Transient electrical signal based methods and devices for characterizing molecular interaction and/or motion in a sample

Abstract

Devices for detecting a transient electrical signal in a sample are provided. Also provided are systems that include the subject devices. The subject devices and systems find use in a variety of applications, particularly in the characterization of a sample, and more particularly in the characterization of molecular entities in the sample.

What is claimed is:  
     
         1 . A method of characterizing a first molecule X and a second immobilized molecule Y in a sample of a conducting medium, said method comprising: 
 (a) providing a system comprising said immobilized second molecule Y, said conducting medium sample, and said first molecule X;    (b) detecting a transient electrical signal produced by a monodirectional movement of said first molecule X through said conducting medium sample relative to said immobilized second molecule Y; and    (c) relating said detected transient electrical signal to at least one characterizing feature of said first molecule X and said second molecule Y in said sample.    
     
     
         2 . The method according to  claim 1 , wherein said at least one characterizing feature is motion, velocity, quantity, structure, charge or binding event.  
     
     
         3 . The method according to  claim 1 , wherein said movement is a movement of X towards Y.  
     
     
         4 . The method according to  claim 1 , wherein said movement is a movement of X away from Y.  
     
     
         5 . The method according to  claim 1 , wherein said conducting medium sample is a fluid medium.  
     
     
         6 . The method according to  claim 1 , wherein said conducting medium sample is a gel or gaseous medium.  
     
     
         7 . The method according to  claim 1 , wherein said immobilized molecule Y is a polymer.  
     
     
         8 . The method according to  claim 7 , wherein said polymer is a polypeptide.  
     
     
         9 . The method according to  claim 7 , wherein said polymer is a nucleic acid.  
     
     
         10 . The method according to  claim 1 , wherein said immobilized second molecule Y is immobilized on a surface of a first working electrode.  
     
     
         11 . The method according to  claim 10 , wherein said transient electrical signal is measured using said first working electrode and a second reference electrode.  
     
     
         12 . The method according to  claim 10 , wherein said transient electrical signal is measured using a plurality of electrodes, which plurality includes said first working electrode.  
     
     
         13 . The method according to  claim 1 , wherein said transient electrical signal is a change in an electrical parameter over time.  
     
     
         14 . The method according to  claim 13 , wherein said electrical parameter is voltage.  
     
     
         15 . The method according to  claim 13 , wherein said electrical parameter is current.  
     
     
         16 . The method according to  claim 13 , wherein said electrical parameter is accumulated charge.  
     
     
         17 . The method according to  claim 13 , wherein said electrical parameter is impedance of said medium.  
     
     
         18 . A method according to  claim 1 , wherein said second immobilized molecule Y is a polymer immobilized on a surface of a working electrode, said conducting medium sample is fluid medium; said transient electrical signal is measured using said first working electrode and a second reference electrode; said movement is a movement of X towards Y; and said at least one characterizing feature is a binding event between X and Y.  
     
     
         19 . The method according to  claim 18 , wherein said immobilized polymer is a polypeptide.  
     
     
         20 . The method according to  claim 19 , wherein said first molecule X is a polypeptide.  
     
     
         21 . The method according to  claim 19 , wherein X and Y are proteins.  
     
     
         22 . The method according to  claim 21 , wherein X and Y are a receptor-ligand pair.  
     
     
         23 . The method according to  claim 21 , wherein X and Y are an antibody-antigen pair.  
     
     
         24 . The method according to  claim 18 , wherein said immobilized polymer is a nucleic acid.  
     
     
         25 . The method according to  claim 24 , wherein said first molecule X is a nucleic acid.  
     
     
         26 . The method according to  claim 24 , wherein said first molecule X is a nucleotide.  
     
     
         27 . The method according to  claim 26 , wherein said method is a method of detecting the covalent bonding of a nucleotide to a 3′ end of a primer containing nucleic acid via a polymerase catalyzed template dependent primer extension reaction.  
     
     
         28 . The method according to  claim 24 , wherein said method is a method of sequencing a nucleic acid.  
     
