Process for the preparation of oligonucleotides
First Claim
1. A process for the preparation of oligonucleotides of the .[.general.]. formula I ##STR13## in which B denotes a nucleoside base, R1 denotes hydrogen, hydroxyl or hydroxyl which is protected by .Iadd., where appropriate, .Iaddend.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 nucleotide 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 ( VIII)where the groups R4 are primary, secondary, or tertiary alkyl radicals having .Badd.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 benzohydroxytriazole substituted in the phenyl moiety.
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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.
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Citations
19 Claims
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1. A process for the preparation of oligonucleotides of the .[.general.]. formula I ##STR13## in which B denotes a nucleoside base, R1 denotes hydrogen, hydroxyl or hydroxyl which is protected by .Iadd., where appropriate, .Iaddend.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 nucleotide 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 ( VIII)where the groups R4 are primary, secondary, or tertiary alkyl radicals having .Badd.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 benzohydroxytriazole substituted in the phenyl moiety. - View Dependent Claims (2, 3)
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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.
- ##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;
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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 .Iadd., where appropriate, .Iaddend.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.
- ##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;
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5. A method of synthesizing oligonucleotides, comprising the steps of:
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(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. - View Dependent Claims (6, 7, 8)
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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.
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10. A method of synthesizing oligonucleotides, comprising the steps of:
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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. - View Dependent Claims (11, 12)
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13. A protected nucleotide having the formula:
- ##STR24## where, B'"'"' is a nucleoside base protected .Iadd., where appropriate, .Iaddend.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 cycloalkyl 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.]. .Iadd.halogen .Iaddend.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. - View Dependent Claims (14, 15, 16)
- ##STR24## where, B'"'"' is a nucleoside base protected .Iadd., where appropriate, .Iaddend.by a base protective group which can be eliminated;
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17. A protected nucleotide having the formula:
- ##STR27## where,
R1 is H, OH, or a hydroxyl group which is protected .Iadd., where appropriate, .Iaddend.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.
- ##STR27## where,
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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. - View Dependent Claims (19)
- ##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;
Specification