Libraries of oligomers labeled with different tags

• US 6,780,981 B1
• Filed: 05/08/2001
• Issued: 08/24/2004
• Est. Priority Date: 05/15/1998
• Status: Expired due to Fees

• Current Assignee: Oxford University Innovation Limited (University of Oxford)
• Original Assignee: Oxford Gene Technology IP Limited (Sysmex Corporation)
• Inventors: Hamilton, Alan Lewis, Elder, John Kenneth, Shchepinov, Mikhail Sergeevich, Southern, Edwin Mellor, Housby, John Nicholas
• Primary Examiner(s): Riley, Jezia
• Application Number:
  US09/700,462
• Time in Patent Office: 1,204 Days
• Field of Search: 536/22.1, 536/23.1, 536/25.3, 536/26.6, 435/6
• US Class Current: 536/23.1
• CPC Class Codes: C07H 21/00 Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6872 involving mass spectrometry
• 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 30/10 by measuring physical properties, e.g. mass
• 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 50/10 involving encoding steps
• CPC Class Codes: C40B 50/16 involving encoding steps
• CPC Class Codes: C40B 60/10 for identifying library members
• CPC Class Codes: C40B 70/00 Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes

Abstract

A method of making a set of labelled compounds by the use of a preferably particulate support, comprises dividing the support into lots, performing a different chemical reaction on each lot of the support, e.g. to couple a chemical moiety to that lot of the support, tagging a fraction of each lot of the support with a different label, and combining the said lots of the support. The steps are repeated several times, preferably to build up oligomer molecules carrying labels which identify the nature and position of a monomer unit of the oligomer, and which are releasable from the support. Preferred labels, which are releasable from the compounds by cleavage to provide charged groups for analysis by mass spectrometry, are groups of the trityl (trimethylphenyl) family. Also claimed are libraries of these labels and their use in assays and nucleic acid analysis methods.

Claims

1. A method of making a set of labeled compounds, by the use of a support and a set of labels, said method comprising the steps of:

a) at least one first or intermediate step comprising dividing the support into lots, performing a different chemical reaction on each lot of the support so as either to modify that lot of the support or to couple a chemical moiety to that lot of the support, tagging a fraction of each lot of the support with a different label, and combining said lots of the support, and

b) at least one intermediate or final step comprising dividing the support into lots, performing a different chemical reaction on each lot of the support, so as either to modify that lot of the support or to couple a chemical moiety to that lot of the support, tagging a fraction of each lot of the support with a different cleavable label, wherein the label is cleavable to give a charged species for mass spectrometry, whereby each different cleavable label is linked to a chemical moiety coupled to the support in a different step and forms with that chemical moiety a labeled compound which is separable from the support, and combining the said lots of the support.

2. The method of claim 1, wherein the support is a particulate solid support.

3. The method of claim 1, wherein step b) is performed to couple the chemical moiety to a chemical moiety previously coupled to the support.

4. The method of claim 3, wherein the chemical moieties are monomer units and the labeled compounds are oligomers.

5. The method of claim 4, wherein the set of labeled compounds is a library of n^s oligomers, wherein the n is the number of different monomer units and the s is the number of monomer units in each labeled oligomer, wherein step a) is performed once to couple a different monomer unit to each of the support, and step b) is performed s−

1 times.

6. The method of claim 5, wherein the set of labeled compounds contains n×

s different labels.

7. The method of claim 1, wherein each labeled compound comprises a single label and at least one chemical moiety.

8. The method of claim 1, wherein the support is treated to release said labeled compounds into solution.

9. The method of claim 1, wherein from 0.25% to 25% of each lot of the support is tagged in each step with a different label.

10. The method of claim 1, wherein the support has cleavable linkers, wherein each cleavable linker has at least one group for chemical synthesis and another group for labeling.

11. The method of claim 1, wherein each label is a group of formula R¹R²R³C—

, where R¹, R² and R³ are the same or different and each is a monocyclic or fused ring aromatic group that is substituted or unsubstituted.

12. The method of claim 11, wherein at leas one of R¹, R², and R³ carries a substituent selected from C1-C20 alkoxy and hydrocarbyl either unsubstituted by carboxylic acid, sulphonic acid, nitro, cyano, hydroxyl, thiol, primary, secondary, or tertiary amino, primary or secondary amido, anhydride, carbonyl halide, or active ester.

