Self-assembly of molecules using combinatorial hybridization

• US 20060199207A1
• Filed: 02/24/2006
• Published: 09/07/2006
• Est. Priority Date: 02/24/2005
• Status: Abandoned Application

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Matysiak, Stefan M.
• Application Number:
  US11/360,576
• Publication Number:
  US 20060199207A1
• Time in Patent Office: Days
• US Class Current: 435/6.18
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00677 Ex-situ synthesis followed by deposition on the substrate
• CPC Class Codes: B01J 2219/0072 Organic compounds
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: B01J 2219/00725 Peptides
• CPC Class Codes: B01J 2219/00729 Peptide nucleic acids [PNA]
• CPC Class Codes: C07K 1/047 Simultaneous synthesis of different peptide species; Peptide libraries
• CPC Class Codes: C07K 9/00 Peptides having up to 20 amino acids, containing saccharide radicals and having a fully defined sequence; Derivatives thereof
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 50/14 : Solid phase synthesis, i.e. wherein one or more library building blocks are bound to a solid support during library creation; Particular methods of cleavage from the solid support
• CPC Class Codes: C40B 50/18 : using a particular method of attachment to the solid support
• CPC Class Codes: G01N 33/54353 : with ligand attached to the carrier via a chemical coupling agent coatings G01N33/54393
• CPC Class Codes: G01N 33/6803 : General methods of protein analysis not limited to specific proteins or families of proteins

Abstract

Simple and convenient methods for arranging molecules of interest in a pre-determined pattern are described. The methods use combinatorial hybridization based on interactions between complementary nucleic acid sequences to arrange the molecules of interest. The resulting arrangements, kits containing the components used in the methods, and methods of using the resulting arrangements are also disclosed.

Claims

1. An array comprising a plurality of conjugates and a plurality of anchors, wherein:

each of the conjugates comprises a molecule bound to a nucleic acid fragment, wherein the molecule of each conjugate is not the same as the molecule of any of the other conjugates;

each of the anchors is immobilized on a surface and comprises at least two nucleic acid fragments; and

the nucleic acid fragment of each conjugate is hybridized to at least one of the nucleic acid fragments of the anchors.

2. The array of claim 1, wherein the molecules are peptides, peptoids, proteins, steroids or analogues thereof, hormones, carbohydrates, polycarbohydrates, aminoglycosides, aptamers of L or D oligoribonucleotides, nucleoside antibiotics, L-nucleoside analogues, oligoglycosids, macrolids, polyenes, oligolactones, polyethers, tetracycline, anthracycline, p-chinoid macrolactams, terpenoids, isopren and analogues thereof, peptide antibiotics, or benzodiazepine.

3. The array of claim 2, wherein the peptides are tri-peptides.

4. The array of claim 1, wherein at least two of the anchors comprise the same nucleic acid fragment.

5. The array of claim 1, wherein the nucleic acid fragment in each conjugate is L-DNA or PNA.

6. The array of claim 1, wherein at least one of the nucleic acid fragments in each anchor is L-DNA or PNA.

7. The array of claim 6, wherein at least one of the nucleic acid fragments in each anchor is L-DNA.

8. A method of arranging molecules comprising:

(a) immobilizing a first set of nucleic acid fragments with known sequences in a predetermined pattern on a surface to form anchors;

(b) contacting the anchors with a mixture comprising conjugates of a second set of nucleic acid fragments and the molecules, wherein the nucleic acid fragment in each conjugate has a sequence complementary to at least part of one of the nucleic acid fragments in the anchors; and

(c) incubating the anchors and the mixture for a time and under conditions sufficient for the conjugates to bind to the anchors, thereby arranging the molecules.

9. The method of claim 8, wherein the molecules to be arranged are peptides, peptoids, proteins, steroids or analogues thereof, hormones, carbohydrates, polycarbohydrates, aminoglycosides, aptamers of L or D oligoribonucleotides, nucleoside antibiotics, L-nucleoside analogues, oligoglycosids, macrolids, polyenes, oligolactones, polyethers, tetracycline, anthracycline, p-chinoid macrolactams, terpenoids, isopren and analogues thereof, peptide antibiotics, or benzodiazepine.

