Characterization of individual polymer molecules based on monomer-interface interactions

Abstract

The invention relates to a method for detecting a double-stranded region in a nucleic acid by (1) providing two separate, adjacent pools of a medium and a interface between the two pools, the interface having a channel so dimensioned as to allow sequential monomer-by-monomer passage of a single-stranded nucleic acid, but not of a double-stranded nucleic acid, from one pool to the other pool; (2) placing a nucleic acid polymer in one of the two pools; and (3) taking measurements as each of the nucleotide monomers of the single-stranded nucleic acid polymer passes through the channel so as to differentiate between nucleotide monomers that are hybridized to another nucleotide monomer before entering the channel and nucleotide monomers that are not hybridized to another nucleotide monomer before entering the channel.

What is claimed is:  
     
         1 - 24 . (canceled) 
     
     
         25 . A method for characterizing a target polynucleic acid comprising:
 a) providing a surface containing more than one channel of a dimension sufficient to allow sequential monomer-by-monomer passage of a target polynucleic acid;   b) providing a source of target polynucleic acid at the surface;   c) inducing passage of the target polynucleic acid through the channels;   d) making one or more measurements over time as the target polynucleic acid moves relative to the channels yielding data suitable to determine a characteristic of the target polynucleic acid.   
     
     
         26 . A method according to  claim 25 , wherein the channels connect two separate pools of solution and comprising providing a source of target polynucleic acid in one of the two pools. 
     
     
         27 . A method according to  claim 25  comprising measuring ionic flow through the channels in the presence of a potential difference between the two pools. 
     
     
         28 . A method according to  claim 25 , wherein the measurements are optical. 
     
     
         29 . A method according to  claim 28 , comprising detecting optical deflection at the interface. 
     
     
         30 . A method according to  claim 29 , comprising directing a laser at the interface and observing the optical deflection using a detector. 
     
     
         31 . A method according to  claim 30 , wherein the laser is pulsed. 
     
     
         32 . A method according to  claim 25 , wherein the channels are ion-permeable channels. 
     
     
         33 . A method according to  claim 25 , wherein the channels are protein pores. 
     
     
         34 . A method according to  claim 33 , wherein the protein pores are bacterial porins. 
     
     
         35 . A method according to  claim 33 , wherein the protein pores are naturally occurring, recombinant or natural. 
     
     
         36 . A method according to  claim 33 , wherein the channels are voltage sensitive. 
     
     
         37 . A method according to  claim 25  wherein the channels are synthetic.