Labile Linkers for Biomarker Detection

A method of detecting the presence or absence of a target molecule or condition suspected to be present in a sample, comprising:

• contacting the sample with a fusion molecule comprising a cleavable linker, wherein said cleavable linker is specifically cleaved in the presence of said target molecule or condition;
• loading said sample into a device comprising a nanopore, wherein said nanopore separates an interior space of the device into two volumes;
• configuring the device to pass a polymer scaffold through said nanopore, wherein a first portion of said fusion molecule is bound to said polymer scaffold, wherein a second portion of said fusion molecule is bound to a payload molecule, and wherein the device comprises a sensor configured to identify objects passing through the nanopore;
• and
• determining with the sensor whether the cleavable linker has been cleaved, thereby detecting the presence or absence of the target molecule or condition in said sample.

A method for detecting the presence or absence of a target molecule or condition suspected to be present in a sample, comprising:

• contacting the sample with a fusion molecule, a polymer scaffold, and a payload molecule, said fusion molecule comprising a cleavable linker, wherein said target molecule specifically cleaves said cleavable linker, a polymer scaffold binding domain, and a payload molecule binding domain;
• loading said fusion molecule, said polymer scaffold, said payload molecule, and said sample into a device comprising a nanopore, wherein said nanopore separates an interior space of the device into two volumes;
• configuring the device to pass the polymer scaffold through said nanopore, wherein the device comprises a sensor configured to identify objects passing through the nanopore;
• and
• determining with the sensor whether the cleavable linker is bound to the payload molecule, thereby detecting the presence or absence of the target molecule or condition.

A method for detecting a target molecule or condition suspected to be present in a sample, comprising:

• contacting the sample with a polymer scaffold, wherein the scaffold comprises a cleavable domain, wherein said cleavable domain is specifically cleaved in the presence of said target molecule;
• loading said polymer scaffold and said sample into a device comprising a nanopore, wherein said nanopore separates an interior space of the device into two volumes;
• configuring the device to pass the polymer scaffold through said nanopore, wherein the device comprises a sensor configured to identify objects passing through the nanopore;
• and
• determining with the sensor whether the cleavable domain has been cleaved, thereby detecting the presence or absence of the target molecule or condition in said sample.

A method of quantitating a target molecule or condition suspected to be present in a sample, comprising:

• contacting the sample with a fusion molecule, a polymer scaffold, and a payload molecule, said fusion molecule comprising a cleavable linker, wherein said cleavable linker is specifically cleaved in the presence of said target molecule or condition, a polymer scaffold binding domain, and a payload molecule binding domain;
• loading said fusion molecule, said polymer scaffold, said payload molecule, and said sample into a device comprising a nanopore, wherein said nanopore separates an interior space of the device into two volumes;
• configuring the device to pass the polymer scaffold through said nanopore, wherein the device comprises a sensor configured to identify objects passing through the nanopore;
• determining with the sensor whether the polymer scaffold is bound to the payload molecule, thereby detecting the presence or absence of target molecule;
• and
• estimating the concentration or activity of the target molecule or condition suspected to be present in a sample using measurements from said sensor.

A method of quantitating a target molecule suspected to be present in a sample, comprising:

• contacting the sample with a fusion molecule comprising a cleavable linker, wherein said cleavable linker is specifically cleaved in the presence of said target molecule;
• loading said sample into a device comprising a nanopore, wherein said nanopore separates an interior space of the device into two volumes;
• configuring the device to pass a polymer scaffold through said nanopore, wherein a first portion of said fusion molecule is bound to said polymer scaffold, wherein a second portion of said fusion molecule is bound to a payload molecule, and wherein the device comprises a sensor configured to identify objects passing through the nanopore;
• determining with the sensor whether the cleavable linker has been cleaved, thereby detecting the presence or absence of the target molecule in said sample;
• and
• estimating the concentration of the target molecule or condition suspected to be present in a sample using measurements from said sensor.

A kit comprising:

• a device comprising a nanopore, wherein said nanopore separates an interior space of the device into two volumes, and configuring the device to pass the nucleic acid through one or more pores, wherein the device comprises a sensor for each pore that is configured to identify objects passing through the nanopore;
• a fusion molecule comprising a cleavable linker, wherein said cleavable linker is specifically cleaved in the presence of a target molecule;
• a payload molecule;
• a polymer scaffold;
• and
• instructions for use to detect the presence or absence of said target molecule in a sample.