10. The method of claim 9, wherein the peptides are tri-peptides.

11. The method of claim 9, wherein the peptides comprise peptoids or D-amino acids.

12. The method of claim 8, wherein each of the anchors comprises two or more nucleic acid fragments, each of which is capable of binding at least one of the conjugates.

13. The method of claim 12, wherein at least two of the anchors comprise the same nucleic acid fragment.

14. The method of claim 8, wherein the surface is a porous surface.

15. The method of claim 8, wherein the surface is a well of a multi-well plate.

16. The method of claim 8, wherein at least one of the nucleic acid fragments in each anchor is L-DNA or PNA.

17. The method of claim 16, wherein at least one of the nucleic acid fragments in each anchor is L-DNA.

18. The method of claim 8, wherein the immobilization is achieved using chemical conjugation or oxime coupling.

19. The method of claim 8, which further comprises stabilizing the anchor/conjugate complexes using photo-induced crosslinking.

20. The method of claim 8, wherein the nucleic acid fragment in each conjugate is L-DNA or PNA.

21. A method of characterizing a protein comprising:

(a) immobilizing a first set of nucleic acid fragments with known sequences in a predetermined pattern on a surface to form anchors;

(b) contacting the anchors with a mixture comprising conjugates of a second set of nucleic acid fragments and peptide fragments, wherein the nucleic acid fragment in each conjugate has a sequence complementary to at least part of one of the nucleic acid fragments in the anchors;

(c) incubating the anchors and the mixture for a time and under conditions sufficient for the conjugates to bind to the anchors to provide an array of anchor-conjugate complexes;

(d) contacting the array with the protein for a time and under conditions sufficient for the protein to bind to one or more of the complexes; and

(e) detecting the binding of the protein to the complexes to obtain a binding pattern;

wherein the binding pattern is characteristic of the protein.

22. The method of claim 21, wherein the characteristics of two or more of proteins are combined to provide an analytical probe for proteins.

23. The method of claim 22, wherein the analytical probe is a protein chip.

24. The method of claim 22, wherein the analytical probe is an arrangement of peptide sequences in a capillary tube.

25. The method of claim 21, wherein the protein is a Major Histo-Compatibility (MHC) complex.

26. The method of claim 21, wherein the binding is detected by chemiluminescence, bioluminescence, silver staining, radioisotopes, or proximity ligation.

27. The method of claim 21, wherein each of the anchors comprises two or more nucleic acid fragments, each of which is capable of binding at least one of the conjugates.

28. The method of claim 27, wherein at least two of the anchors comprise the same nucleic acid fragment.

29. The method of claim 21, wherein the peptide fragments are tri-peptides.

30. The method of claim 21, wherein the surface is a porous surface.

31. The method of claim 21, wherein the surface is a well on a multi-well plate.

32. The method of claim 21, wherein at least one of the nucleic acid fragments in each of the anchors is L-DNA or PNA.

33. The method of claim 32, wherein at least one of the nucleic acid fragments in each of the anchors is L-DNA.

34. The method of claim 21, wherein the immobilization is achieved using chemical conjugation or oxime coupling.

35. The method of claim 21, which further comprises stabilizing the anchor/conjugate complexes using photo-induced crosslinking.

36. The method of claim 21, wherein the method further comprises stabilizing the anchor/conjugate/protein complexes using photo-induced crosslinking.

37. The method of claim 35, wherein the method further comprises stabilizing the anchor/conjugate/protein complexes using photo-induced crosslinking.

38. The method of claim 21, wherein the nucleic acid fragment in the conjugate is L-DNA or PNA.

39. A kit for a protein assay comprising:

a multi-well plate, each well containing anchors, each of which is immobilized on the surface of the well and comprises one or more of nucleic acid fragments; and

one or more peptide libraries, each library comprising conjugates, each of which comprising a nucleic acid fragment and a peptide, and wherein the nucleic acid fragment in each conjugate has a sequence complementary to at least part of one of the immobilized nucleic acid fragments in the anchors.

40. The kit of claim 39, wherein each of the immobilized nucleic acid fragments is L-DNA or PNA.

41. The kit of claim 40, wherein each of the immobilized nucleic acid fragments is L-DNA.

42. The kit of claim 41, wherein the nucleic acid fragment in each of the conjugate is L-DNA or PNA.