Compositions, Devices, Systems, and Methods for Using a Nanopore

Abstract

Devices and methods that can detect and control an individual polymer in a mixture is acted upon by another compound, for example, an enzyme, in a nanopore are provided. The devices and methods also determine (˜>50 Hz) the nucleotide base sequence of a polynucleotide under feedback control or using signals generated by the interactions between the polynucleotide and the nanopore. The invention is of particular use in the fields of molecular biology, structural biology, cell biology, molecular switches, molecular circuits, and molecular computational devices, and the manufacture thereof.

What is claimed is: 
     
         1 . A method for nucleic acid sequencing, comprising:
 (a) providing a chip comprising a plurality of individually addressable nanopores, an individually addressable nanopore of said plurality of individually addressable nanopores containing at least one nanopore formed in a membrane disposed adjacent to an electrode, wherein each individually addressable nanopore is adapted to detect a nucleic acid molecule or a portion thereof;   (b) directing a plurality of nucleic acid molecules to said individually addressable nanopores; and   (c) characterizing, with the aid of a processor coupled to said chip, a nucleic acid sequence of each of said nucleic molecules based on electrical signals received from said plurality of individually addressable nanopores.   
     
     
         2 . The method of  claim 1 , wherein said plurality of nucleic acid molecules are derived from a nucleic acid sample. 
     
     
         3 . The method of  claim 2 , wherein each of said plurality of nucleic acid molecules has a shorter nucleic acid sequence than said nucleic acid sample. 
     
     
         4 . The method of  claim 3 , further comprising, prior to (b), fragmenting said nucleic acid sample to provide said plurality of nucleic acid molecules. 
     
     
         5 . The method of  claim 2 , further comprising characterizing a nucleic acid sequence of said nucleic acid sample based upon a characterization of a nucleic acid sequence of each of said nucleic molecules. 
     
     
         6 . The method of  claim 1 , wherein said electrode is adapted to supply an electrical stimulus across said membrane, which stimulus enables the generation of a detectable signal upon molecular flow of said nucleic acid molecule or portion thereof. 
     
     
         7 . The method of  claim 1 , wherein said membrane has a capacitance greater than about 5 fF/μm 2  as measured across said membrane. 
     
     
         8 . The method of  claim 1 , wherein said membrane has a resistance greater than or equal to about 500 MΩ as measured across said membrane. 
     
     
         9 . The method of  claim 8 , wherein said resistance is measured with the aid of opposing electrodes disposed adjacent to said membrane. 
     
     
         10 . The method of  claim 1 , wherein said membrane has a resistance less than or equal to about 1 GΩ across said membrane. 
     
     
         11 . The method of  claim 10 , wherein said resistance is measured with the aid of opposing electrodes disposed adjacent to said membrane. 
     
     
         12 . The method of  claim 1 , wherein each individually addressable nanopore is adapted to regulate molecular flow. 
     
     
         13 . The method of  claim 12 , wherein each individually addressable nanopore is adapted to regulate molecular flow with the aid of an electrical stimulus applied to said nanopore. 
     
     
         14 . The method of  claim 13 , wherein said electrical stimulus comprises one or more voltage pulses. 
     
     
         15 . The method of  claim 1 , wherein each individually addressable nanopore is adapted to regulate molecular flow adjacent to said at least one nanopore. 
     
     
         16 . The method of  claim 1 , wherein each individually addressable nanopore is adapted to regulate molecular flow through said at least one nanopore. 
     
     
         17 . The method of  claim 1 , wherein each individually addressable nanopore is adapted to detect said nucleic acid molecule or a portion thereof upon molecular flow of said nucleic acid molecule or portion thereof through or adjacent to said at least one nanopore. 
     
     
         18 . The method of  claim 1 , wherein said nucleic acid sequence is characterized upon movement of each of said plurality of nucleic acid molecules or portions thereof. 
     
     
         19 . The method of  claim 1 , wherein said electrode is coupled to an integrated circuit that processes a signal detected with the aid of said electrode. 
     
     
         20 . A system for nucleic acid sequencing, comprising:
 (a) a chip comprising a plurality of individually addressable nanopores, an individually addressable nanopore of said plurality of individually addressable nanopores containing at least one nanopore formed in a membrane disposed adjacent to an electrode, wherein each individually addressable nanopore is adapted to aid in the detection of said nucleic acid molecule or a portion; and   (b) a processor coupled to said chip, wherein said processor is programmed to aid in characterizing a nucleic acid sequence of said nucleic acid molecule based on electrical signals received from said plurality of individually addressable nanopores.   
     
     
         21 . The system of  claim 20 , wherein said electrode is adapted to supply an electrical stimulus across said membrane, which stimulus enables the generation of a detectable signal upon molecular flow of said nucleic acid molecule or portion thereof. 
     
     
         22 . The system of  claim 20 , wherein said membrane has a capacitance greater than about 5 fF/μm 2  as measured across said membrane. 
     
     
         23 . The system of  claim 20 , wherein said membrane has a resistance greater than or equal to about 500 MΩ as measured across said membrane. 
     
     
         24 . The system of  claim 23 , wherein said resistance is measured with the aid of opposing electrodes disposed adjacent to said membrane. 
     
     
         25 . The system of  claim 20 , wherein said membrane has a resistance less than or equal to about 1 GΩ across said membrane. 
     
     
         26 . The system of  claim 25 , wherein said resistance is measured with the aid of opposing electrodes disposed adjacent to said membrane. 
     
     
         27 . The system of  claim 20 , wherein each individually addressable nanopore is adapted to regulate molecular flow. 
     
     
         28 . The system of  claim 27 , wherein each individually addressable nanopore is adapted to regulate molecular flow with the aid of an electrical stimulus applied to said nanopore. 
     
     
         29 . The system of  claim 28 , wherein said electrical stimulus comprises one or more voltage pulses. 
     
     
         30 . The system of  claim 20 , wherein each individually addressable nanopore is adapted to regulate molecular flow adjacent to said at least one nanopore. 
     
     
         31 . The system of  claim 20 , wherein each individually addressable nanopore is adapted to regulate molecular flow through said at least one nanopore. 
     
     
         32 . The system of  claim 20 , wherein each individually addressable nanopore is adapted to detect said nucleic acid molecule or a portion thereof upon molecular flow of said nucleic acid molecule or portion thereof through or adjacent to said at least one nanopore. 
     
     
         33 . The system of  claim 20 , wherein said processor is in a workstation that is in proximity to said chip. 
     
     
         34 . The system of  claim 20 , wherein said electrode is coupled to an integrated circuit that processes a signal detected with the aid of said electrode.