A method of selecting high affinity binding to a target nucleic acid by two-dimensional separation

The invention relates to a method of selection, by two-dimensional separation, of nucleic acids that bind to a target molecule with high affinity from a mixture of nucleic acids. The inventive method comprises the following steps: a) subjecting the mixture of nucleic acids to a physico-chemical separation step, thereby obtaining a set of mixed fractions containing the nucleic acids, a run parameter window being associated with every mixed fraction containing the nucleic acids, b) contacting a mixed fraction containing the nucleic acids with the target molecule, thereby obtaining a binding mixture containing nucleic acid/target molecule complexes, and c) subjecting the binding mixture from step b) to the same physico-chemical separation step as in step a), thereby selecting nucleic acid/target molecule complexes whose run parameters are outside the run parameter window.