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

• US 20090163381A1
• Filed: 12/26/2006
• Published: 06/25/2009
• Est. Priority Date: 03/09/2001
• Status: Abandoned Application

• 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.
• Application Number:
  US11/616,110
• Publication Number:
  US 20090163381A1
• Time in Patent Office: Days
• US Class Current: 506/16
• 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 compound library comprising a bifunctional single set of oligomer blocks that are suitable for producing both terminal oligomer blocks and condensation oligomer blocks by the removal of different protecting groups wherein the oligomer blocks of the bifunctional set are peptide nucleic acid oligomer, PNA chimera or PNA combination oligomer;

provided however that;

(a) the oligomer blocks are selected to comprise functional moieties that form a linker of at least three atoms in length that covalently links the two-oligomer blocks when a terminal oligomer block is condensed with a condensation oligomer block;

(b) the oligomer blocks are not support bound; and

(c) the oligomer blocks do not comprise nucleobase-protecting groups.

3. The compound library of claims 1 or 2, wherein each oligomer block comprises from 3 to 15 nucleobase containing subunits.

4. The compound library of claims 1 or 2, wherein the oligomer blocks of the library are peptide nucleic acid.

5. The compound library of claims 1 or 2, wherein the oligomer blocks of the library are independently either trimers, tetramers, pentamers, hexamers, heptamers or octamers.

6. The compound library of claim 1, wherein the oligomer blocks contain at least one region of constant nucleobase sequence and at least one region containing variable nucleobase sequence.

9. The compound library of claims 6 or 8, wherein the number of different oligomer blocks of a set is 4ⁿ, wherein n is a whole number in the range of 3-8 representing the number of variable nucleobase positions of the variable nucleobase sequence in the blocks of the set.

2. A compound library comprising at least one set of terminal oligomer blocks and at least one set of condensing oligomer blocks, wherein each set of blocks comprises two or more different oligomers and said oligomer blocks are selected from the group consisting of:

peptide nucleic acid oligomer, PNA chimera and PNA combination oligomer, provided however that;

(a) the oligomer blocks are selected to comprise functional moieties that form a linker of at least three atoms in length when a terminal oligomer block is condensed with a condensation oligomer block;

(b) the oligomer blocks are not support bound; and

(c) the oligomer blocks do not comprise nucleobase-protecting groups.

7. The compound library of claim 2, wherein the terminal blocks contain at least one region of constant nucleobase sequence and at least one region containing variable nucleobase sequence and/or the condensing blocks contain at least one region of constant nucleobase sequence and at least one region containing variable nucleobase sequence.

8. The compound library of claim 7, wherein the constant nucleobase sequence is from 1-10 nucleobase containing subunits in length and the variable nucleobase sequence is from 3-8 nucleobase containing subunits in length.

10. The compound library of claim 2, wherein the number of different terminal oligomer blocks of a set is 4ⁿ, wherein n is a whole number in the range of 3-8 representing the number of variable nucleobase positions in the terminal blocks of the set and/or the number of different condensing oligomer blocks of a set is 4ⁿ, wherein n is a whole number in the range of 3-8 representing the number of variable nucleobase positions in the condensation blocks of the set.

11. The compound library of claim 2, wherein the terminal oligomer blocks of the library are peptide nucleic acids having a C-terminal amide and an N-terminal natural amino acid.

12. The compound library of claim 11, wherein the N-terminal natural amino acid is selected from the group consisting of:

glycine, lysine, cystine, glutamic add and aspartic acid.

13. The compound library of claim 2, wherein the terminal oligomer blocks of the library are peptide nucleic acids having a C-terminal amide and an N-terminal reactive moiety selected from the group consisting of:

aminooxyacetyl, 2-thioacetyl, 3-thiopropionyl and malimido.

14. The compound library of claim 2, wherein the condensation oligomer blocks of the library are peptide nucleic acids having a C-terminal natural amino acid moiety and a capped, protected or labeled N-terminus.

15. The compound library of claim 14, wherein the C-terminal natural amino acid moiety is selected from the group consisting of:

glycine, lysine, cystine, glutamic acid and aspartic acid.

16. The compound library of claim 2, wherein the condensation oligomer blocks of a set are peptide nucleic acids having a capped, protected or labeled N-terminus and a C-terminal haloacetyl moiety selected from the group consisting of:

chloroacetyl bromoacetyl and iodoacetyl.

17. The compound library of claim 2, wherein condensation of a terminal oligomer block with a condensing oligomer block forms a linker that is a substrate for an enzyme.

18. The compound library of claim 2, wherein condensation of a terminal oligomer block of the set with a condensing oligomer block of the set forms a linker selected from the group consisting of:

one amino acid residue, two amino add 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.

19. The compound library of claim 18, 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.

20. The compound library of claims 2, wherein the oligomer blocks of at least one set further comprise one or more reporter moieties.

21. The compound library of claim 20, wherein the reporter moieties are selected from the group consisting of:

a chromophore, a fluorochrome, a quencher, a radioisotope and a hapten.

22. The compound library of claim 2, wherein the library comprises three or more sets of oligomer blocks wherein at least two sets are substantially identical except that they differ in the nature of an attached label such that the two or more different labeling schemes (one labeling scheme being common to each set of oligomer blocks) renders each set of oligomer blocks independently detectable.

23. The compound library of claim 22, wherein the library further comprises at least one set of oligomer blocks each comprising an acceptor or non-fluorescent quencher moiety such that the oligomer blocks of this set are suitable for ligation to the oligomer blocks of either of the two or more sets of oligomer blocks comprising independently detectable labels.

24. The compound library of claim 23, wherein pairs of independently detectable self-indicating combination oligomers are formed by the ligation of each of two independently detectable oligomer blocks to an oligomer block comprising an acceptor or quencher moiety.

25. The compound library of claim 2, wherein at least one set of terminal oligomer blocks is unlabeled.

27. The compound library of claim 2, wherein the oligomers of one of the sets of oligomer blocks are support bound.

28. The compound library of claim 2, wherein the oligomer blocks of at least one set of terminal oligomer blocks is support bound.

26. The compound library of claim, wherein at least one set of condensation oligomer blocks is unlabeled.