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

• US 7,745,126 B2
• Filed: 12/26/2006
• Issued: 06/29/2010
• 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:
  US11/616,141
• Publication Number:
  US 20080085837A1
• Time in Patent Office: 1,281 Days
• Field of Search: 435/6, 536/23.1, 536/24.3, 536/25.3, 536/26.6
• US Class Current: 435/6.14
• 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. An array of at least two oligomers, wherein at least one of the oligomers is a combination oligomer that comprises a segment having the formula:

A-B-C

wherein;

each of A and C is an oligomer block independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer and each of A and C is optionally linked to other moieties; and

B is a linker of at least three atoms in length that covalently links oligomer block A to oligomer block C;

wherein;

oligomer blocks A and C 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.

3. The array 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.

4. The array of claim 3, 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.

5. The array of claim 1, wherein at least one of the at least two oligomers 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.

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

7. The array of claim 1, wherein at least one of the at least two 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 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.

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

9. The array of claim 8, wherein the energy transfer set of each combination oligomer comprises a single donor moiety and a single acceptor moiety.

10. The array of claim 9, wherein both the donor and acceptor moieties are fluorophores.

11. The array of claim 9, wherein the donor moiety is a donor fluorophore and the acceptor moiety is a non-fluorescent quencher moiety.

12. The array of claim 1, wherein each combination oligomer further comprises one or more reporter moieties.

13. The array of claim 1, wherein each combination oligomer is unlabeled.

2. The away of clam 1, wherein the linker is not part of a nucleobase containing backbone subunit of the polymer.

14. A method comprising:

(a) reacting, at a site on a solid surface, a first oligomer block, a second oligomer block, and optionally a condensation reagent or reagents under condensation conditions to thereby form a combination oligomer having a linker of at least three atoms in length that covalently links the first oligomer block to the second oligomer block;

wherein;

(i) one of said two oligomer blocks is support bound;

(ii) each of the first and second oligomer blocks independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer;

(iii) one or both oligomer blocks do not comprise nucleobase protecting groups; and

(iv) the combination oligomer forms in the absence of a template; and

(b) repeating step (a) at one or more sites until the array of combination oligomers is constructed,

with the further proviso that 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.

15. The method of claim 14, wherein the linker is not part of a nucleobase containing backbone subunit of the polymer.

16. A method comprising:

(a) reacting, at a site on a solid surface, a combination oligomer having a linker of at least three atoms in length that covalently links the first oligomer block to the second oligomer block with a surface functional group to thereby attached the combination oligomer to the surface of the array, wherein;

(i) each of the first and second oligomer blocks independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer;

(ii) one or both oligomer blocks do not comprise nucleobase protecting groups; and

(b) repeating step (a) at one or more sites until the array of combination oligomers is constructed,

with the further proviso that the combination oligomer hybridizes juxtaposed to a target sequence of contiguous nucleobases, with no gap or gap base.

17. The method of claim 16, wherein the linker is not part of a nucleobase containing backbone subunit of the polymer.

18. An array of at least two oligomers, wherein at least one of the oligomers is a combination oligomer that comprises a segment having the formula:

A-B-C

wherein;

each of A and C is an oligomer block independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer and each of A and C is optionally linked to other moieties; and

B is a linker of at least three atoms in length that covalently links oligomer block A to oligomer block C;

wherein;

oligomer blocks A and C 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,

with the further proviso that the linker is not part of a nucleobase containing backbone subunit of the polymer.

19. An array of at least two oligomers, wherein at least one of the oligomers is a combination oligomer that comprises a segment having the formula:

A-B-C

wherein;

each of A and C is an oligomer block independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer and each of A and C is optionally linked to other moieties; and

B is a linker of at least three atoms in length that covalently links oligomer block A to oligomer block C;

wherein;

oligomer blocks A and C 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

wherein at least one of the at least two 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 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.

20. The array of claim 19, wherein the labels of the energy transfer set are linked to the distal-most termini of the oligomer blocks or to sites within the oligomer blocks.

21. The array of claim 20, wherein the energy transfer set of each combination oligomer comprises a single donor moiety and a single acceptor moiety.

22. The array of claim 21, wherein both the donor and acceptor moieties are fluorophores.

23. The array of claim 21, wherein the donor moiety is a donor fluorophore and the acceptor moiety is a non-fluorescent quencher moiety.

24. A method comprising:

(a) reacting, at a site on a solid surface, a first oligomer block, a second oligomer block, and optionally a condensation reagent or reagents under condensation conditions to thereby form a combination oligomer having a linker of at least three atoms in length that covalently links the first oligomer block to the second oligomer block, wherein;

(i) one of said two oligomer blocks is support bound;

(ii) each of the first and second oligomer blocks independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer;

(iii) one or both oligomer blocks do not comprise nucleobase protecting groups; and

(iv) the combination oligomer forms in the absence of a template; and

(b) repeating step (a) at one or more sites until the array of combination oligomers is constructed,

with the further proviso that the linker is not part of a nucleobase containing backbone subunit of the polymer.

25. The method of claim 24, wherein 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.

26. A method comprising:

(a) reacting, at a site on a solid surface, a combination oligomer having a linker of at least three atoms in length that covalently links the first oligomer block to the second oligomer block with a surface functional group to thereby attached the combination oligomer to the surface of the array, wherein;

(i) each of the first and second oligomer blocks independently selected from the group consisting of a peptide nucleic acid, a PNA chimera and a PNA combination oligomer;

(ii) one or both oligomer blocks do not comprise nucleobase protecting groups; and

(b) repeating step (a) at one or more sites until the array of combination oligomers is constructed,

with the further proviso that the linker is not part of a nucleobase containing backbone subunit of the polymer.

27. The method of claim 26, wherein 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.