     
         29 . The method according to  claim 24 , wherein said method is a method of detecting a nucleic acid analyte in a sample.  
     
     
         30 . The method according to  claim 29 , wherein said nucleic acid analyte comprises a SNP.  
     
     
         31 . The method according to  claim 29 , wherein said method quantitatively determines the amount of said nucleic acid analyte in said sample.  
     
     
         32 . The method according to  claim 31 , wherein said method is a method of gene expression profiling.  
     
     
         33 . The method according to  claim 26 , wherein said method is a PCR method.  
     
     
         34 . A method of detecting the occurrence of a polymerase mediated template dependent primer extension reaction in a medium, said method comprising: 
 (a) providing a system comprising an immobilized template primer duplex nucleic acid made up of template and primer nucleic acids in contact with said medium, wherein said medium comprises a polymerase and at least one nucleotide;    (b) detecting a transient electrical signal produced in said medium by covalent bonding of said at least one nucleotide to a terminus of said primer nucleic acid; and    (c) relating said detected transient electrical signal to the occurrence of a polymerase mediated template dependent primer extension reaction in said medium.    
     
     
         35 . The method according to  claim 34 , wherein said transient electrical signal is a change in an electrical parameter over time.  
     
     
         36 . The method according to  claim 35 , wherein said detected polymerase mediated template dependent primer extension reaction is the covalent addition of at least one nucleotide to said primer nucleic acid's 3′ end.  
     
     
         37 . The method according to  claim 33 , wherein said duplex nucleic acid is immobilized on a surface of a first working electrode.  
     
     
         38 . The method according to  claim 37 , wherein said transient electrical signal is measured using said first working electrode and a second reference electrode.  
     
     
         39 . The method according to  claim 37 , wherein said transient electrical signal is measured using a plurality of electrodes, which plurality includes said first working electrode.  
     
     
         40 . The method according to  claim 33 , wherein said medium is an aqueous fluid medium.  
     
     
         41 . The method according to  claim 33 , wherein said medium comprises only one type of nucleotide.  
     
     
         42 . The method according to  claim 33 , wherein said medium comprises at least two different types of nucleotides.  
     
     
         43 . The method according to  claim 42 , wherein said medium comprises ATP, GTP, CTP and TTP.  
     
     
         44 . The method according to  claim 33 , wherein said method is a method of sequencing a nucleic acid.  
     
     
         45 . The method according to  claim 33 , wherein said method is a method of detecting a nucleic acid analyte and said method further comprises relating the occurrence of a polymerase mediated template dependent primer extension reaction to the presence of said nucleic acid analyte in said medium.  
     
     
         46 . The method according to  claim 45 , wherein said nucleic acid analyte is a SNP.  
     
     
         47 . The method according to  claim 45 , wherein said nucleic acid analyte is a nucleic acid from a pathogenic organism.  
     
     
         48 . The method according to  claim 33 , wherein said method is a method of gene expression profiling.  
     
     
         49 . The method according to  claim 33 , wherein said method is a method of monitoring a PCR reaction in real time.  
     
     
         50 . A method of sequencing a nucleic acid, said method comprising: 
 (a) providing a system comprising an immobilized template primer duplex nucleic acid made up of said nucleic acid hybridized to a primer nucleic acid, wherein said immobilized template primer duplex nucleic acid is immobilized on a surface of a working electrode and is in contact with a medium comprising a polymerase and at least one nucleotide;    (b) detecting a transient electrical signal produced in said medium by covalent bonding of said at least one nucleotide to a terminus of said template nucleic acid; and    (c) determining said sequence of said nucleic acid using said detected transient electrical signal.    
     
     
         51 . The method according to  claim 50 , wherein said method comprises producing said template primer duplex nucleic acid and then immobilizing said duplex nucleic acid.  
     
     
         52 . The method according to  claim 50 , wherein said method comprises immobilizing said template nucleic acid followed by hybridization of said immobilized template nucleic acid to said primer nucleic acid.  
     
     
         53 . The method according to  claim 50 , wherein said method comprises immobilizing said primer nucleic acid followed by hybridization of said immobilized primer nucleic acid to said template nucleic acid.  
     
