Manipulating the translation of dna strands across and through nanopore sequencing systems using raman signatures to identify dna bases and methods

Abstract

Nucleic acid sequencing methods and systems, the systems including nanochannel chip including: a nanochannel formed in an upper surface of the nanochannel chip and; a roof covering the nanochannel and comprising nanopores and a field enhancement structure; and a barrier disposed in the nanochannel. The method including: introducing a buffer solution including long-chain nucleic acids to the nanochannel chip; applying a voltage potential across the nanochannel chip to drive the nucleic acids through the nanochannel, towards the barrier, and to translocate the nucleic acids through nanopores adjacent to the barrier, such that bases of each of the nucleic acids pass through the field enhancement structure one base at a time and emerge onto an upper surface of the roof; detecting the Raman spectra of the bases of the nucleic acids as each base passes through the electromagnetic-field enhancement structure; and sequencing the nucleic acids based on the detected Raman spectra.

What is claimed is: 
     
         1 . A nanochannel chip comprising:
 a substrate;   nanochannels formed on an upper surface of the substrate;   wells disposed on the substrate and fluidly connected to opposing open ends of the nanochannels;   a nanoparticle layer covering the nanochannels and comprising nanopores;   pillars disposed on an upper surface of the nanoparticle layer;   a cover disposed on the pillars, such that a gap is formed between the cover and the upper surface of the nanoparticle layer; and   an adhesive layer disposed between the cover and the pillars.   
     
     
         2 . The nanochannel chip of  claim 1 , wherein the adhesive layer comprises a polydimethylsiloxane (PDMS) coating. 
     
     
         3 . The nanochannel chip of  claim 1 , wherein the pillars are configured such that the cover and the upper surface of the roof are separated by a distance ranging from about 0.5 µm to about 2.0 µm. 
     
     
         4 . The nanochannel chip of  claim 1 , wherein the cover is optically transparent and non-porous. 
     
     
         5 . The nanochannel chip of  claim 1 , wherein the cover is optically transparent and electrically conductive. 
     
     
         6 . A nanochannel chip comprising:
 a substrate;   nanochannels formed on an upper surface of the substrate;   wells disposed on the substrate and fluidly connected to opposing open ends of the nanochannels;   a nanoparticle layer covering the nanochannels and comprising nanopores;   an alignment layer disposed on the nanoparticle layer and comprising a porous crystalline material; and   an electromagnetic-field enhancement layer disposed on the alignment layer and configured to spatially localize incident electromagnetic fields to a spatial scale of about 1 nm 3 ,   wherein the alignment layer has a higher pore density and a smaller average pore size than the nanoparticle layer.   
     
     
         7 . The nanochannel chip of  claim 6 , wherein tortuous nanopores of the nanoparticle layer are each aligned with at least one of the pores of the alignment layer. 
     
     
         8 . The nanochannel chip of  claim 6 , wherein:
 the electromagnetic-field enhancement layer comprises pores; and   the alignment layer is configured to fluidly connect the nanopores of the nanoparticle layer with the pores of the electromagnetic-field enhancement layer.   
     
     
         9 . The nanochannel chip of  claim 8 , wherein the alignment layer has a substantially uniform porosity and an average pore size ranging from about 0.3 nm to about 3 nm. 
     
     
         10 . The nanochannel chip of  claim 6 , wherein the alignment layer comprises graphene or mesoporous or microporous silica. 
     
     
         11 . The nanochannel chip of  claim 6 , further comprising a nanopore sealing layer disposed between the nanoparticle layer and the alignment layer, the nanopore sealing layer configured to seal a portion of the nanopores of the nanoparticle layer. 
     
     
         12 . The nanochannel chip of  claim 6 , further comprising:
 pillars disposed on an upper surface of the nanoparticle layer; and   an optically transparent cover disposed on the pillars, such that a gap is formed between the cover and the upper surface of the nanoparticle layer.   
     
     
         13 . A sequencing system comprising:
 a nanochannel chip comprising: 
 a substrate; 
 nanochannels formed on an upper surface of the substrate; 
 wells disposed on the substrate and fluidly connected to opposing open ends of the nanochannels; 
 a nanoparticle layer covering the nanochannels and comprising nanopores; 
 an alignment layer disposed on the nanoparticle layer and comprising a porous crystalline material; and 
 an electromagnetic-field enhancement layer disposed on the alignment layer and configured, in combination with the nanopores, to spatially localize incident electromagnetic fields to a spatial scale of about 1 nm 3 , 
 wherein the alignment layer has a higher pore density and a smaller average pore size than the nanoparticle layer; 
   a coherent light source configured to illuminate a linear region of the nanochannel chip;   a spectrometer configured to separate light emitted from the linear region into Raman spectral components;   an objective configured to focus light emitted from the linear region on an inlet of the spectrometer;   a camera configured to generate image data using the Raman spectral components output from the spectrometer into image data; and   a processor configured to sequence the nucleic acids based on the image data.