chain.

40. The process according to claim 39 wherein the oligonucleotide chain comprises from about 10 to about 30 nucleosides attached through the 5'"'"' --O and 3'"'"' --O positions.

41. The process according to claim 39 wherein the phosphate triester product is hydrolyzed to form the oligonucleotide and silica gel, and the oligonucleotide is separated therefrom.

42. The process according to claim 41 including the further step of removing blocking groups from the oligonucleotide.

43. A process for producing polynucleotides which comprises the step of condensing the 3'"'"' --OH or 5'"'"' --OH of a nucleoside linked to a functionalized inorganic polymer with a compound which is the reaction product of nucleoside and blocked phosphodichloridite.