Method and probe composition for detecting multiple sequences in a single assay

A method of detecting the presence or absence of a plurality of selected target sequences in a target polynucleotide, comprising

• adding to a target polynucleotide, a plurality of different-sequence probe pairs, where each probe pair includes two polynucleotide probe elements which are complementary in sequence to adjacent portions of a selected one of the target sequences in the target polynucleotide, and one of the elements in each probe pair contains a nonpolynucleotide polymer chain which imparts a distinctive elution characteristic in a chromatographic separation medium to the associated probe pair, when the elements in the pair are ligated,
• hybridizing the probe pairs with the target polynucleotide,
• treating the hybridized polynucleotides under conditions effective to ligate the end subunits of target-bound probe elements when their end subunits are base-paired with adjacent target bases,
• releasing the ligated probe pairs from the target polynucleotide,
• separating the released, ligated probe pairs by chromatography in such a chromatographic separation medium,
• and detecting the ligated probe pairs formed, to determine the presence or absence of the selected target sequences.

A method of detecting the presence or absence of a plurality of selected target sequences in a target polynucleotide, comprising

• adding to the target polynucleotide, a plurality of sequence-specific probes, each comprising an oligonucleotide-binding polymer having a probe-specific sequence of subunits designed for base-specific binding of the binding polymer to a target sequence, and attached to the binding polymer, a nonpolynucleotide polymer chain which imparts to the probe a distinctive electrophoretic mobility in a sieving matrix,
• reacting the probes with the target polynucleotide under conditions favoring binding of the probes in a base-specific manner to the target polynucleotide,
• treating the probes to selectively modify those probes which have bound to the target polynucleotide in a sequence-specific manner, to form modified, labeled probes, each having a detectable reporter label and a distinctive electrophoretic mobility in a sieving matrix,
• fractionating the modified, labeled probe(s) by electrophoresis in a sieving matrix, and
• detecting the modified, labeled probe(s) to determine the presence or absence of the selected target sequences.

A method of detecting the presence or absence of a plurality of selected target sequences in a target polynucleotide, comprising

• adding to the target polynucleotide, a plurality of sequence-specific probes, each comprising an oligonucleotide-binding polymer having a probe-specific sequence of subunits designed for base-specific binding of the binding polymer to a target sequence, and attached to the binding polymer, a nonpolynucleotide polymer chain which imparts to the probe a distinctive elution characteristic in a chromatographic separation medium,
• reacting the probes with the target polynucleotide under conditions favoring binding of the probes in a base-specific manner to the target polynucleotide,
• treating the probes to selectively modify those probes which have bound to the target polynucleotide in a sequence-specific manner, to form modified, labeled probes, each having a detectable reporter label and a distinctive elution characteristic in a chromatographic separation medium,
• fractionating the modified, labeled probe(s) by chromatography in a chromatographic medium, and
• detecting the modified, labeled probe(s) to determine the presence or absence of the selected target sequences.