Patent ID: 7264925

Claim:
A method of separating a population of duplexes, each comprising one of a population of different, substantially uncharged oligomeric analyte molecules and a specific probe molecule, wherein said substantially uncharged analyte molecules are oligonucleotide analogs composed of linked subunits of which at least 90% are uncharged, and said specific probe molecule is a fully charged nucleic acid or fully charged nucleic acid analog, the method comprising: (a) applying to an ion exchange medium a mixture of (i) the different substantially uncharged analyte molecules and (ii) the specific probe molecule, under conditions such that the probe forms stable duplexes with a plurality of or all of the different substantially uncharged analyte molecules, thereby forming a plurality of different probe-analyte duplexes, which differ from each other with respect to the presence, length or position of an unhybridized portion of the probe molecule, and (b) separating said different probe-analyte duplexes from each other and from single stranded analyte or probe molecules within the medium.