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 sequences, wherein the method comprises the steps of:
- providing one or more modified, high stringency oligonucleotide conjugates (“
MHSO”
) comprising a nucleotide sequence that is complementary to a target sequence and a linking molecule;
incubating a sample of nucleic acids comprising the target sequence to be captured with the MHSO conjugate under non-denaturing conditions, thereby forming one or more hybridized duplexes, wherein each duplex comprises a target sequence 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 sequences utilizing modified, high stringency nucleic acids and strand displacement stategies. In this method, one or more modified, high stringency oligonucleotide (MHSO) conjugates are selected in which the conjugates are constructed from at least one modified nucleic acid, such as, for example, a locked nucleic acid (“LNA”) and a linking molecule. When incubated with a sample of nucleic acids, these MHSO conjugates capture the target sequence 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 sequence portion and a MHSO conjugate portion. The captured target sequences 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.
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Citations
37 Claims
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1. An in vitro method of capturing one or more target sequences, wherein the method comprises the steps of:
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providing one or more modified, high stringency oligonucleotide conjugates (“
MHSO”
) comprising a nucleotide sequence that is complementary to a target sequence and a linking molecule;
incubating a sample of nucleic acids comprising the target sequence to be captured with the MHSO conjugate under non-denaturing conditions, thereby forming one or more hybridized duplexes, wherein each duplex comprises a target sequence 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, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 32, 35)
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12. An in vitro method of capturing one or more target sequences, wherein the method comprises the steps of:
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providing one or more LNA conjugates comprising a nucleotide sequence that is complementary to a target sequence and a linking molecule, wherein at least in one of the LNA conjugates 85% of the nucleobases are locked nucleoside analogues (LNAs);
incubating a sample of nucleic acids comprising the target sequence to be captured with the LNA conjugate in a low stringency buffer solution under non-denaturing conditions, thereby forming one or more hybridized duplexes, wherein each duplex comprises a target sequence 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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28. An in vitro method of capturing one or more target sequences, wherein the method comprises the steps of:
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providing one or more LNA conjugates comprising a nucleotide sequence that is complementary to a target sequence and a linking molecule, wherein at least in one of the LNA conjugates 100% of the nucleobases are locked nucleoside analogues (LNAs);
incubating a sample of nucleic acids comprising the target sequence to be captured with the LNA conjugate in a low stringency buffer solution with a salt conentration of between 10 mM and 100 mM under non-denaturing conditions at a temperature of between about 65°
C. to about 80°
C., thereby forming one or more hybridized duplexes, wherein each duplex comprises a target sequence 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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33. 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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34. A hybridized duplex comprising a locked nucleic acid portion, and a simple sequence repeat portion.
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36. 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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37. 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