Methods and systems for integrated on-chip single-molecule detection

Abstract

The present disclosure provides methods and systems for performing single-molecule detection using fabricated integrated on-chip devices. In an aspect, the present disclosure provides a method for on-chip detection of an array of biological, chemical, or physical entities, comprising: (a) providing an array of light sensing devices; (b) immobilizing the array of biological, chemical, or physical entities on a substrate of the array of light sensing devices; (c) exposing the array of biological, chemical, or physical entities to electromagnetic radiation sufficient to excite the array of biological, chemical, or physical entities, thereby producing an emission signal of the array of biological, chemical, or physical entities; (d) using the array of light sensing devices, acquiring pixel information of the emission signal of the array of biological, chemical, or physical entities without scanning the array of light sensing devices across the array of biological, chemical, or physical entities; and (d) detecting the array of biological, chemical, or physical entities based at least in part on the acquired pixel information.

1 .- 27 . (canceled) 
     
     
         28 . A method comprising:
 (a) obtaining a plurality of structured nucleic acid particles that are each attached to only one biological or chemical entity comprising an antibody, wherein said structured nucleic acid particles comprises nucleic acid origami; and   (b) attaching said plurality of structured nucleic acid particles to an array of spatially separated attachment sites on a solid support, such that each said attachment site on the solid support is attached to said only one biological or chemical entity comprising an antibody via said structured nucleic acid particle.   
     
     
         29 . The method of  claim 28 , wherein the attachment of the structured nucleic acid particles to the attachment sites is non-covalent. 
     
     
         30 . The method of  claim 28 , wherein the attachment of the structured nucleic acid particles to the attachment sites is through bioconjugation. 
     
     
         31 . The method of  claim 28 , wherein the attachment of the structured nucleic acid particles to the attachment sites is through biotin. 
     
     
         32 . The method of  claim 28 , wherein the attachment of the structured nucleic acid particles to the attachment sites utilizes nucleic acids. 
     
     
         33 . The method of  claim 28 , wherein the structured nucleic acid particle comprises at least one long nucleic acid strand and a plurality of short nucleic acid strands. 
     
     
         34 . The method of  claim 28 , wherein each of the biological or chemical entities is attached to a seed for growing a polymeric molecule. 
     
     
         35 . The method of  claim 34 , wherein the seed comprises a monomer for rolling circle amplification. 
     
     
         36 . The method of  claim 34 , wherein the seed is used for fluorescent visualization. 
     
     
         37 . The method of  claim 28 , wherein the structured nucleic acid particle comprising nucleic acid origami comprises a landing surface that preferentially contacts the solid support. 
     
     
         38 . The method of  claim 37 , wherein the nucleic acid origami comprises a region that creates steric or electrostatic interactions with the support. 
     
     
         39 . The method of  claim 28 , wherein the biological or chemical entities are cleaved from the solid support. 
     
     
         40 . The method of  claim 39 , wherein the cleaving is performed through a photo-cleavable bond. 
     
     
         41 . The method of  claim 39 , wherein the cleaving is performed by chemical or enzymatic digestion. 
     
     
         42 . The method of  claim 28 , wherein the solid support is part of a flow cell. 
     
     
         43 . A solid support comprising an array of spatially separated structured nucleic acid particles, the solid support prepared by:
 (a) obtaining a plurality of structured nucleic acid particles that are each attached to only one biological or chemical entity comprising an antibody, wherein said structured nucleic acid particles comprises nucleic acid origami; and   (b) attaching said plurality of structured nucleic acid particles to an array of spatially separated attachment sites on a solid support, such that each said attachment site on the solid support is attached to said only one biological or chemical entity comprising an antibody via said structured nucleic acid particle.