Probe composition containing a binding domain and polymer chain and methods of use
First Claim
1. A probe composition for use in detecting one or more of a plurality of different target sequences in a polynucleotide sample, comprisinga 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.
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Abstract
Method and composition for detecting one or more selected polynucleotide regions in a target polynucleotide. In the method, a mixture of sequence-specific probes are reacted with the target polynucleotide under hybridization conditions, and the hybridized probes are treated to selectively modify those probes which are bound to the target polynucleotide in a base-specific manner. The resulting labeled probes include a polymer chain which imparts to each different-sequence probe, a distinctive ratio of charge/translational frictional drag, and a detectable label. The labeled probes are fractionated by electrophoresis in a non-sieving matrix, and the presence of one or more selected sequences in the target polynucleotide are detected according to the observed electrophoretic migration rates of the labeled probes in a non-sieving medium.
128 Citations
11 Claims
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1. A probe composition for use in detecting one or more of a plurality of different target sequences in a polynucleotide sample, comprising
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.
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8. 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.
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10. 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.
Specification