     
         54 . The method according to  claim 50 , wherein said medium comprises a single type of nucleotide and said method comprises two or more iterations of said steps (a) and (b) to produce a plurality of transient electrical signals from which said sequence of said nucleic acid is determined.  
     
     
         55 . The method according to  claim 50 , wherein said medium comprises at least two different nucleotides.  
     
     
         56 . The method according to  claim 55 , wherein said medium comprises GTP, ATP, CTP and TTP and said determining step comprises reading said sequence from a single detected transient electrical signal.  
     
     
         57 . A method of detecting the occurrence of a binding event between a first molecule and an immobilized second molecule in a medium, said method comprising: 
 (a) providing a system comprising said immobilized second molecule immobilized on a surface of a working electrode and in contact with a medium comprising said first molecule;    (b) detecting a transient electrical signal in said medium produced by a binding event between said first molecule said immobilized second molecule; and    (c) relating said detected transient electrical signal to the occurrence of said binding event between said first and second molecule.    
     
     
         58 . The method according to  claim 57 , wherein first and second molecules are proteins.  
     
     
         59 . The method according to  claim 57 , wherein said first and second molecules are a receptor-ligand pair.  
     
     
         60 . The method according to  claim 57 , wherein said first and second molecules are an antibody-antigen pair.  
     
     
         61 . The method according to  claim 57 , wherein said first and second molecules are nucleic acids.  
     
     
         62 . An apparatus comprising: 
 (a) a medium containment element containing a medium having a first molecule;    (b) a working electrode having a second molecule immobilized on a surface thereof, wherein said surface is in contact with said medium;    (c) a driver to drive said working electrode; and    (e) a signal processor to obtain a response of said first and to generate a transient electrical signal based thereon.    
     
     
         63 . The apparatus according to  claim 62 , wherein said apparatus further comprises a reference electrode in contact with said medium and said signal processor compares responses from said working and reference electrode to generate said transient electrical signal.  
     
     
         64 . The apparatus according to  claim 63 , wherein said driver comprises a differential amplifier to create a charge difference between said electrodes in said medium.  
     
     
         65 . The apparatus according to  claim 63 , wherein said working and reference electrodes are present on a planar surface of a semiconductor substrate.  
     
     
         66 . A device for use in practicing the method of  claim 1 , said device comprising: 
 (a) a transient electrical signal detection element for detecting a transient electrical signal caused by movement of said first molecule X through a conducting medium sample relative to said immobilized second molecule Y; and    (b) a computer readable medium on which is recorded an algorithm that relates said transient electrical signal generated by said movement of said first molecule X relative to said immobilized second molecule Y to at least one characterizing feature of said first molecule X and said second molecule Y in said sample.    
     
     
         67 . The device according to  claim 66 , wherein said at least one characterizing feature is motion, velocity, quantity, structure, charge or binding event.  
     
     
         68 . The device according to  claim 66 , wherein said at least one characterizing feature is a binding event between said first molecule X and said second molecule Y.  
     
     
         69 . The device according to  claim 66 , wherein said transient electrical signal detection element comprises at least one working electrode.  
     
     
         70 . The device according to  claim 69 , wherein said transient electrical signal detection element comprises said at least one working electrode and a reference electrode.  
     
     
         71 . The device according to  claim 69 , wherein said transient electrical signal detection element comprises a plurality of electrodes, one of which is said at least one working electrode.  
     
     
         72 . The device according to  claim 66 , wherein said device further comprises a differential amplifier.  
     
     
         73 . The device according to  claim 72 , wherein said differential amplifier is a differential voltage amplifier.  
     
     
         74 . The device according to  claim 72 , wherein said differential amplifier is a differential current amplifier.  
     
     
         75 . The device according to  claim 66 , wherein said device further includes a sample containment element.  
     
     
         76 . The device according to  claim 75 , wherein said device is an integrated device.  
     
     
         77 . The device according to  claim 75 , wherein said device comprises at least two distinct sample containment means each having its one transient electrical signal detection element.  
     
