Tag reagent and assay method

Abstract

This invention provides reagents, libraries and sets of the reagents, and assay methods using the reagents, the reagents comprising an analyte moiety and a tag moiety, wherein the tag moiety contains information defining the identify and location of the analyte residues of the analyte moiety which is detectable by mass spectrometry.

1 . A reagent comprising 
 a) an analyte moiety comprising at least two analyte residues, and linked to    b) a tag moiety comprising one or more reporter groups suitable for detection by mass spectrometry, excluding oligonucleotides,    wherein a reporter group designates an analyte residue, and the reporter group at each position of the tag moiety is chosen to designate an analyte residue at a defined position of the analyte moiety.    
     
     
         2 . A reagent as claimed in    claim 1   , wherein there is provided a linker group to which is attached the analyte moiety and the tag moiety.  
     
     
         3 . A reagent as claimed in    claim 1    or    claim 2   , wherein the analyte moiety is a chain of n analyte residues, and the tag moiety is a chain of up to n reporter groups, the reporter group at each position of the tag chain being chosen to designate the analyte residue at a corresponding position of the analyte chain.  
     
     
         4 . A reagent as claimed in any one of    claims 1    to    3   , wherein the analyte moiety is linked to the tag moiety by a photocleavable link.  
     
     
         5 . A reagent as claimed in any one of    claims 1    to    4   , having a formula A - L - R where A is a chain of n analyte residues constituting the analyte moiety, L is the linker, R is a chain of up to n reporter groups constituting the tag moiety, and n is 2 - 20, wherein the tag moiety contains information defining the location of analyte residues in the analyte moiety.  
     
     
         6 . A reagent as claimed in any one of    claims 2    to    5   , wherein the linker comprises an aromatic group carrying a hydroxy, amino or sulphydryl group for analyte moiety synthesis, and a reactive group for tag moiety synthesis.  
     
     
         7 . A reagent as claimed in    claim 6   , wherein the aromatic group carrying a hydroxy, amino or sulphydryl group for analyte moiety synthesis, also carries an o-nitro group for photocleavage.  
     
     
         8 . A reagent as claimed in any one of    claims 1    to    7   , wherein there is present a charged group for analysis by mass spectrometry.  
     
     
         9 . A reagent as claimed in any one of    claims 1    to    8   , wherein the analyte moiety is a peptide chain.  
     
     
         10 . A reagent as claimed in any one of    claims 1    to    8   , wherein the analyte moiety is an oligonucleotide chain.  
     
     
         11 . A library of the reagents claimed in any one of    claims 1    to    10   , wherein the library consists of a plurality of reagents each comprising a different analyte moiety.  
     
     
         12 . A library as claimed in    claim 11   , wherein the library consists of 4 n  reagents each comprising a different analyte moiety which is a different oligonucleotide chain of n nucleotides.  
     
     
         13 . A library as claimed in    claim 12   , wherein the reagents are mixed together in solution.  
     
     
         14 . An assay method which comprises the steps of: providing a target substance; incubating the target substance with the library of reagents claimed in any one of    claims 11    to    13    under conditions to cause at least one reagent to bind to the target substance; removing non-bound reagents; recovering the tag moieties of the or each bound reagent; and analysing the recovered tag moieties as an indication of the nature of the analyte moieties bound to the target substance.  
     
     
         15 . An assay method as claimed in    claim 14   , wherein the target substance is an organism or tissue or group of cells.  
     
     
         16 . A method of sequencing a target nucleic acid, which method comprises the steps of: 
 a) providing an oligonucleotide immobilised on a support,    b) hybridising the target nucleic acid with the immobilised oligonucleotide,    c) incubating the hybrid from b) with the library claimed in    claim 13   , so that an oligonucleotide chain of a first reagent of the library becomes hybridised to the target nucleic acid adjacent the immobilised oligonucleotide,    d) ligating the adjacent oligonucleotides, thus forming a ligated first reagent,    e) removing other non-ligated reagents, and    f) recovering and analysing the tag moiety of the ligated first reagent as an indication of the sequence of a first part of the target nucleic acid.    
     
