Device and methods for directed synthesis of chemical libraries

• US 20030182068A1
• Filed: 10/30/2002
• Published: 09/25/2003
• Est. Priority Date: 10/30/2001
• Status: Abandoned Application

• Current Assignee: Nanomics Biosystems Pty Limited
• Original Assignee: Nanomics Biosystems Pty Limited
• Inventors: Miller, Christopher R., Johnston, Angus, Way, Jeffery C., Battersby, Bronwyn J., Trau, Mathias
• Application Number:
  US10/283,741
• Publication Number:
  US 20030182068A1
• Time in Patent Office: Days
• US Class Current: 702/22
• 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 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00454 by chemical cleavage from the solid support
• CPC Class Codes: B01J 2219/00463 Directed sorting
• CPC Class Codes: B01J 2219/00466 in a slurry
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00502 Particles of irregular geometry
• CPC Class Codes: B01J 2219/00545 Colours
• CPC Class Codes: B01J 2219/00554 Physical means
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00592 Split-and-pool, mix-and-divide processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00689 using computers
• CPC Class Codes: B01J 2219/00695 Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00698 Measurement and control of process parameters
• CPC Class Codes: B01J 2219/00702 Processes involving means for analysing and characterising the products
• 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: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07K 1/047 : Simultaneous synthesis of different peptide species; Peptide libraries
• 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 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes

Abstract

The invention features a sort computer which interfaces with a sorting device in order to control the sorting of beads on a bead by bead basis. The invention further features novel methods for the directed synthesis of encoded libraries of oligomers, e.g., oligonucleotides, on beads. These methods allow the synthesis of libraries that are sufficiently large to permit complex genomic analyses to be carried out. New methods of using the encoded libraries also are described.

Claims

1. A method for directing the synthesis of a combinatorial library of oligomers, said method comprising the steps of:

(a) prior to coupling, assigning a predetermined oligomer sequence to each of a plurality of carriers, wherein each of said plurality of carriers comprises a distinguishable feature;

(b) sorting said plurality of carriers into a plurality of reaction vessels, wherein the vessel into which each carrier is sorted is determined by the oligomer assigned to each carrier based on said distinguishable feature, and wherein each carrier is sorted independently of the other carriers;

(c) performing a reaction to couple a chemical moiety to each carrier in each vessel, wherein the chemical moiety is the same or different in different vessels;

(d) repeating steps (b) and (c) at least once, wherein, in each step, a subsequent chemical moiety is coupled to the previously added chemical moiety to produce a plurality of oligomers, thereby directing the synthesis of a combinatorial library of oligomers.

2. The method of claim 1, further comprising the step, between steps (c) and (d), of pooling the carriers in each of said vessels.

3. The method of claim 1, wherein each carrier in said plurality of carriers comprises a unique distinguishable feature.

4. The method of claim 1, wherein said chemical moiety comprises a deoxyribonucleotide, a ribonucleotide, an amino acid, a saccharide, a peptide nucleic acid, a carbonate, a sulphone, a sulfoxide, a nucleoside, a carbohydrate, a urea, a phosphonate, a lipid, or an ester.

5. The method of claim 1, wherein said chemical moiety is protected.

6. The method of claim 1, wherein prior to step (c), a linker is coupled to each of said plurality of carriers.

7. The method of claim 6, wherein said linker is cleavable.

8. The method of claim 7, further comprising, after step (e), cleaving said linker.

9. The method of claim 6, wherein said linker is not cleavable.

10. The method of claim 1, wherein each carrier comprises a reactive group.

11. The method of claim 1, wherein in step (a), said plurality of carriers is sorted into at least four vessels.

12. The method of claim 1, wherein in step (a), said carriers are sorted in a flow cytometer.

13. The method of claim 1, wherein said distinguishable feature is detectable by fluorescence, light scatter, color, luminescence, phosphorescence, infrared radiation, x-ray scatter, light absorbance, surface plasmon resonance, electrical impedance, or a combination thereof.

14. The method of claim 1, further comprising step (e), cleaving at least one of said plurality of oligomers from one of said plurality of carriers.

15. The method of claim 1, wherein said carrier is a bead.

16. A library of encoded carriers, said library comprising a plurality of carriers wherein each of said carriers comprises a unique distinguishing feature and a unique oligomer bound to said carrier.

17. The library of claim 16, wherein said library comprises at least 1,000, 10,000, 100,000, or 1,000,000 carriers.

18. The library of claim 16, wherein said library comprises between 1,000 and 1,000,000 carriers.

19. The library of claim 16, wherein said oligomer comprises a deoxyribonucleotide, a ribonucleotide, an amino acid, a saccharide, a peptide nucleic acid, a carbonate, a sulphone, a sulfoxide, a nucleoside, a carbohydrate, a urea, a phosphonate, a lipid, or an ester.

20. The library of claim 16, wherein said unique oligomer is bound to said carrier via a linker.

21. The library of claim 20, wherein said linker is cleavable.

22. The library of claim 20, wherein said linker is not cleavable.

23. The library of claim 16, wherein said carriers are beads.

24. A device for sorting carriers, said device comprising:

(a) a sorter comprising a flow path that splits into at least two branches into which carriers can be sorted;

(b) one or more detectors capable of detecting said carriers in said flow path, wherein said one or more detectors are disposed to detect said carriers prior to passing into one of said branches;

(c) a computer that determines the branch into which each carrier is sorted based on one or more signals from each carrier obtained from said one or more detectors.

25. The device of claim 24, wherein said sorter is a flow cytometer.

26. The device of claim 24, wherein said flow path splits into at least four branches.

27. The device of claim 24, wherein one of said one or more detectors detects fluorescence, light scatter, color, luminescence, phosphorescence, infrared radiation, x-ray scatter, light absorbance, surface plasmon resonance, or electrical impedance.

28. A sort computer, said computer comprising:

(a) an interface that is capable of receiving data that encodes a distinguishable feature of a carrier as it is passed through a sorting device comprising a flow path that splits into at least two branches;

(b) one or more memories that store the number of carriers having each distinguishable feature;

(c) a controller that is capable of controlling said sorting device to sort said carrier into one of said branches; and

(d) a sorting selector that determines into which branch said carrier is sorted based on the number of carriers having that distinguishable feature stored in said one or more memories.