Methods, Kits and Compositions Pertaining to Combination Oligomers and Libraries for Their Preparation

• US 20080206747A1
• Filed: 12/22/2006
• Published: 08/28/2008
• Est. Priority Date: 03/09/2001
• Status: Active Grant

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applera Corporation (Thermo Fisher Scientific Incorporated)
• Inventors: Coull, James M., Hyldig-Nielsen, Jens J., Fiandaca, Mark J., Kristjanson, Mark D., Creasey, Theresa S.
• Granted Patent: US 7,638,279 B2
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C07B 2200/11 Compounds covalently bound to a solid support
• CPC Class Codes: C12Q 1/6816 characterised by the detection means C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2525/107 incorporating a peptide nucleic acid
• CPC Class Codes: C12Q 2531/113 PCR
• CPC Class Codes: C12Q 2565/137 Chromatographic separation
• CPC Class Codes: C40B 20/04 Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: C40B 40/00 Libraries per se, e.g. arrays, mixtures
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: Y10S 435/81 Packaged device or kit

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.

Claims

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.

2. The composition of claim 1, which further comprises a third oligomer block that is linked covalently to the first or second oligomer block by a second linker that is at least three atoms in length, such that the second linker is the same or different in kind from the first said linker.

3. The composition of claim 1, wherein the first and second oligomer blocks are peptide nucleic acids.

4. The composition of claim 1, wherein the linker is selected from the group consisting of:

one amino acid residue, two amino acid residues, three amino acid residues, one E-linker residue, two E-Linker residues, one O-linker residue, two O-linker residues, one X-linker residue and two X-linker residues.

5. The composition of claim 4, wherein the linker is selected from the group consisting of:

the amino acid glycine, the amino acid dimer gly-gly, the amino acid dimer gly-lys, the amino acid dimer lys-gly, the amino acid dimer glu-gly, the amino acid dimer gly-cys, the amino acid dimer cys-gly and the amino acid dimer asp-gly.

6. The composition of claim 1, wherein the combination oligomer further comprises at least one energy transfer set of labels such that at least one acceptor moiety of the energy transfer set is linked to one of the linked oligomer blocks of the combination oligomer whilst at least one donor moiety of the energy transfer set is linked to another of the linked oligomer blocks of the combination oligomer wherein the labels of the set are linked to the oligomer blocks at positions that facilitate a change in detectable signal of at least one label when the combination oligomer is hybridized to the target sequence as compared to when the combination oligomer is in a non-hybridized state.

7. The composition of claim 6, wherein the labels of the energy transfer set are linked to the distal-most termini of the oligomer block or to sites within the oligomer blocks.

8. The composition of claim 6, wherein the energy transfer set comprises a single donor moiety and a single acceptor moiety.

9. The composition of claim 8, wherein both the donor and acceptor moieties are fluorophores.

10. The composition of claim 8, wherein the donor moiety is a donor fluorophore and the acceptor moiety is a non-fluorescent quencher moiety.

11. The composition of claim 1, wherein the combination oligomer further comprises one or more reporter moieties.

12. The composition of claim 11, wherein the one or more reporter moieties are linked at the oligomer block termini, linked at a position internal to the oligomer blocks or linked at a position integral to the linker.

13. The composition of claim 11, wherein the reporter moieties are each independently selected from the group consisting of:

a chromophore, a fluorochrome, a quencher, a spin label, a radioisotope, an enzyme, a hapten and a chemluminescent compound.

14. The composition of claim 1, wherein the composition is support bound.

15. The composition of claim 1, wherein the composition exists at a unique position of an array.

16. A method comprising:

(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.

17. The method of claim 16, wherein the target sequence is a subsequence of a nucleic acid that has been amplified by a nucleic acid amplification process.

18. The method of claim 17, wherein the nucleic acid amplification process is selected from the group consisting of:

Polymerase Chain Reaction (PCR), Ligase Chain Reaction (LCR), Strand Displacement Amplification (SDA), Transcription-Mediated Amplification (TMA), Q-beta replicase amplification (Q-beta) and Rolling Circle Amplification (RCA).

19. The method of claim 16, wherein the target sequence is contained within a cell or organism.

20. The method of claim 16, wherein the target sequence is contained within nucleic acid that has been extracted from a cell or organism.

21. The method of claim 16, wherein the combination oligomer further comprises a third oligomer block that is linked covalently to the first or second oligomer block by a second linker that is at least three atoms in length, such that the second linker is the same or different in kind from the first said linker.

22. The method of claim 16, wherein the first and second oligomer blocks are peptide nucleic acids.

23. The method of claim 16, wherein the linker is selected from the group consisting of:

one amino acid residue, two amino acid residues, three amino acid residues, one E-linker residue, two E-Linker residues, one O-linker residue, two O-linker residues, one X-linker residue and two X-linker residues.

