Process for the preparation of oligonucleotides

• US 4,725,677 A
• Filed: 06/18/1985
• Issued: 02/16/1988
• Est. Priority Date: 08/18/1983
• Status: Expired

• Current Assignee: Millipore Corporation
• Original Assignee: Biosyntech GmbH
• Inventors: Sinha, Nanda D., Koster, Hubert
• Primary Examiner(s): GRIFFIN, RONALD
• Application Number:
  US06/752,178
• Time in Patent Office: 973 Days
• Field of Search: 536/27, 536/28, 536/29
• US Class Current: 536/25.34
• CPC Class Codes: C07F 9/26 containing P-halide groups
• 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

The invention relates to a process for the preparation of oligonucleotides by the following steps: reaction of a nucleoside with a phosphine derivative, reaction of the nucleotide derivative thus obtained with a nucleoside bonded to a polymeric carrier, oxidation of the carrier-bound nucleoside-nucleotide thus obtained with formation of phosphotriester groups, blocking of free primary 5'"'"'-OH groups, elimination of a protective group from the terminal 5'"'"'-OH group, where appropriate single or multiple repetition of the abovementioned steps to introduce further nucleoside phosphate or oligonucleoside phosphate units, and cleavage of the nucleoside-carrier bond and, where appropriate, elimination of all protective groups present in the oligonucleoside phosphates. The phosphine derivative used is a compound of the general formula III ##STR1## in which X and L can react with OH groups of the sugar units in the oligonucleotides, and R³ is a protective group which can be liberated by β-elimination.

Claims

1. A process for the preparation of oligonucleotides of the general formula I

in which B denotes a nucleoside base, R¹ denotes hydrogen, hydroxyl or hydroxyl which is protected by a removable protective group and n denotes an integer from 1 to 200, comprising the steps of

(a) reacting a nucleoside of the general formula II ##STR14## in which R¹ as defined as above, and R² denotes a removable protective group and B'"'"' denotes the nucleoside base B protected by the protective groups which can be eliminated, with a phosphine derivative of the general formula III ##STR15## in which R³ is a protective group which can be eliminated, and X and L are groups which react with hydroxyl groups in the sugar moieties of the nucleotides or nucleosides, in the presence of a base to thereby form a nucleotide phosphite

(b) reacting the nucleotide phosphite obtained in step (a) and represented by the formula IV:

##STR16## in which B'"'"', R¹, R², R³ and L are as defined above, with a nucleoside, of the general formula V, bound to a polymeric carrier ##STR17## in which B'"'"' and R¹ are as defined above and C denotes the polymeric carrier;

(c) oxidizing the carrier-bound nucleoside-nucleotides obtained in step (b) and represented by the formula;

##STR18## in which B'"'"', R¹, R², R³ and C are as defined above, with formation of phosphotriester groups,

(d) blocking free primary 5'"'"'-OH groups, which have not been reacted in the reaction according to step (b), with permanent protective groups;

(e) eliminating the protective group R² ;

(f) optionally repeating steps (a) to (e) to introduce further nucleoside phosphate or oligonucleoside phosphate units; and

(g) cleaving the nucleoside carrier bond and optionally eliminating the protective groups present in the oligonucleoside phosphates,

which process comprises using in step (a) as the phosphine derivative of the general formula III a compound in which R³ denotes a group of the formula VII ##STR19## in which the groups Y, which can be identical or different, represent hydrogen, methyl, and/or ethyl and Z represents an electron-attracting group, where, in the phosphine derivative of the formula III, X is chlorine, bromine, CN or SCN and L is CN or SCN, a secondary amino radical of the formula (VIII)

space="preserve" listing-type="equation">--NR.sub.2.sup.4

where the groups R⁴ are primary, secondary, or tertiary alkyl radicals having 1-10 carbon atoms, or together form a cycloalkyl radical having 5-7 carbon atoms, which can contain one or two nitrogen, oxygen, or sulfur atoms as hereoatoms, or are imidazole, triazole, tetrazole, 3-nitro-1,2,4-triazole, thiazole, pyrrole, benzotriazole, benzohydroxytriazole, imidazole substituted in the phenyl moiety, triazole substituted in the phenyl moiety, tetrazole substituted in the phenyl moiety, 3-nitro-1,2,4-triazole substituted in the phenyl moiety, thiazole substituted in the phenyl moiety, pyrrole substituted in the phenyl moiety, benzotriazole substituted in the phenyl moiety, or benzohydroxytrizole substituted in the phenyl moiety.

