Universal molecular processor for precision medicine

A method for identifying a nucleotide within a target nucleic acid molecule from a sample, said method comprising:

• providing a device comprising:
• a biomolecular processor, each biomolecular processor comprising:
• a bioreactor chamber defined by a solid substrate;
• a plurality of spaced support structures within said bioreactor chamber and attached to the solid substrate;
• one or more capture molecules immobilized to some or all of said plurality of spaced support structures, said one or more capture molecules suitable to bind to a portion of a target nucleic acid molecule in a sample;
• one or more nanotubes defined by the solid substrate and fluidically coupled to the bioreactor chamber, each of said one or more nanotubes having a passage extending between an input end proximate to said bioreactor chamber and an output end distal to said bioreactor chamber and comprising one or more nanopores within the passage with each nanopore having a reduced diameter relative to the passage;
• electrodes positioned at locations upstream of said bioreactor chamber and downstream of said one or more nanotubes;
• a voltage source electrically coupled to said electrodes to establish a voltage gradient between a location upstream of said bioreactor chamber and downstream of said one or more nanotubes causing molecules to pass from said bioreactor chamber through said one or more nanotubes to the output end;
• and
• a detector positioned to measure changes in current levels across the one or more nanopores as molecules pass through said one or more nanotubes;
• feeding a sample comprising a target nucleic acid molecule into said biomolecular processor under conditions effective for the target nucleic acid molecule to bind to the capture molecules and to be immobilized to the spaced support structures;
• contacting the immobilized target nucleic acid molecules or immobilized extension products that are complementary to the target nucleic acid molecule with a solution to form a nucleotide extension reaction mixture, said solution comprising one or more oligonucleotide primers complementary to a portion of the immobilized target nucleic acid molecules or the immobilized extension product thereof, a polymerase, and a collection of nucleotide triphosphates, each type of nucleotide triphosphate having (1) a different cleavable identifying signature-generating moiety and (2) a cleavable blocking moiety that blocks further nucleotide extension reactions;
• subjecting the nucleotide extension mixture to a hybridization treatment, wherein the one or more oligonucleotide primers hybridize in a base-specific manner to their complementary immobilized target nucleic acid molecules or immobilized extension products thereof;
• extending the hybridized oligonucleotide primers by single base-specific addition of a nucleotide triphosphate from the collection of nucleotide triphosphates to the 3′end of the hybridized primers;
• cleaving the identifying signature-generating moiety from each nucleotide added to the hybridized oligonucleotide primer after said extending;
• passing the cleaved identifying signature-generating moiety through the one or more nanotubes;
• detecting, with said detector, the identifying signature generated by the cleaved identifying signature-generating moiety when the cleaved identifying signature-generating moiety passes through the one or more nanotubes;
• and
• identifying, based on said detecting, the nucleotide from the collection of nucleotides that was added during said extending, thereby identifying one or more nucleotides in the target nucleic acid molecule in the sample.