In vitro capture of nucleic acids via modified oligonucleotides and magnetic beads
First Claim
1. An in vitro method of capturing one or more target simple sequence repeats, wherein the method comprises the steps of:
- providing one or more modified oligonucleotide conjugates, wherein each of the modified oligonucleotide conjugates comprises at least one locked nucleic acid and a linking molecule;
incubating a sample of nucleic acids with the modified oligonucleotide conjugates, thereby forming one or more hybridized duplexes, wherein each duplex comprises a target simple sequence repeat portion and a modified oligonucleotide conjugate portion;
contacting substantially all of the hybridized duplexes with a linking source, such that the linking molecule of each duplex that contacts the linking source forms a bond with the linking source; and
separating substantially all of the hybridized duplexes from the sample of nucleic acids by extracting the linking source from the sample.
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Abstract
A method is disclosed for capturing one or more target simple sequence repeats (SSRs) utilizing locked nucleic acids and strand displacement stategies. In this method, one or more modified oligonucleotide conjugates are selected in which the conjugates are constructed from at least one locked nucleic acid (“LNA”) and a linking molecule, hereinafter referred to as “LNA conjugates”. When incubated with a sample of nucleic acids, these LNA conjugates capture SSRs by selectively binding to complementary sequences of DNA or RNA, which may be either single or double stranded. Once bound, the resulting complexes constitute hybridized duplexes containing both a targeted simple sequence repeat portion and a LNA conjugate portion. The captured SSRs are separated from the sample by using a linking source that binds to the linking molecule of the hybridized duplex and extracting the linking source with the bound duplex from the sample. In a preferred embodiment, the SSRs may be detached from the LNA conjugates by treatment with an alkaline buffer.
11 Citations
30 Claims
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1. An in vitro method of capturing one or more target simple sequence repeats, wherein the method comprises the steps of:
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providing one or more modified oligonucleotide conjugates, wherein each of the modified oligonucleotide conjugates comprises at least one locked nucleic acid and a linking molecule;
incubating a sample of nucleic acids with the modified oligonucleotide conjugates, thereby forming one or more hybridized duplexes, wherein each duplex comprises a target simple sequence repeat portion and a modified oligonucleotide conjugate portion;
contacting substantially all of the hybridized duplexes with a linking source, such that the linking molecule of each duplex that contacts the linking source forms a bond with the linking source; and
separating substantially all of the hybridized duplexes from the sample of nucleic acids by extracting the linking source from the sample. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 26, 29, 30)
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24. An in vitro method of capturing one or more target simple sequence repeats, wherein the method comprises the steps of:
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providing one or more modified oligonucleotide conjugates, wherein each of the modified oligonucleotide conjugates comprises at least one locked nucleic acid and a linking molecule;
incubating a sample of nucleic acids with the modified oligonucleotide conjugates, thereby forming one or more hybridized duplexes, wherein each duplex comprises a target simple sequence repeat portion and a modified oligonucleotide conjugate portion;
binding the linking molecule biotin on the modified oligonucleotides to streptavidin on coated magnetic beads, such that the magnetic beads are linked to the hybridization duplexes;
separating the hybridized duplexes from other materials with a magnet;
washing the hybridized duplexes;
incubating the hybridized duplexes with buffer of pH of about 9.5 such that the targeted simple sequence repeat dissociates from the modified oligonucleotide conjugate and the magnetic bead;
transforming the simple sequence repeats in E coli; and
sequencing the transformed simple sequence repeats.
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25. A hybridized duplex comprising:
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a locked nucleic acid portion, and a simple sequence repeat portion.
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27. A strand displacement method of capturing target nucleic acids, wherein the improvement comprises using one or more target nucleic acid molecules having a nucleotide sequence which comprises one or more simple sequence repeats.
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28. A kit for capturing target simple sequence repeats, comprising:
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one or more modified oligonucleotide conjugates, wherein each of the modified oligonucleotide conjugates comprises at least one locked nucleic acid and a linking molecule. a hybridized duplex comprised of a simple sequence repeat portion and a modified oligonucleotide conjugate portion;
a linking source, wherein the linking source is attachable to the linking molecule of the modified oligonucleotide conjugate; and
a means for separating the hybridized duplexes from a sample of nucleic acids.
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Specification