How to choose the flanking sequence that brings to the ligand binding site relative binding affinity

摘要

Methods of ranking the relative reactivity of nucleotide sequences flanking a ligand binding site. The invention involves, and is useful for, ranking populations of nucleic acid molecules, each containing a ligand binding site and flanking sequences on either side of the binding site. In an embodiment a method of ranking reactivities of polynucleotide flanking sequences is disclosed wherein the method includes (a) providing a plurality of different nucleic acid molecules, wherein each of the molecules has the same ligand binding site located adjacent to at least one flanking sequence; (b) exposing the molecules to a ligand selective for the binding site under conditions such that the relative binding affinity of the ligand for the binding site within at least two of the molecules is determined; and (c) ranking the relative binding affinities determined in step (b) to rank the relative reactivities of said polynucleotide flanking sequences. In another embodiment, a higher relative binding affinity for the ligand binding site within the molecule(s) corresponds to a higher relative reactivity of the flanking sequence(s).