Method and apparatus for the analysis and identification of molecules

Abstract

An apparatus and method for performing analysis and identification of molecules have been presented. In one embodiment, a portable molecule analyzer includes a sample input/output connection to receive a sample, a nanopore-based sequencing chip to perform analysis on the sample substantially in real-time, and an output interface to output result of the analysis.

1 - 21 . (canceled) 
     
     
         22 . A structure for use in an apparatus for analysis of a sample liquid containing biological substances, comprising:
 a set of guiding channels comprising a single inlet  1501  and multiple outlets  1502 , wherein said inlet  1501  to any of the outlets  1502  has a same path length; 
 wherein said sample liquid is to be fed into said inlet  1501  which breaks up into smaller, but equal, volumes at each successive level in a hierarchical fluidic network of said set of guiding channels to arrive at each of said multiple outlets. 
     
     
         23 . The structure of  claim 22 , wherein said biological substances comprises molecules. 
     
     
         24 . The structure of  claim 22 , wherein said multiple outlets are connected to a nanopore-based sequencing chip comprising a plurality of nanopores, wherein each of said multiple outlets is separately connected to each of said plurality of nanopores. 
     
     
         25 . The structure of  claim 22 , said biological substances are dsDNA and said structure further comprises:
 a) a chamber  1401  comprising a nicking mechanism for nicking said dsDNA at a specific restriction site to form nicked dsDNA;   b) a dissociation zone comprising a dissociation mechanism for dissociating said nicked dsDNA into a plurality of short strands of ssDNA in a controlled manner;   c) a set of guiding electrodes within said set of guiding channels for transporting said plurality of short strands of ssDNA; 
 wherein said dissociation zone connects said chamber to said single inlet to feed said plurality of short strands of ssDNA into said set of guiding channels; said set of guiding electrodes assign each of said plurality of short strands of ssDNA entering the inlet into different channels and ensure the ssDNA arrives at each of said multiple outlets in a known order to be reconstructed with a concatenation algorithm. 
     
     
         26 . The structure of  claim 25 , wherein said nicking mechanism comprises one or more nickases selected from the group consisting of mutated type II S endonucleoases, CRISPR/cas9 derived nickases and TALEN like fokI based nickases. 
     
     
         27 . The structure of  claim 26 , wherein said mutated type II S endonucleoase is fokI based nickase. 
     
     
         28 . The structure of  claim 25 , wherein said nicking mechanism comprises one or more nickases selected from New England BioLab’s REBASE database. 
     
     
         29 . The structure of  claim 25 , wherein said dissociation mechanism is heating, helicase, bacteriophage T7 gene product 4, or bacteriophage T7 gene product gp4. 
     
     
         30 . The structure of  claim 25 , wherein said dissociation zone further comprises a straightening mechanism for straightening said nicked dsDNA. 
     
     
         31 . The structure of  claim 30 , wherein said straightening mechanism comprises an array of micro-or nano-pillars or a DNA pump. 
     
     
         32 . The structure of  claim 24 , wherein said set of guiding electrodes is arranged in a H-tree structure. 
     
     
         33 . A method for analysing a sample liquid containing biological substances using an apparatus comprising the structure of claim  21 , comprising the steps of:
 a. Feeding said sample liquid into said single inlet  1501 ; and   b. Receiving an equal volume of said sample liquid at each of said multiple outlets.   
     
     
         34 . The method of  claim 33 , wherein said biological substances comprises molecules. 
     
     
         35 . The method of  claim 33 , wherein said biological substances are dsDNA and said structure further comprises:
 a) a chamber  1401  comprising a nicking mechanism for nicking said dsDNA at a specific restriction site to form nicked dsDNA;   b) a dissociation zone comprising a dissociation mechanism for dissociating said nicked dsDNA into a plurality of short strands of ssDNA in a controlled manner;   c) a set of guiding electrodes within said set of guiding channels for transporting said plurality of short strands of ssDNA; 
 wherein said dissociation zone connects said chamber to said single inlet to feed said plurality of short strands of ssDNA into said set of guiding channels; said set of guiding electrodes assign each of said plurality of short strands of ssDNA entering the inlet into different channels and ensure the ssDNA arrives at each of said multiple outlets in a known order to be reconstructed with a concatenation algorithm. 
     
     
         36 . The method of  claim 35 , wherein said nicking mechanism comprises one or more nickases selected from the group consisting of mutated type II S endonucleoases, CRISPR/cas9 derived nickases and TALEN like fokI based nickases. 
     
     
         37 . The method of  claim 36 , wherein said mutated type II S endonucleoase is fokI based nickase. 
     
     
         38 . The method of  claim 35 , wherein said nicking mechanism comprises one or more nickases selected from New England BioLab’s REBASE database. 
     
     
         39 . The method of  claim 35 , wherein said dissociation mechanism is heating, helicase, bacteriophage T7 gene product 4, or bacteriophage T7 gene product gp4. 
     
     
         40 . The method of  claim 33 , wherein said dissociation zone further comprises a straightening mechanism for straightening said nicked dsDNA. 
     
     
         41 . The method of  claim 33 , wherein said straightening mechanism comprises an array of micro-or nano-pillars or a DNA pump. 
     
     
         42 . The method of  claim 33 , wherein said set of guiding electrodes is arranged in a H-tree structure.