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

• US 20080269074A1
• Filed: 12/26/2006
• Published: 10/30/2008
• 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 7,851,155 B2
• Time in Patent Office: Days
• US Class Current: 506/26
• 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 method comprising:

reacting 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) the first and second oligomer blocks are each independently a peptide nucleic acid oligomer, PNA chimera or PNA combination oligomer;

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

(iii) the combination oligomer forms in the absence of a template.

2. The method of claim 1, wherein the combination oligomer, as formed, is further elongated;

said method further comprising;

(a) optionally deprotecting the previously formed combination oligomer; and

(b) reacting the combination oligomer with a third oligomer block and optionally a condensation reagent or reagents under condensation conditions to thereby form an elongated combination oligomer having a covalent linkage of at least three atoms in length that covalently links the third oligomer block to the combination oligomer wherein, the elongated combination oligomer forms in the absence of a template.

3. The method of claim 2, wherein steps (a)-(b) are repeated until the combination oligomer is of the desired length.

4. The method of claim 1, wherein the combination oligomer forms in greater than fifty percent yield.

5. The method of claim 1 wherein at least one of the oligomer blocks contains at least one region of constant nucleobase sequence and at least one region containing variable nucleobase sequence.

6. The method of claim 5 wherein the constant nucleobase sequence is from 1 to 10 nucleobase containing subunits in length.

7. The method of claim 5, wherein the variable nucleobase sequence is from 3 to 8 nucleobase containing subunits in length.

8. The method of claim 1, wherein one of the two oligomer blocks is a peptide nucleic acid having a C-terminal amide and an unprotected N-terminal natural amino acid.

9. The method of claim 8, wherein the unprotected N-terminal amino acid is selected from the group consisting of:

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

10. The method of claim 1, wherein one of the two oligomer blocks is a peptide nucleic acid having a C-terminal natural amino acid moiety and a capped or protected N-termini.

11. The method of claim 10, wherein the C-terminal natural amino acid is selected from the group consisting of:

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

12. The method of claim 1, wherein the oligomer blocks contain from 3 to 15 nucleobase containing subunits.

13. The method of claim 1, wherein the condensation is performed in an aqueous solution using a water-soluble carbodiimide as the condensation reagent.

14. The method of claim 13, wherein the condensation is performed in the presence of an activating reagent.

15. The method of claim 13, wherein the water-soluble carbodiimide is EDC and the pH of the reaction is less than 6.5.

16. The method of claim 14, wherein the activating agent is HOAt or HOBt.

17. The method of claim 1, wherein the combination oligomer, as formed by the ligation reaction, comprises from 6 to 30 nucleobase containing subunits.

18. The method of claim 1, wherein the first and second oligomer blocks are peptide nucleic acid.

19. The method 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.

20. The method of claim 19, 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.

21. The method of claim 1, wherein the each of the two oligomer blocks comprise at least one label of an energy transfer set of labels 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 that is formed by the ligation reaction is hybridized to a target sequence as compared to when the combination oligomer is in a non-hybridized state.

22. The method of claim 21, wherein the labels of the energy transfer set are linked to the distal-most termini of the oligomer blocks of the formed combination oligomer or linked to sites within the oligomer blocks.

23. The method of claim 22, wherein the energy transfer set comprises a single donor moiety and a single acceptor moiety.

24. The method of claim 23, wherein both the donor and acceptor moieties are fluorophores.

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

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

27. The method of claim 26, 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.

28. The method of claim 26, wherein the reporter moieties are selected from the group consisting of:

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

29. The method of claim 1, wherein the linker comprises a cleavage site for an enzyme.

30. The method of claim 1, wherein the combination oligomer, as formed, is support bound.

31. The method of claim 1, wherein the combination oligomer, as formed, exists at a unique position of an array.

32. The method of claim 1, wherein the combination oligomer, as formed, comprises a probing nucleobase sequence that is designed to sequence specifically hybridize juxtaposed to a target sequence of contiguous nucleobases in a polynucleobase strand such that there is no gap or gap base.