METHOD OF SEQUENCING AND MAPPING TARGET NUCLEIC ACIDS
First Claim
1. A method of determining the methylation profile of a target nucleic acid comprising;
- ligating a first adapter to an extendable 3′
end of a 5′
dephosphorylated target nucleic acid, wherein the target nucleic acid comprises a first native strand and a complementary second strand, and wherein a nick is between a 3′
extendable end of the adapter and the second strand of the target nucleic acid;
extending the extendable 3′
end of the adapter with a strand-replacing polymerase and dATP, dGTP, dTTP, 5-methyl-dCTP, to form a fully methylated second strand, wherein the fully methylated strand is complementary to the first strand;
phosphorylating the first strand to form a phosphorylated 5′
end;
ligating the phosphorylated 5′
end of the first strand to an extendable 3′
end of a second adapter, and ligating an extendable 3′
end of the fully-methylated second strand to a phosphoryated 5′
end of the second adapter, to form a dual-adapter ligation product;
converting non-methylated cytosine in the first native strand of the dual-adapter ligation product to uracil to form a converted native strand in a converted dual-adapter ligation product; and
,comparing the identity of the cytosine positions in the fully methylated strand with the identity of the cytosine positions in the converted native strand to determine the methylation profile of the target nucleic acid.
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Accused Products
Abstract
The present teachings pertain to methods, compositions, reaction mixtures, and kits for mapping a low complexity sequence to a locus in a genome. In some embodiments, the low complexity sequence can be used to determine the methylation profile of a target nucleic acid. A strand-replacing reaction results in a product containing a first strand and a second strand, which can be connected together with a stem-loop adapter to form a single strand. A sequencing reaction can compare the two strands of the product, allowing the experimentalist to both map the sequence to a locus in a reference genome, as well as ascertain the methylation profile of the original target nucleic acid.
65 Citations
24 Claims
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1. A method of determining the methylation profile of a target nucleic acid comprising;
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ligating a first adapter to an extendable 3′
end of a 5′
dephosphorylated target nucleic acid, wherein the target nucleic acid comprises a first native strand and a complementary second strand, and wherein a nick is between a 3′
extendable end of the adapter and the second strand of the target nucleic acid;extending the extendable 3′
end of the adapter with a strand-replacing polymerase and dATP, dGTP, dTTP, 5-methyl-dCTP, to form a fully methylated second strand, wherein the fully methylated strand is complementary to the first strand;phosphorylating the first strand to form a phosphorylated 5′
end;ligating the phosphorylated 5′
end of the first strand to an extendable 3′
end of a second adapter, and ligating an extendable 3′
end of the fully-methylated second strand to a phosphoryated 5′
end of the second adapter, to form a dual-adapter ligation product;converting non-methylated cytosine in the first native strand of the dual-adapter ligation product to uracil to form a converted native strand in a converted dual-adapter ligation product; and
,comparing the identity of the cytosine positions in the fully methylated strand with the identity of the cytosine positions in the converted native strand to determine the methylation profile of the target nucleic acid. - View Dependent Claims (2, 3, 4, 5, 6)
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7. A method of determining the methylation profile of a target nucleic acid comprising;
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ligating a first adapter to an extendable 3′
end of the target nucleic acid, wherein the first adapter is a stem-loop molecule comprising an extendable 3′
end and a phosphorylated 5′
end, wherein the target nucleic acid comprises a native first strand and a complementary second strand, and wherein a nick is between the 3′
extendable end of the first adapter and the second strand of the target nucleic acid;extending the 3′
end of the stem-loop adapter with dATP, dGTP, dTTP, 5-methyl-dCTP to form a fully methylated strand, wherein the fully methylated strand is complementary to the first native strand;providing a second adapter, wherein the second adapter comprises a first strand and a second strand, wherein the first strand comprises a first primer portion, and an extendable 3′
end, and the second strand comprises a second primer portion and a phosphorylated 5′
end;ligating the fully methylated second strand to the phosphorylated 5′
end of the second adapter and ligating the first native strand of the target nucleic acid to the extendable 3′
end of the second adapter, to form a dual-adapter ligation product;converting non-methylated cytosine in the first native strand of the dual-adapter ligation product to uracil to form a converted native strand in a converted dual-adapter ligation product; immobilizing the converted dual-adapter ligation product on a solid support; hybridizing a primer to the second primer portion of the converted dual-adapter ligation product; sequencing the converted dual-adapter ligation product; and
,comparing the identity of the cytosine positions in the fully-methylated second strand with the identity of the cytosine positions in the converted strand to determine the methylation profile of the target nucleic acid. - View Dependent Claims (8, 9, 10, 11)
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12. A reaction mixture comprising;
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(a) an adapter ligated to a first strand of a target nucleic acid, wherein the target nucleic acid comprises the first strand and a second strand, wherein the adapter is a stem-loop adapter comprising an extendable 3′
end, and,wherein a nick exists between the extendable 3′
end of the stem-loop adapter and the second strand of the target nucleic;(b) a strand-replacing polymerase; (c) 5-methyl-dCTP; and
,(d) at least one of DATP, dTTP, dGTP.
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- 13. A strand replacement product, wherein the strand replacement product comprises a high complexity fully methylated strand and a low complexity converted native strand.
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15. A kit for determining the methylation profile of a target nucleic acid comprising;
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(a) a first adapter, wherein the first adapter is a stem-loop adapter, and wherein the stem-loop adapter comprises a phosphorylated 5′
end and an extendable 3′
end;(b) a second adapter, wherein the second adapter comprises a phosphorylated 5′
end;(c) a strand-replacing polymerase; (d) a converting agent; (e) a kinase; (f) 5-methyl-dCTP; and
,(g) at least one of dATP, dTTP, dGTP. - View Dependent Claims (16, 17, 18)
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19. A method of mapping a low complexity sequence to a locus of a genome comprising;
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generating a strand replacement product comprising a high complexity strand and a low complexity strand; sequencing the high complexity strand; and
,comparing the sequence of the high complexity strand to the genome in order to map the low complexity strand to a locus of the genome. - View Dependent Claims (20, 21, 22)
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23. A method of forming a single-stranded dual-adapter ligation product comprising;
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forming an adapter-ligated single-stranded target nucleic acid; hybridizing a primer to the adapter of the adapter-ligated single-stranded target nucleic acid; extending the primer in the presence of 5-methyl dCTP to form a double-stranded product comprising a fully methylated strand; and
,ligating a stem-loop adapter to the double-stranded product to form a single-stranded dual adapter ligation product. - View Dependent Claims (24)
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Specification