Probe composition containing a binding domain and polymer chain and methods of use

A kit for detecting one or more of a plurality of different nucleotide sequences in a nucleic acid sample, comprising

• a ligase enzyme, and
• a mixture of sequence-specific probes, each capable of binding specifically to a different target sequence, wherein each probe is characterized by (a) an oligonucleotide binding polymer having a probe-specific sequence of subunits designed for base-specific binding of the polymer to one of the target sequences under selected binding conditions, and (b) attached to the binding polymer, a polymer chain which imparts to the probe a charge/translational frictional drag ratio that is distinctive relative to the charge/translational frictional drag ratio of the other probe(s) in said mixture,
• wherein each sequence-specific probe further includes a second binding polymer, where the first-mentioned and second binding polymers in each sequence-specific probe are effective to bind in a base-specific manner to adjacent and contiguous regions of a selected target sequence, allowing ligation of the two binding polymers when bound to the target sequence in a sequence-specific manner, and the polymer chain attached to the first binding polymer imparts to each ligated probe pair, a distinctive combined ratio of charge/translational frictional drag.

A kit for detecting one or more of a plurality of different nucleotide sequences in a nucleic acid sample, comprising

• a polymerase enzyme, and
• a mixture of sequence-specific probes, each capable of binding specifically to a different target sequence, wherein each probe is characterized by (a) an oligonucleotide binding polymer having a probe-specific sequence of subunits designed for base-specific binding of the polymer to one of the target sequences under selected binding conditions, and (b) attached to the binding polymer, a polymer chain which imparts to the probe a charge/translational frictional drag ratio that is distinctive relative to the charge/translational frictional drag ratios of the other probe(s) in said mixture,
• wherein each sequence-specific probe further includes a second binding polymer, where the first-mentioned and second binding polymers in each sequence-specific probe are effective to bind in a base-specific manner to opposite end regions of opposite strands of a selected duplex target sequence, allowing primer-initiated polymerase extension of each binding polymer when bound to such target sequence, and the polymer chain attached to the first binding polymer imparts to each polymerized region a distinctive combined ratio of charge/translational frictional drag.