Methods, kits and compositions pertaining to combination oligomers and libraries for their preparation

• US 7,566,420 B1
• Filed: 12/26/2006
• Issued: 07/28/2009
• Est. Priority Date: 03/09/2001
• Status: Expired due to Fees

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Boston Probes, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Coull, James M., Hyldig-Nielsen, Jens J., Fiandaca, Mark J., Kristjanson, Mark D., Creasey, Theresa S.
• Primary Examiner(s): Riley; Jezia
• Application Number:
  US11/616,071
• Time in Patent Office: 945 Days
• Field of Search: 435/6, 435/91.1, 422/68.1, 536/23.1, 536/24.3, 536/24.33, 536/25.3, 536/26.6
• US Class Current: 422/68.1
• 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 kit comprising:

(a) two or more independently detectable combination oligomers wherein,

(i) each of said independently detectable combination oligomers comprises a first oligomer block and a second oligomer block that are each independently a peptide nucleic acid, a PNA chimera or PNA combination oligomer and are linked covalently to each other by a linker that is at least three atoms in length that is not part of a nucleobase containing backbone subunit of the polymer,

(ii) in each independently detectable combination oligomer, 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, to thereby form a double stranded target sequence/combination oligomer complex, and the probing nucleobase sequence in each independently detectable combination oligomer differs from the probing nucleobase sequences of the other independently detectable combination oligomer(s) by at least one nucleobase, and

(iii) each independently detectable combination oligomer contains at least one independently detectable label;

(b) optionally one or more oligonucleotides;

(c) optionally one or more buffers;

(d) optionally one or more nucleotide triphosphates;

(e) optionally a nucleic acid amplification master mix; and

(f) optionally one or more polymerase enzymes.

2. The kit of claim 1, which optionally comprises two or more oligonucleotide primers.

3. The kit of claim 1, wherein each combination oligomer comprises 6 to 30 nucleobase containing subunits.

4. The kit of claim 1, wherein the oligomer blocks of each combination oligomer are peptide nucleic acid.

5. The kit of claim 1, wherein the linker of the combination oligomers 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.

6. The kit of claim 5, 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.

7. The kit of claim 1, wherein the independently detectable reporter moieties are independently linked at the oligomer block termini, linked at a position internal to the oligomer blocks or linked at a position integral to the linker.

8. The kit of claim 7, wherein the reporter moieties are selected from the group consisting of:

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

9. The kit of claim 1, wherein the linker of each combination oligomer comprises a cleavage site for an enzyme.

10. The kit of claim 1, wherein each combination oligomer is support bound.

11. The kit of claim 1, wherein at least one of the combination oligomers 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 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.

12. The kit of claim 11, wherein all of the combination oligomers comprise an energy transfer set and each of the combination oligomers is an independently detectable self-indicating combination oligomer.

13. The kit of claim 11, wherein the labels of the energy transfer set are linked at the distal-most termini of the oligomer block or to sites within the oligomer blocks.

14. The kit of claim 11, wherein the energy transfer set comprises a single donor moiety and a single acceptor moiety.

15. The kit of claim 14, wherein both the donor and acceptor moieties are fluorophores.

16. The kit of claim 14, wherein the donor moiety is a donor fluorophore and the acceptor is a non-fluorescent quencher moiety.

17. A kit comprising:

(a) two or more independently detectable combination oligomers wherein,

(i) each of said independently detectable combination oligomers comprises a first oligomer block and a second oligomer block that are each independently a peptide nucleic acid, a 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,

(ii) in each independently detectable combination oligomer, 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 to thereby form a double stranded target sequence/combination oligomer complex, and the probing nucleobase sequence in each independently detectable combination oligomer differs from the probing nucleobase sequences of the other independently detectable combination oligomer(s) by at least one nucleobase, and

(iii) each independently detectable combination oligomer contains at least one independently detectable label;

(b) optionally one or more oligonucleotides;

(c) optionally one or more buffers;

(d) optionally one or more nucleotide triphosphates;

(e) optionally a nucleic acid amplification master mix; and

(f) optionally one or more polymerase enzymes.

18. The kit of claim 17, which optionally comprises two or more oligonucleotide primers.

19. The kit of claim 17, wherein each combination oligomer comprises 6 to 30 nucleobase containing subunits.

20. The kit of claim 17, wherein the oligomer blocks of each combination oligomer are peptide nucleic acid.

21. The kit of claim 17, wherein the linker of the combination oligomers 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.

22. The kit of claim 21, 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.

23. The kit of claim 17, wherein the independently detectable reporter moieties are independently linked at the oligomer block termini, linked at a position internal to the oligomer blocks or linked at a position integral to the linker.

24. The kit of claim 23, wherein the reporter moieties are selected from the group consisting of:

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

25. The kit of claim 17, wherein the linker of each combination oligomer comprises a cleavage site for an enzyme.

26. The kit of claim 17, wherein each combination oligomer is support bound.

27. The kit of claim 17, wherein at least one of the combination oligomers 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 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.

28. The kit of claim 27, wherein all of the combination oligomers comprise an energy transfer set and each of the combination oligomers is an independently detectable self-indicating combination oligomer.

29. The kit of claim 27, wherein the labels of the energy transfer set are linked at the distal-most termini of the oligomer block or to sites within the oligomer blocks.

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

31. The kit of claim 30, wherein both the donor and acceptor moieties are fluorophores.

32. The kit of claim 30, wherein the donor moiety is a donor fluorophore and the acceptor is a non-fluorescent quencher moiety.