Methods, kits and compositions pertaining to combination oligomers and libraries for their preparation
First Claim
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1. A composition comprising:
- (a) a polynucleobase strand; and
(b) a combination oligomer that comprises a first oligomer block and a second oligomer block that are each independently a peptide nucleic acid, PNA chimera or PNA combination oligomer;
wherein the first and second oligomer blocks are linked covalently to each other by a linker that is at least three atoms in length, and the first and second oligomer blocks are sequence specifically hybridized juxtaposed to a target sequence of contiguous nucleobases in the polynucleobase strand to thereby form a double stranded target sequence/combination oligomer complex such that there is no gap or gap base.
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Abstract
This invention pertains to the field of combination oligomers, including the block synthesis of combination oligomers in the absence of a template, as well as related methods, kits, libraries and other compositions.
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Citations
49 Claims
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1. A composition comprising:
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(a) a polynucleobase strand; and (b) a combination oligomer that comprises a first oligomer block and a second oligomer block that are each independently a peptide nucleic acid, PNA chimera or PNA combination oligomer; wherein the first and second oligomer blocks are linked covalently to each other by a linker that is at least three atoms in length, and the first and second oligomer blocks are sequence specifically hybridized juxtaposed to a target sequence of contiguous nucleobases in the polynucleobase strand to thereby form a double stranded target sequence/combination oligomer complex such that there is no gap or gap base. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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16. A method comprising:
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(a) contacting a polynucleobase strand comprising a target sequence of contiguous nucleobases with a combination oligomer under suitable hybridization conditions; wherein the combination oligomer comprises a first oligomer block and a second oligomer block that are each independently a peptide nucleic acid, PNA chimera or PNA combination oligomer; wherein the first and second oligomer blocks are linked covalently to each other by a linker that is at least three atoms in length; and wherein the first and second oligomer blocks are sequence specifically hybridized juxtaposed to the target sequence of contiguous nucleobases such that there is no gap or gap base, to thereby form a double stranded target sequence/combination oligomer complex; and (b) determining the complex to thereby determine the target sequence. - View Dependent Claims (17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35)
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36. A method comprising:
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(a) contacting a nucleic acid sample with at least two independently detectable combination oligomers, wherein (i) each independently detectable combination oligomer comprises a first oligomer block and a second oligomer block that are each independently a peptide nucleic acid, PNA chimera or PNA combination oligomer and are linked covalently to each other by a linker that is at least three atoms in length; and (ii) the first and second oligomer blocks taken together encode a probing nucleobase sequence that is designed to sequence specifically hybridize juxtaposed to a target sequence of contiguous nucleobases, such that there is no gap or gap base, in a polynucleobase strand of the nucleic acid sample to thereby form a double stranded target sequence/independently detectable combination oligomer complex, and the probing nucleobase sequence in each independently detectable combination oligomer differs from the other by at least one nucleobase; (b) contacting the nucleic acid sample and combination oligomers with one or more reagents suitable for performing a nucleic acid amplification reaction that amplifies nucleic acid present in the sample; (c) performing the nucleic acid amplification reaction in the presence of the nucleic acid, the combination oligomers and the reagents; (d) determining complex formation for each independently detectable combination oligomer/target sequence complex to thereby determine whether the nucleic acid present in the sample is heterozygous or homozygous for a particular single nucleotide polymorphism. - View Dependent Claims (37, 38, 39, 40, 41, 42, 43, 44, 45, 46)
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47. A method comprising:
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(a) contacting a combination oligomer with a possible binding partner under suitable binding conditions to thereby possibly form a combination oligomer/binding partner complex;
wherein the combination oligomer is a polymer comprising a segment of the formula;
A-W-C;wherein, A and C are oligomer blocks that are each independently a peptide nucleic acid, PNA chimera or PNA combination oligomer and are optionally linked to other moieties; and W is a linker of at least three atoms in length and; (i) covalently links oligomer block A to oligomer block C; and (ii) is a cleavage site for an enzyme; and (b) treating the product of step (a) with an enzyme suitable for cleaving the cleavage site under suitable enzyme cleaving conditions; and (c) determining whether or not the combination oligomer has been cleaved by the activity of the enzyme to thereby determine whether or not the combination oligomer/binding partner complex formed wherein, if the combination oligomer/binding partner complex forms, the combination oligomer binds juxtaposed to the binding partner complex such that there is no gap or gap base. - View Dependent Claims (48, 49)
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Specification