24. The method of claim 23, wherein the linker is selected from the group consisting of:

the amino acid glycine, the amino acid dimer gly-gly, the amino acid dimer gly-lys, the amino acid dimer lys-gly, the amino acid dimer glu-gly, the amino acid dimer gly-cys, the amino acid dimer cys-gly and the amino acid dimer asp-gly.

25. The method of claim 16, wherein the combination oligomer further comprises at least one energy transfer set of labels such that at least one acceptor moiety of the energy transfer set is linked to one of the linked oligomer blocks of the combination oligomer whilst at least one donor moiety of the energy transfer set is linked to another of the linked oligomer blocks of the combination oligomer wherein the labels of the set are linked to the oligomer blocks at positions that facilitate a change in detectable signal of at least one label when the combination oligomer is hybridized to the target sequence as compared to when the combination oligomer is in a non-hybridized state.

26. The method of claim 25, wherein the labels of the energy transfer set are linked to the distal-most termini of the oligomer blocks or linked at a position internal to the oligomer blocks.

27. The method of claim 26, wherein the energy transfer set comprises a single donor moiety and a single acceptor moiety.

28. The method of claim 27, wherein both the donor and acceptor moieties are fluorophores.

29. The method of claim 27, wherein the donor moiety is a donor fluorophore and the acceptor moiety is a non-fluorescent quencher moiety.

30. The method of claim 16, wherein the combination oligomer further comprises one or more reporter moieties.

31. The method of claim 16, wherein the target sequence is labeled with a reporter moiety.

32. The method of claim 16, wherein neither of the target sequence nor the combination oligomer are labeled with a reporter moiety and the complex is determined using a labeled antibody that specifically binds to said complex.

33. The method of claim 16, wherein the linker comprises a cleavage site for an enzyme.

34. The method of claim 16, wherein the combination oligomer is support bound.

35. The method of claim 16, wherein the combination oligomer exists at a unique position of an array.

36. 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

(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.

37. The method of claim 36, wherein each independently detectable combination oligomer comprises an independently detectable energy transfer set of labels such that at least one acceptor moiety of the set is linked to one of the linked oligomer blocks of the combination oligomer whilst at least one donor moiety of the set is linked to another of the linked oligomer blocks of the combination oligomer to thereby produce a change in detectable signal of at least one label when each combination oligomer is sequence specifically hybridized to its target sequence of contiguous nucleobases as compared to when the combination oligomer is in a non-hybridized state.

38. The method of claim 36, wherein the nucleic acid amplification reaction is selected from the group consisting of:

Polymerase Chain Reaction (PCR), Ligase Chain Reaction (LCR), Strand Displacement Amplification (SDA), Transcription-Mediated Amplification (TMA), Q-beta replicase amplification (Q-beta) and Rolling Circle Amplification (RCA).

39. The method of claim 37, wherein the nucleic acid amplification reaction is selected from the group consisting of:

Polymerase Chain Reaction (PCR), Ligase Chain Reaction (LCR), Strand Displacement Amplification (SDA), Transcription-Mediated Amplification (TMA), Q-beta replicase amplification (Q-beta) and Rolling Circle Amplification (RCA).

40. The method of claim 36, wherein the first and second oligomer blocks are peptide nucleic acids.

41. The method of claim 37, wherein the first and second oligomer blocks are peptide nucleic acids.

42. The method of claim 37, wherein the labels of each energy transfer set are linked to the distal-most termini of the oligomer blocks or to sites within the oligomer blocks.

43. The method of claim 37, wherein each energy transfer set comprises a single donor moiety and a single acceptor moiety.

44. The method of claim 43, wherein the donor moiety is a donor fluorophore and the acceptor is a non-fluorescent quencher moiety.

45. The method of claim 36, wherein one or more of the target sequence/independently detectable combination oligomer complexes is support bound.

46. The method of claim 37, wherein one or more of the target sequence/independently detectable combination oligomer complexes is support bound.

47. 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 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.

48. The method of claim 47, wherein the combination oligomer is a self-indicating combination oligomer comprising an energy transfer set of labels such that at least one acceptor moiety of the energy transfer set is linked to one of the linked oligomer blocks of the combination oligomer whilst at least one donor moiety of the energy transfer set is linked to another of the linked oligomer blocks of the combination oligomer wherein the labels of the set are linked to the oligomer blocks at positions that facilitate a change in detectable signal of at least one label when the combination oligomer is hybridized to a target sequence as compared to when the combination oligomer is in a non-hybridized state.

49. The method of claim 47, wherein the combination oligomer is support bound.