Enzymatic synthesis of oligonucleotides using digestible templates
First Claim
Patent Images
1. A method of synthesizing two or more oligonucleotides comprising the steps of:
- (a) providing a nucleic acid template comprising a primer binding region and an oligonucleotide complementary region located 5'"'"' to said primer binding region, said primer binding region being complementary to a nucleic acid primer and said oligonucleotide complementary region comprising two or more subregions, each said subregion being complementary to an oligonucleotide to be synthesized, wherein said template is used to direct the synthesis of a primer extension product comprising;
an oligonucleotide product comprising said oligonucleotides and one or more cleavage sites, each said cleavage site separating a pair of said oligonucleotides positioned adjacent to one another on said oligonucleotide product;
a nucleic acid primer; and
a cleavage site separating said primer from said oligonucleotide product;
(b) contacting said template with said primer under conditions such that said primer is able to hybridize to the primer binding region of said template to form a template-primer hybrid;
(c) incubating said template-primer hybrid in the presence of at least one DNA polymerase under conditions such that DNA synthesis occurs to form said primer extension product;
(d) cleaving said primer extension product such that said primer is separated from said oligonucleotide product and the oligonucleotides of said oligonucleotide product are separated from each other; and
(e) digesting said template before, simultaneous with or subsequent to step (d), so that said template is separated from said primer extension product.
1 Assignment
0 Petitions
Accused Products
Abstract
The present invention describes methods of synthesizing oligonucleotides. In particular, it relates to methods of enzymatically synthesizing chirally pure oligonucleotides using templates which can be digested after synthesis. By using digestible templates, separation and purification of the synthesized oligonucleotides are greatly facilitated.
-
Citations
86 Claims
-
1. A method of synthesizing two or more oligonucleotides comprising the steps of:
-
(a) providing a nucleic acid template comprising a primer binding region and an oligonucleotide complementary region located 5'"'"' to said primer binding region, said primer binding region being complementary to a nucleic acid primer and said oligonucleotide complementary region comprising two or more subregions, each said subregion being complementary to an oligonucleotide to be synthesized, wherein said template is used to direct the synthesis of a primer extension product comprising;
an oligonucleotide product comprising said oligonucleotides and one or more cleavage sites, each said cleavage site separating a pair of said oligonucleotides positioned adjacent to one another on said oligonucleotide product;
a nucleic acid primer; and
a cleavage site separating said primer from said oligonucleotide product;(b) contacting said template with said primer under conditions such that said primer is able to hybridize to the primer binding region of said template to form a template-primer hybrid; (c) incubating said template-primer hybrid in the presence of at least one DNA polymerase under conditions such that DNA synthesis occurs to form said primer extension product; (d) cleaving said primer extension product such that said primer is separated from said oligonucleotide product and the oligonucleotides of said oligonucleotide product are separated from each other; and (e) digesting said template before, simultaneous with or subsequent to step (d), so that said template is separated from said primer extension product. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
-
-
16. A method of synthesizing an oligonucleotide comprising the steps of:
-
(a) providing a nucleic acid template comprising a primer binding region and an oligonucleotide complementary region located 5'"'"' to said primer binding region, said primer binding region being complementary to a nucleic acid primer and said oligonucleotide complementary region being complementary to an oligonucleotide to be synthesized, wherein said primer contains a deoxyuridine located at or near the 3'"'"'-terminus of said primer, and wherein said template is used to direct the synthesis of a primer extension product comprising said oligonucleotide, said primer, and a cleavage site separating said primer from said oligonucleotide; (b) contacting said template with said primer under conditions such that said primer is able to hybridize to the primer binding region of said template to form a template-primer hybrid; (c) incubating said template-primer hybrid in the presence of at least one DNA polymerase under conditions such that DNA synthesis occurs to form a primer extension product; (d) cleaving said primer extension product at said cleavage site to separate said primer from said oligonucleotide; and (e) digesting said template before, simultaneous with or subsequent to step (d), so that said template is separated from said primer extension product. - View Dependent Claims (17, 18, 19, 20, 21, 22, 23, 24, 25, 26)
-
-
27. A method of synthesizing an oligonucleotide comprising the steps of:
-
(a) providing a nucleic acid template comprising a primer binding region and an oligonucleotide complementary region located 5'"'"' of said primer binding region, said primer binding region being complementary to a nucleic acid primer and said oligonucleotide complementary region being complementary to an oligonucleotide to be synthesized, wherein said template and said primer are contained on the same nucleic acid strand, such that said template is a self-priming template comprising a self-complementary region and an oligonucleotide complementary region, said primer comprising the 3'"'"'-terminus of said self-complementary region, and wherein said template is used to direct the synthesis of a primer extension product comprising said oligonucleotide, said primer, and a cleavage site separating said primer from said oligonucleotide; (b) contacting said template with said primer under conditions such that said primer is able to hybridize to the primer binding region of said template to form a template-primer hybrid; (c) incubating said template-primer hybrid in the presence of at least one DNA polymerase under conditions such that DNA synthesis occurs to form a primer extension product; (d) cleaving said primer extension product at said cleavage site to separate said primer from said oligonucleotide; and (e) digesting said template before, simultaneous with or subsequent to step (d), so that said template is separated from said primer extension product. - View Dependent Claims (28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38)