13. The method of claim 1, wherein the labeled compounds are labeled oligonucleotides.

16. The method of claim 11, wherein R¹²R³C—

is a substituted monomethoxytrityl group.

18. The method of claim 12, wherein R¹R²R³C—

is a substituted monomethoxytrityl group.

20. The compound of claim 16, wherein R¹R²R³C—

is a substituted monomethoxytrityl group.

14. A set of labeled compounds wherein a molecule of a compound of the set is tagged with a single cleavable label which identifies the nature and/or the position of a component of that molecule, wherein each label is cleavable to give a charsed species for mass spectrometry, and different molecules of the same compound are tagged with different labels, wherein each label is a group of formula R¹R²R³C—

, where R¹, R² and R³ are the same or different and each is a monocyclic or fused ring aromatic group that is substituted or unsubstituted.

15. A set of labeled compounds wherein a molecule of a compound of the set is tagged with a single cleavable label which identifies the nature and/or the position of a component of that molecule, wherein the label is cleavable to give a charged species for mass spectrometry, and different molecules of the same compound are tagged with different labels, wherein each label is a group of formula R¹R²R³C—

, where R¹, R² and R³ are the same or different and each is a monocyclic or fused ring aromatic group that is substituted or unsubstituted; and

wherein at least one of R¹, R² and R³ carries a substituent selected from C₁-C₂₀ alkoxy or hydrocarbyl either unsubstituted or substituted by carboxylic acid, sulphonic acid, nitro, cyano, hydroxyl, thiol, primary, secondary or tertiary amino, primary or secondary amido, anhydride, carbonyl halide or active ester.

17. A set of labeled compounds wherein a molecule of a compound of the set is tagged with a single cleavable label which identifies the nature and/or the position of a component of that molecule, wherein the label is cleavable to give a charged species for mass spectrometry, and different molecules of the same compound are tagged with different labels, wherein each label is a group of formula R¹R²R³C—

, where R¹, R² and R³ are the same or different and each is a monocyclic or fused ring aromatic group that is substituted or unsubstituted and wherein R¹R²R³C—

is a substituted monomethoxytrityl group.

19. A set of labeled compounds wherein a molecule of a compound of the set is tagged with a single cleavable label which identifies the nature and/or the position of a component of that molecule, wherein the label is cleavable to give a charred species for mass spectrometry, and different molecules of the same compound are tagged with different labels, wherein each label is a group of formula R¹R²R³C—

, where R¹, R² and R³ are the same or different and each is a monocyclic or fused ring aromatic group that is substituted or unsubstituted; and

wherein at least one of R¹, R² and R³ carries a substituent selected from C₁-C₂₀ alkoxy or hydrocarbyl either unsubstituted or substituted by carboxylic acid, sulphonic acid, nitro, cyano, hydroxyl, thiol, primary, secondary or tertiary amino, primary or secondary amido, anhydride, carbonyl halide or active ester; and

wherein R¹R²R³C—

is a substituted monomethoxytrityl group.

21. A library consisting of a set of labeled compounds wherein a molecule of a compound of the set is tagged with a single cleavable label which identifies the nature and/or the position of a component of that molecule, wherein the label is cleavable to give a charged species for mass spectrometry, and different molecules of the same compound are tagged with different labels;

wherein each label is a group of formula R¹R²R³C—

, where R¹, R² and R³ are the same or different and each is a monocyclic or fused ring aromatic group that is substituted or unsubstituted.

22. A library consisting of a set of labeled compounds wherein a molecule of a compound of the set is tagged with a single cleavable label which identifies the nature and/or the position of a component of that molecule, wherein the label is cleavable to give a charged species for mass spectrometry, and different molecules of the same compound are tagged with different labels, wherein each label is a group of formula R¹R²R³C—

, where R¹, R² and R³ are the same or different and each is a monocyclic or fused ring aromatic group that is substituted or unsubstituted; and

wherein at least one of R¹, R² and R³ carries a substituent selected from C₁-C₂₀ alkoxy or hydrocarbyl either unsubstituted or substituted by carboxylic acid, sulphonic acid, nitro, cyano, hydroxyl, thiol, primary, secondary or tertiary amino, primary or secondary amido, anhydride, carbonyl halide or active ester.