Methods of determining polynuceotide intramolecular structure

Abstract

A method of identifying one or a combination of ligands, e.g. oligonucleotides or analogues, that interact specifically with a target, e.g. a DNA or an RNA molecule having a secondary or tertiary structure. One ligand may be pre-reacted to open up the target for interaction with other ligands forming an array on a solid surface.

1 . A method of designing a reagent, which method comprises providing a target, applying the target to ligands which form an array on a solid surface, observing interaction between the ligands and the target, and using the observation to design a reagent to interact with the target.  
     
     
         2 . A method of determining combinations of ligands specific for a target, which method comprises the steps of: 
 a) binding at least one ligand to the target, to form a target complex,    b) applying the target complex to other ligands which form an array on a solid surface, under conditions which allow interaction between the other ligands and the target complex, and    c) identifying at least one other ligand which interacts with the target complex.    
     
     
         3 . A method as claimed in  claim 2 , comprising the additional step of binding the at least one other ligand to the target complex and then repeating steps b) and c).  
     
     
         4 . A method as claimed in any one of  claims 1  to  3 , wherein the target is a nucleic acid and the ligands are oligonucleotides or oligonucleotide analogues.  
     
     
         5 . A method as claimed in  claim 2  or  claim 3 , wherein one ligand is an oligonucleotide or oligonucleotide analogue and another ligand is a peptide.  
     
     
         6 . A method as claimed in any one of  claims 2  to  5 , wherein two ligands are joined together by means of a linker.  
     
     
         7 . A method as claimed in any one of  claims 4  to  6 , wherein the ligands are oligonucleotide analogues modified by the addition or substitution of other chemical moieties selected from oligoaliphatic ethers, intercalating agents, positively charged residues, chelating agents and lipophilic agents.  
     
     
         8 . A method as claimed in any one of  claims 1  to  7 , wherein the ligands form the basis of a ribozyme.  
     
     
         9 . A method as claimed in any one of  claims 1  to  8 , wherein the target and one or more ligands are different chemical types.  
     
     
         10 . A method as claimed in any one of  claims 1  to  9 , wherein at least one ligand becomes covalently bound to the target.  
     
     
         11 . A method as claimed in any one of  claims 2  to  10 , wherein the at least one ligand to be bound to the target to form a target complex in step a), is chosen by mixing the target with a library of ligands and choosing from the library at least one ligand that binds to the target.  
     
     
         12 . A method as claimed in any one of  claims 1  to  11 , wherein the target is an RNA.  
     
     
         13 . A method as claimed in any one of  claims 1  to  12 , wherein the target is a molecule having a secondary or tertiary structure, and is caused to interact with the array of ligands under conditions such that the secondary or tertiary structure is retained.