-
-
39. A method of synthesizing an oligonucleotide comprising the steps of:
-
(a) providing a nucleic acid template comprising a primer binding region and an oligonucleotide complementary region located 5'"'"' of said primer binding region, said primer binding region being complementary to a nucleic acid primer and said oligonucleotide complementary region being complementary to an oligonucleotide to be synthesized, wherein said primer comprises DNA and a ribonucleotide located at or near the 3'"'"'-terminus of said primer, and wherein said template is used to direct the synthesis of a primer extension product comprising said oligonucleotide, said primer, and a cleavage site separating said primer from said oligonucleotide; (b) contacting said template with said primer under conditions such that said primer is able to hybridize to the primer binding region of said template to form a template-primer hybrid; (c) incubating said template-primer hybrid in the presence of at least one DNA polymerase under conditions such that DNA synthesis occurs to form a primer extension product; (d) cleaving said primer extension product at said cleavage site to separate said primer from said oligonucleotide; and (e) digesting said template before, simultaneous with or subsequent to step (d), so that said template is separated from said primer extension product. - View Dependent Claims (40, 41, 42, 43, 44, 45, 46, 47, 48, 49)
-
-
50. A method of synthesizing an oligonucleotide comprising the steps of:
-
(a) providing a nucleic acid template comprising a primer binding region and an oligonucleotide complementary region located 5'"'"' of said primer binding region, said primer binding region being complementary to a nucleic acid primer and said oligonucleotide complementary region being complementary to an oligonucleotide to be synthesized, wherein said template is used to direct the synthesis of a primer extension product comprising said oligonucleotide, said primer, and a cleavage site separating said primer from said oligonucleotide, wherein said cleavage site comprises a restriction endonuclease recognition sequence, and wherein said primer is separated from said oligonucleotide using a restriction endonuclease able to recognize said restriction endonuclease recognition sequence; (b) contacting said template with said primer under conditions such that said primer is able to hybridize to the primer binding region of said template to form a template-primer hybrid; (c) incubating said template-primer hybrid in the presence of at least one DNA polymerase under conditions such that DNA synthesis occurs to form a primer extension product; (d) cleaving said primer extension product at said cleavage site to separate said primer from said oligonucleotide; and (e) digesting said template before, simultaneous with or subsequent to step (d), so that said template is separated from said primer extension product. - View Dependent Claims (51, 52, 53, 54, 55, 56, 57, 58)
-
-
59. A method of synthesizing at least one oligonucleotide comprising the steps of:
-
(a) providing first and second nucleic acid templates, each said template comprising a primer complementary region and an oligonucleotide complementary region located 5'"'"' to the primer complementary region, under conditions such that the primer complementary region of said first template is able to hybridize with the primer complementary region of said second template, thus forming a hybrid between the primer complementary regions of said first and second templates, wherein the primer complementary region of said first template comprises a primer for said second template, wherein the primer complementary region of said second template comprises a primer for said first template, wherein each said oligonucleotide complementary region is complementary to an oligonucleotide to be synthesized, said oligonucleotides being the same or different, and wherein each said template is used to direct the synthesis of a primer extension product comprising said oligonucleotide, said primer, and a cleavage site separating said primer from said oligonucleotide; (b) incubating said hybrid in the presence of at least one DNA polymerase under conditions such that DNA synthesis occurs to form said primer extension products; (c) cleaving said primer extension products such that said primers are separated from said oligonucleotides; and (d) digesting said templates before, simultaneous with or subsequent to step (c), so that said templates are separated from said primer extension products. - View Dependent Claims (60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70)
-
-
71. A method of synthesizing two or more oligonucleotides comprising the steps of:
-
(a) providing first and second nucleic acid templates, each said template comprising a primer complementary region and an oligonucleotide complementary region located 5'"'"' to the primer complementary region, under conditions such that the primer complementary region of said first template is able to hybridize with the primer complementary region of said second template, thus forming a hybrid between the primer complementary regions of said first and second templates, wherein the primer complementary region of said first template comprises a primer for said second template, wherein the primer complementary region of said second template comprises a primer for said first template, wherein each said oligonucleotide complementary region comprises two or more subregions, each said subregion being complementary to an oligonucleotide, and wherein each said template is used to direct the synthesis of a primer extension product comprising;
an oligonucleotide product comprising two or more of said oligonucleotides and one or more cleavage sites, each said cleavage site separating a pair of said oligonucleotides positioned adjacent to one another on said oligonucleotide product;
said primer; and
a cleavage site separating said primer from said oligonucleotide product;(b) incubating said hybrid in the presence of at least one DNA polymerase under conditions such that DNA synthesis occurs to form said primer extension products; (c) cleaving said primer extension products such that said primers are separated from said oligonucleotide products and the oligonucleotides of said oligonucleotide products are separated from each other; and (d) digesting said templates before, simultaneous with or subsequent to step (c), so that said templates are separated from said primer extension products. - View Dependent Claims (72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86)
-
Specification