     
         78 . The device according to  claim 77 , wherein said device has a chip configuration.  
     
     
         79 . The device according to  claim 77 , wherein said device has an array configuration.  
     
     
         80 . The device according to  claim 66 , wherein said immobilized second molecule Y is a polymer.  
     
     
         81 . The device according to  claim 80 , wherein said polymer is immobilized on a surface of a working electrode component of said transient electrical signal detection element.  
     
     
         82 . The device according to  claim 81 , wherein said polymer is a polypeptide.  
     
     
         83 . The device according to  claim 81 , wherein said polymer is a nucleic acid.  
     
     
         84 . A system for use in practicing the method of  claim 1 , wherein said system comprises: 
 (a) a transient electrical signal detection element for detecting a transient electrical signal caused by movement of a first molecule X through a conducting medium sample relative to immobilized second molecule Y;    (b) an algorithm present on a computer readable medium that relates said transient electrical signal generated by said movement of said first molecule X relative to said immobilized second molecule Y to at least one characterizing feature of said first molecule X and said second molecule Y in said sample; and    (c) a conducting medium sample comprising first molecule X in contact with said immobilized second molecule Y.    
     
     
         85 . The system according to  claim 84 , wherein said at least one characterizing feature is motion, velocity, quantity, structure, charge or binding event.  
     
     
         86 . The system according to  claim 84 , wherein said at least one characterizing feature is a binding event between said first molecule X and said second molecule Y.  
     
     
         87 . The system according to  claim 84 , wherein said conducting medium sample is a fluid medium.  
     
     
         88 . The system according to  claim 84 , wherein said conducting medium sample is a gel or a gaseous medium.  
     
     
         89 . The system according to  claim 84 , wherein said transient electrical signal detection element comprises at least one working electrode.  
     
     
         90 . The system according to  claim 89 , wherein said transient electrical signal detection element further comprises a reference electrode.  
     
     
         91 . The system according to  claim 89 , wherein said transient electrical signal detection element comprises a plurality of electrodes, wherein said plurality comprises said at least one working electrode.  
     
     
         92 . The system according to  claim 84 , wherein said system further comprises a differential amplifier.  
     
     
         93 . The system according to  claim 92 , wherein said differential amplifier is a differential voltage amplifier.  
     
     
         94 . The system according to  claim 92 , wherein said differential amplifier is a differential current amplifier.  
     
     
         95 . The system according to  claim 84 , wherein said immobilized second molecule Y is a polymer.  
     
     
         96 . The system according to  claim 95 , wherein said polymer is a polypeptide.  
     
     
         97 . The system according to  claim 95 , wherein said polymer is a nucleic acid.  
     
     
         98 . A computer readable medium on which is recorded an algorithm for relating a transient electrical signal caused by movement of a first molecule X through a conducting medium relative to second immobilized molecule Y to at least one characterizing feature of said first molecule X and said second molecule Y in said medium.  
     
     
         99 . The computer readable medium according to  claim 98 , wherein said at least one characterizing feature is motion, velocity, quantity, structure, charge or binding event.  
     
     
         100 . The computer readable medium according to  claim 99 , wherein said at least one characterizing feature is a binding event between said first molecule X and said second molecule Y.  
     
     
         101 . The computer readable medium according to  claim 98 , wherein said second immobilized molecule Y is a polymer.  
     
     
         102 . The computer readable medium according to claim  101 , wherein said polymer is a polypeptide.  
     
     
         103 . The computer readable medium according to claim  102 , wherein said first molecule X is a polypeptide.  
     
     
         104 . The computer readable medium according to claim  101 , wherein said polymer is a nucleic acid.  
     
     
         105 . The computer readable medium according to claim  104 , wherein said first molecule X is a nucleic acid.  
     
     
         106 . The computer readable medium according to claim  104 , wherein said first molecule X is a nucleotide.  
     
     
         107 . The computer readable medium according to claim  106 , wherein said algorithm provides the identity of said nucleotide.  
     
     
         108 . The computer readable medium according to claim  106 , wherein said algorithm provides the sequence of said immobilized nucleic acid.