2. The process as claimed in claim 1, in which is used a phosphine derivative of the formula III in which X is chlorine or bromine, and L is a secondary amino radical of the formula (VIII)

3. The process as claimed in claim 1 or 2, in which is used a phosphine derivative of the formula (III) in which X is chlorine, L is an N,N-dimethylamino, -diethylamino or -diisopropylamino group or N-morpholino group, and R³ is a β

-cyanoethyl group.

4. A method of preparing oligonucleotides of the general formula:

##STR20## wherein B is a nucleoside base, R¹ is hydrogen, hydroxyl or hydroxyl which is protected by removable nucleoside protective groups, and n denotes an integer from 1 to 200, comprising the steps of;

(a) reacting a nucleotide phosphite represented by the formula;

##STR21## wherein B'"'"' is a nucleoside base B protected by a base protective group which can be eliminated, R¹ is as defined above, R² is 4,4'"'"' dimethoxytrityl or 4,4'"'"',4" trimethoxytrityl; and

L is N,N-dimethylamino, N,N-diethylamino, N,N-diisopropylamino, or N-morpholino, with a nucleoside bound to a polymeric carrier, of the general formula;

##STR22## wherein B'"'"' and R¹ are as defined above and C represents the polymeric carrier, to produce a carrier bound nucleoside-nucleotide of the formula;

##STR23## wherein B'"'"', R¹, R², R³ and C are as defined above;

(b) oxidizing the carrier bound nucleoside-nucleotide;

(c) blocking free primary 5'"'"'-OH groups, which have not been reacted in the reaction of step (a), with permanent protective groups;

(d) eliminating the protecting group R² ;

(f) repeating steps (a) to (d) to introduce further nucleoside phosphate units; and

(g) cleaving the nucleoside-carrier bond and optionally eliminating protective groups present in the oligonucleoside phosphates.

5. A method of synthesizing oligonucleotides, comprising the steps of:

(a) coupling a nucleoside β

-cyanoethyl-protected phosphoramidite to a carrier-bound nucleoside to produce a carrier bound nucleoside-nucleotide having a phosphite triester linkage;

(b) oxidizing the phosphite triester to form a phosphate triester;

(c) optionally coupling additional nucleoside β

-cyanoethyl-protected phosphoramidites to the carrier bound nucleoside-nucleotide and, after each coupling step, oxidizing the resulting phosphite triester to form a phosphate triester, to form a carrier bound polynucleotide;

(d) removing the β

-cyanoethyl protecting groups; and

(e) removing the polynucleotide from the carrier.

6. A method of claim 5, wherein the nucleoside β

-cyanoethyl phosphoramidite is a nucleoside β

-cyanoethyl N,N-dimethylphosphoramidite, N,N-diethylphosphoramidite, N,N-dipropylphosphoramidite or N,N-morpholino phosphoramidite.

7. A method of claim 6, wherein the carrier is controlled pore glass.

8. A method of claim 7, wherein the β

-cyanoethyl protecting group is removed with simultaneous removal of the polynucleotide from the carrier, by concentrated aqueous ammonia.

9. In a method of polynucleotide synthesis, comprising sequentially coupling nucleotide phosphoramidites to produce a polynucleotide, wherein the phosphorus atoms of the nucleotide phosphoramidites are protected by methyl groups, the improvement wherein the phosphorus protecting group are cyanoethyl groups.