     
         17 . A method as claimed in    claim 16   , comprising the additional steps of 
 ci) incubating the hybrid from f) with the library claimed in    claim 13   , so that an oligonucleotide chain of a second reagent of the library becomes hybridised to the target nucleic acid adjacent the oligonucleotide chain of the first reagent,    di) ligating the adjacent oligonucleotides, thus forming a ligated second reagent,    ei) removing other non-ligated reagents, and    fi) recovering and analysing the tag moiety of the ligated second reagent as an indication of the sequence of a second part of the target nucleic acid.    
     
     
         18 . A method as claimed in    claim 16    or    claim 17   , wherein: in step a) the oligonucleotide is immobilised on the ends of a series of pins as the support; in step b) an individual clone of target DNA is hybridised to the oligonucleotide immobilised on each individual pin; in steps c) and d) there are formed a series of ligated reagents, with different pins carrying different ligated reagents; and in step f) the tag moiety of each ligated reagent is recovered and analysed as an indication of the sequence of a part of the target DNA.  
     
     
         19 . A method as claimed in    claim 16    or    claim 17   , wherein: in step b) each individual clone of target DNA is hybridised to the oligonucleotide immobilised at an individual spaced location of the support; in steps c) and d) there are provided a series of ligated reagents with different spaced locations of the support carrying different ligated reagents; and in step f) the tag moiety of each ligated reagent is recovered and analysed as an indication of the sequence of a part of the target DNA.  
     
     
         20 . A method as claimed in    claim 16    or    claim 17   , wherein the method comprises the steps of: 
 a) providing an array of oligonucleotides immobilised at spaced locations on a support, an oligonucleotide at one location being different from oligonucleotides at other locations,  
 b) incubating the target nucleic acid with the array of immobilised oligonucleotides, so as to form hybrids at one or more spaced locations on the support,  
 c) incubating the hybrids from b) with the library claimed in    claim 13   , so that an oligonucleotide chain of a reagent of the library becomes hybridised to the target nucleic acid adjacent each immobilised oligonucleotide,  
 d) ligating adjacent oligonucleotides, thus forming ligated reagents at the one or more spaced locations on the support,  
 e) removing other non-ligated reagents, and  
 f) recovering and analysing the tag moiety of each ligated reagent as an indication of the sequence of a part of the target nucleic acid.  
 
     
     
         21 . A method as claimed in    claim 20   , wherein the sequence is known of the oligonucleotide immobilised by a covalent bond at each spaced location on the support.  
     
     
         22 . A method of analysing a target DNA, which method comprises the steps of: 
 i) providing the target DNA immobilised on a support,    ii) incubating the immobilised target DNA from i) with a plurality of the reagents claimed    claim 10   , so that the oligonucleotide chains of different reagents become hybridised to the target DNA on the support,    iii) removing non-hybridised reagents, and    iv) recovering and analysing the tag moiety of each reagent as an indication of the sequence of a part of the target DNA.    
     
     
         23 . A method as claimed in    claim 22   , comprising the additional steps of: 
 iia) incubating the hybrid from iv) with the library of reagents claimed in    claim 13   , so that oligonucleotide chains of different reagents become hybridised to the target DNA,    iiia) ligating adjacent oligonucleotides hybridised to the target DNA and removing non-ligated reagents, and    iva) recovering and analysing the tag moiety of each ligated reagent as an indication of the sequence of part to the target DNA.    
     
     
         24 . A method as claimed in    claim 22    or    claim 23   , wherein individual clones of the target nucleic acid are immobilised at spaced locations on the support, whereby in step ii) the oligonucleotide chains of different reagents become hybridised to the target nucleic acid at different spaced locations on the support.  
     
     
         25 . A method as claimed in any one of    claims 14    to    24   , wherein each tag moiety is recovered by photocleavage from its associated reagent.  
     
     
         26 . A method as claimed in any one of    claims 14    to    25   , wherein the tag moiety is analysed by mass spectrometry.  
     
     
         27 . Assay equipment comprising: a support having two or more spaced locations thereon; individual clones of a target nucleic acid immobilised at the spaced locations on the support; and different reagents according to    claim 10    hybridised to the individual clones of the target nucleic acid at the spaced locations on the support.