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US 7,256,275 B2Granted
Methods, kits and compositions pertaining to combination oligomers and libraries for their preparation
AssigneeBoston Probes, Inc.
InventorsJames M. Coull, Mark J. Fiandaca, Mark D. Kristjanson, Jens J. Hyldig-Nielsen, Theresa S. Creasey
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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.
Claims68
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 that is not part of a nucleobase containing backbone subunit of the polymer and the first and second oligomer blocks are sequence specifically hybridized to a target sequence of contiguous nucleobases in the polynucleobase strand to thereby form a double stranded target sequence/combination oligomer complex.
1 more element
A method comprising:
- (a) contacting a palynucleobase 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 tat 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 that is not part of a nucleobase containing backbone subunit of the polymer;
- and
- wherein the first and second oligomer blocks are sequence specifically hybridized to the target sequence of contiguous nucleobases to thereby form a double stranded target sequence/combination oligoiner complex;
- and
- (b) determining the complex to thereby determine the target sequence.
4 more elements
A method comprising:
- (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 that is not part of a nucleobase containing backbone subunit of the polymer;
- and
- (ii) the first and second oligomer blocks taken together encode a probing nucleobase sequence that is designed to sequence specifically hybridize to a target sequence of contiguous nucleobases in a polynucleobase strand of the nucleic add 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 the nucleic acid present in the sample;
- (c) performing the nucleic add amplification 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 add is heterozygous or homozygous for a particular SNP.
4 more elements
A method comprising:
- (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 pep tide nucleic add, 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 that is not part of a nucleobase containing backbone subunit of the polymer and that:
- (i) covalently links oligomer block A to oligomer block C;
- and
- (ii) is a deavage site for an enzyme;
- (b) freating 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.
10 more elements
Dependencies are inferred from the claim text.