10. A method of synthesizing oligonucleotides, comprising the steps of:

a. coupling a nucleoside β

-cyanoethyl-protected phosphoramidite to a nucleoside, the nucleoside being bound to a polymeric carrier via an ester bond to produce a carrier-bound nucleoside-nucleotide having a phosphite triester linkage;

b. oxidizing the phosphite triester to form a phosphate triester linkage;

c. sequentially coupling additional nucleoside β

-cyanoethyl protected phosphoramidite to the carrier-bound nucleoside-nucleotide, and after each coupling step, oxidizing the resulting phosphite triester linkage to a phosphate triester to produce a carrier-bound polynucleotide;

d. treating the carrier bound polynucleotide with concentrated ammonia to remove the β

-cyanoethyl phosphate protecting group and hydrolyzing the ester bond to the carrier to remove the polynucleotide from the carrier.

11. A method of claim 10, wherein the nucleoside β

-cyanoethyl phosphoramidite is a nucleoside β

-cyanoethyl N,N-dimethylphosphoramidite, N,N-diethylphosphoramidite;

N,N-dispropylphosphoramidite or N,N-morpholino phosphoramidite.

12. A method of claim 10, wherein the carrier is controlled pore glass.

13. A protected nucleotide having the formula:

##STR24## where, B'"'"' is a nucleoside base protected by a base protective group which can be eliminated;

R¹ is H, OH, or a hydroxyl group which is protected by a removable nucleoside protective group;

R² is a removable protective group;

R³ is ##STR25## L is CN, SCN, or NR₂⁴ ;

R⁴ is a primary, secondary or tertiary alkyl radical having 1-10 carbon atoms, or R₂⁴ is a cyloalkyl radical having 5-7 carbon atoms or a cycloalkyl radical having 5-7 atoms comprising atoms and one or two nitrogen, oxygen or sulfur atoms as heteroatoms;

Y is H, CH₃, or CH₂ CH₃ ; and

Z is a halgen, CN, NO₂, phenyl substituted in the o, o'"'"' or p positions with a halogen, CN or NO₂ radical, phenylthio, phenylsulfoxy, or phenylsulfonyl, where the phenyl radicals, may be substituted in the o, o'"'"' or p positions with a halgen, CN or NO₂ radical, or where the group ##STR26## may be replaced by CF₃, CCl₃, or CBr₃.

14. A protected nucleotide as in claim 13, wherein Z is CN.

15. A protected nucleotide as in claim 14, wherein R₃ is CH₂ --CH₂ --CN.

16. A protected nucleotide as in claim 13, wherein R₂ is 4,4'"'"'-dimethoxytrityl or 4,4"-trimethoxytrityl.

17. A protected nucleotide having the formula:

##STR27## where, R¹ is H, OH, or a hydroxyl group which is protected by a removable nucleoside protective group;

R² is 4,4'"'"'-dimethoxytrityl or 4,4'"'"',4"-trimethoxytrityl;

B'"'"' is a nucleoside base protected by a base protective group which can be eliminated

R³ is CH₂ --CH₂ --CN; and

L is N,N-dimethylamino, N,N-diethylamino, N,N-diisopropylamino or N-morpholino.

18. A protected nucleotide having the formula:

##STR28## where, R¹ is H, OH, or a hydroxyl group which is protected by a protective group selected from the group consisting of trityl groups, acyl groups and silyl ether groups;

R² is 4,4'"'"'-dimethoxytrityl or 4,4'"'"',4"-trimethoxytrityl;

B'"'"' is a nucleoside base selected from the group consisting of adenine, guanine, cytosine, thymine, uracil and analogs thereof which are protected by acyl groups or Schiff bases;

R³ is CH₂ --CH₂ --CN; and

L is N,N-dimethylamino, N,N-diethylamino, N,N-diisopropylamino, or N-morpholino.

19. A protected nucleotide of claim 18, wherein R₁ is H and B'"'"' is adenine, guanine, cytosine, thymine or uracil wherein the adenine or guanine is protected by a benzoyl group and the guanine is protected by an isobutyl group.