Nanonozzle device arrays: their preparation and use for macromolecular analysis

Abstract

Constricted nanochannel devices suitable for use in analysis of macromolecular structure, including DNA sequencing, are disclosed. Also disclosed are methods for fabricating such devices and for analyzing macromolecules using such devices.

1 .- 85 . (canceled) 
     
     
         86 . A method for characterizing one or more features of a macromolecule, comprising:
 linearizing a macromolecule residing at least in part within a nanochannel,
 the nanochannel comprising nanochannel segments capable of physically constraining at least a portion of the macromolecule so as to maintain in linear form that portion of the macromolecule, wherein at least one of the nanochannel segments comprises a cross-sectional dimension that is different than the cross-sectional dimension of another of the fluidic nanochannel segments, and wherein the nanochannel segments:
 are curved in form; 
 are tortuous in form; and/or 
 have a varying cross-sectional dimension; and 
 
 the nanochannel segments comprising at least one constriction; 
   transporting at least a portion of the macromolecule within at least a portion of the nanochannel segments such that at least a portion of the macromolecule passes through the constriction;   monitoring at least one signal arising in connection with the macromolecule passing through the constriction; and   correlating the at least one signal to one or more features of the macromolecule.   
     
     
         87 . The method of  claim 86 , wherein the macromolecule comprises a polynucleotide, a polynucleoside, a polymer, a copolymer, a dendrimer, a surfactant, a lipid, a carbohydrate, a polypeptide, a protein, or any combination thereof. 
     
     
         88 . The method of  claim 86 , wherein a feature of the macromolecule comprises the size of the macromolecule, the molecular composition of the macromolecule, the molecular sequence of the macromolecule, an electrical property of one or more molecules of the macromolecule, a chemical property of one or more molecules of the macromolecule, a radioactive property of one or more molecules of the macromolecule, a magnetic property of one or more molecules of the macromolecule, or any combination thereof. 
     
     
         89 . The method of  claim 88 , wherein the molecular composition of the macromolecule comprises the position of one or more molecules of the macromolecule, DNA polymorphisms, DNA copy number polymorphisms, amplifications within DNA, deletions within DNA, translocations within DNA, inversions of particular loci within DNA, the location of a methyl group within the macromolecule, or any combination thereof. 
     
     
         90 . The method of  claim 86 , wherein the macromolecule resides within a fluid. 
     
     
         91 . The method of  claim 86 , wherein the transporting comprises exposing the macromolecule to a gradient, wherein the gradient comprises an electroosmotic field, an electrophoretic field, a magnetic field, an electric field, an electromagnetic field, a flow field, a radioactive field, a mechanical force, an electroosmotic force, an electrophoretic force, an electrokinetic force, a temperature gradient, a pressure gradient, a surface property gradient, a capillary flow, or any combination thereof. 
     
     
         92 . The method of  claim 86 , wherein the signal comprises a visual signal, an infrared signal, an ultraviolet signal, a radioactive signal, a magnetic signal, an electrical signal, an electromagnetic signal, or any combination thereof. 
     
     
         93 . The method of  claim 86 , wherein the signal is inherently emitted by the macromolecule. 
     
     
         94 . The method of  claim 86 , wherein the signal is generated by illuminating the macromolecule. 
     
     
         95 . The method of  claim 94 , wherein the illuminating comprises exposing at least a portion of the macromolecule to visible light, ultraviolet light, infrared light, x-rays, gamma rays, electromagnetic radiation, radio waves, radioactive particles, or any combination thereof. 
     
     
         96 . The method of  claim 86 , wherein the macromolecule comprises one or more labels. 
     
     
         97 . The method of  claim 96 , wherein a feature of the macromolecule comprises the location of one or more labels of the macromolecule. 
     
     
         98 . The method of  claim 96 , wherein the one or more labels comprise an electron spin resonance molecule, a fluorescent molecule, a chemiluminescent molecule, a radioisotope, and enzyme substrate, a biotin molecule, an avidin molecule, an electrical charged transferring molecule, a semiconductor nanocrystal, a semiconductor nanoparticle, a colloid gold nanocrystal, a ligand, a microbead, a magnetic bead, a paramagnetic particle, a quantum dot, a chromogenic substrate, an affinity molecule, a protein, a peptide, a nucleic acid, a carbohydrate, an antigen, a hapten, an antibody, an antibody fragment, a lipid, a polymer, an electrically charged particle, modified nucleotide, or any combination thereof. 
     
     
         99 . A device for analyzing a polynucleotide macromolecule, the device comprising:
 two or more fluid reservoirs joined by a fluid pathway; and   a nanochannel comprising nanochannel segments capable of physically constraining at least a portion of the polynucleotide macromolecule so as to maintain in linear form that portion of the polynucleotide macromolecule, wherein at least one of the nanochannel segments comprises a cross-sectional dimension that is different than the cross-sectional dimension of another of the nanochannel segments, and wherein the nanochannel segments:
 are curved in form; 
 are tortuous in form; and/or 
 have a varying cross-sectional dimension; 
   wherein the nanochannel segments comprises at least one constriction comprising an effective inner diameter in the range of from about 0.5 nm to about 100 nm; and   wherein the nanochannel places the at least two fluid reservoirs in fluid communication with one another.   
     
     
         100 . The device of  claim 99 , wherein the nanochannel comprises a length of at least about 50 nm. 
     
     
         101 . The device of  claim 99 , further comprising a sensor associated with the device located to detect a signal from at least a portion of the polynucleotide macromolecule as it passes through the constriction. 
     
     
         102 . The device of  claim 101 , wherein the sensor is selected from the group consisting of a charge coupled device (CCD) detection system, a complementary metal-oxide semiconductor (CMOS) detection system, a photo diode detection system, a photo-multiplying tube detection system, a scintillation detection system, a photon counting detection system, an electron spin resonance detection system, a fluorescent detection system, a photon detection system, an electrical detection system, a photographic film detection system, a chemiluminescent detection system, an enzyme detection system, an atomic force microscopy (AFM) detection system, a scanning tunneling microscopy (STM) detection system, a scanning electron microscopy (SEM) detection system, an optical detection system, a nuclear magnetic resonance (NMR) detection system, a near field detection system, a total internal reflection (TIRF) detection system, a patch clamp detection system, an electrical current detection system, an electrical amplification detection system, a resistance measurement system, a capacitive detection system, and any combination thereof. 
     
     
         103 . The device of  claim 99 , further comprising an illuminator selected from the group consisting of a laser, a source of visible light, a magnet, a source of ultraviolet light, a source of infrared light, and any combination thereof. 
     
     
         104 . The device of  claim 99 , wherein the constriction is capable of maintaining a linearized polynucleotide macromolecule passing across the constriction in a linearized form. 
     
     
         105 . The device of  claim 99 , wherein the device further comprises a gradient, wherein the gradient comprises an electroosmotic field, an electrophoretic field, a magnetic field, an electric field, an electromagnetic field, a flow field, a radioactive field, a mechanical force, an electroosmotic force, an electrophoretic force, an electrokinetic force, a temperature gradient, a pressure gradient, a surface property gradient, a capillary flow, or any combination thereof.