Methods and apparatus for synthesizing nucleic acid
First Claim
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1. A method for synthesizing an oligonucleotide, comprising:
- exposing an oligonucleotide attached to a solid support to a nucleotide analog in the presence of a nucleotidyl transferase enzyme and in the absence of a nucleic acid template such that the nucleotide analog is incorporated into the oligonucleotide,wherein the nucleotide analog comprises a nucleotide coupled, by a cleavable linker, to an inhibitor that sterically prevents the nucleotidyl transferase from catalyzing incorporation of either a natural nucleotide or a nucleotide analog into said oligonucleotide until said inhibitor is removed by cleavage of said cleavable linker, andwherein the inhibitor is a macromolecule greater than 50 Å
in diameter.
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Abstract
The invention provides improved methods for synthesizing polynucleotides, such as DNA and RNA, using enzymes and specially designed nucleotide analogs. Using the methods of the invention, specific sequences of polynucleotides can be synthesized de novo, base by base, in an aqueous environment, without the use of a nucleic acid template. Because the nucleotide analogs have an unmodified 3′ OH, i.e., as found in “natural” deoxyribose and ribose molecules, the analogs result in natural polynucleotides suitable for incorporation into biological systems.
30 Citations
23 Claims
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1. A method for synthesizing an oligonucleotide, comprising:
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exposing an oligonucleotide attached to a solid support to a nucleotide analog in the presence of a nucleotidyl transferase enzyme and in the absence of a nucleic acid template such that the nucleotide analog is incorporated into the oligonucleotide, wherein the nucleotide analog comprises a nucleotide coupled, by a cleavable linker, to an inhibitor that sterically prevents the nucleotidyl transferase from catalyzing incorporation of either a natural nucleotide or a nucleotide analog into said oligonucleotide until said inhibitor is removed by cleavage of said cleavable linker, and wherein the inhibitor is a macromolecule greater than 50 Å
in diameter. - View Dependent Claims (2, 3, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23)
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4. A method for synthesizing an oligonucleotide, comprising:
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exposing an oligonucleotide attached to a solid support to a nucleotide analog in the presence of a nucleotidyl transferase enzyme and in the absence of a nucleic acid template such that the nucleotide analog is incorporated into the oligonucleotide, wherein the nucleotide analog comprises a nucleotide coupled, by a cleavable linker, to an inhibitor that sterically prevents the nucleotidyl transferase from catalyzing incorporation of a natural nucleotide or a nucleotide analog into said oligonucleotide until said inhibitor is removed by cleavage of said cleavable linker, and wherein the inhibitor comprises the following structure;
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5. A method for synthesizing an oligonucleotide, comprising:
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exposing an oligonucleotide attached to a solid support to a nucleotide analog in the presence of a nucleotidyl transferase enzyme and in the absence of a nucleic acid template such that the nucleotide analog is incorporated into the oligonucleotide, wherein the nucleotide analog comprises a nucleotide coupled, by a cleavable linker, to an inhibitor that sterically prevents the nucleotidyl transferase from catalyzing incorporation of a natural nucleotide or a nucleotide analog into said oligonucleotide until said inhibitor is removed by cleavage of said cleavable linker, and wherein the inhibitor comprises a polypeptoid.
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6. A method for synthesizing an oligonucleotide, comprising:
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exposing an oligonucleotide attached to a solid support to a nucleotide analog in the presence of a nucleotidyl transferase enzyme and in the absence of a nucleic acid template such that the nucleotide analog is incorporated into the oligonucleotide, wherein the nucleotide analog comprises a nucleotide coupled, by a cleavable linker, to an inhibitor that sterically prevents the nucleotidyl transferase from catalyzing incorporation of a natural nucleotide or a nucleotide analog into said oligonucleotide until said inhibitor is removed by cleavage of said cleavable linker, and wherein the inhibitor comprises a polymer. - View Dependent Claims (7)
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8. A method for synthesizing an oligonucleotide, comprising:
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exposing an oligonucleotide attached to a solid support to a nucleotide analog in the presence of a nucleotidyl transferase enzyme and in the absence of a nucleic acid template such that the nucleotide analog is incorporated into the oligonucleotide, wherein the nucleotide analog comprises a nucleotide coupled, by a cleavable linker, to an inhibitor that sterically prevents the nucleotidyl transferase from catalyzing incorporation of a natural nucleotide or a nucleotide analog into said oligonucleotide until said inhibitor is removed by cleavage of said cleavable linker, and wherein the inhibitor is a protein.
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9. A method for synthesizing an oligonucleotide, comprising:
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exposing an oligonucleotide attached to a solid support to a nucleotide analog in the presence of a nucleotidyl transferase enzyme and in the absence of a nucleic acid template such that the nucleotide analog is incorporated into the oligonucleotide, wherein the nucleotide analog comprises a nucleotide coupled, by a cleavable linker, to an inhibitor that sterically prevents the nucleotidyl transferase from catalyzing incorporation of a natural nucleotide or a nucleotide analog into said oligonucleotide until said inhibitor is removed by cleavage of said cleavable linker, and wherein the inhibitor is a nanoparticle.
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Specification