Methods, compositions, and systems for mapping locations of single molecules in multi-dimensional space

Abstract

The invention(s) cover a composition, where units of the composition are configured to interact with each other (e.g., as neighbors) in order enable decoding of positions of captured target material relative to neighboring units of the composition. In embodiments, the composition includes: a body; and a set of molecules coupled to the body, the set of molecules comprising a first subset and a second subset, wherein the first subset is structured for target analyte capture, and wherein the second subset is structured for interactions with one or more neighboring objects. The invention(s) also cover systems incorporating one or more units of the composition and methods implementing units of the composition.

What is claimed is: 
     
         1 . A system comprising:
 a first body comprising a first subset of molecules and a second subset of molecules coupled to the first body,   wherein a first molecule of the first subset of molecules comprises:
 a capture probe configured to capture an analyte of a sample, and 
   wherein a second molecule of the second subset of molecules comprises:
 a linker region configured to extend the second molecule into space beyond a first terminal end of the first molecule, 
 a first particle identification segment unique to the first body, and 
 a first active segment positioned at a second terminal end of the second molecule; and 
   a second body comprising: a second particle identification segment unique to the second body, and a second active segment configured to interact with the first active segment of the first body.   
     
     
         2 . The system of  claim 1 , wherein the capture probe is configured to capture a polyA sequence of a messenger ribonucleic acid molecule (mRNA) molecule. 
     
     
         3 . The system of  claim 1 , wherein the analyte is a target analyte located within a cell. 
     
     
         4 . The system of  claim 1 , wherein the analyte is a target analyte from a surface of the sample. 
     
     
         5 . The system of  claim 1 , wherein the sample is a tissue sample. 
     
     
         6 . The system of  claim 1 , wherein at least one of the first molecule and the second molecule further comprises a cleavable molecule responsive to cleavage by a photocleaving mechanism. 
     
     
         7 . The system of  claim 1 , wherein the second active segment is configured to interact with the first active segment by hybridization. 
     
     
         8 . The system of  claim 1 , wherein the second active segment is configured to interact with the first active segment by ligation. 
     
     
         9 . The system of  claim 1 , wherein the first active segment is structured to preferentially interact with the second active segment and prevent self-interactions with the first active segment. 
     
     
         10 . The system of  claim 1 , further comprising a substrate retaining the first body and the second body in position. 
     
     
         11 . The system of  claim 1 , wherein the sample comprises a suspension, wherein the first body and the second body are dispersed within the suspension. 
     
     
         12 . The system of  claim 1 , further comprising a film containing the first body and the second body. 
     
     
         13 . The system of  claim 1 , wherein the first particle identification segment comprises a first random sequence and wherein the second particle identification segment comprises a second random sequence. 
     
     
         14 . The system of  claim 1 , wherein the first subset of molecules of the first body provides at least 300 functional sites for capture of analytes from the sample 
     
     
         15 . A method comprising:
 positioning a first body and a second body in proximity to a sample comprising a set of targets;   capturing a first target of the set of targets by a first capture probe coupled to the first body;   capturing a second target of the set of targets by a second capture probe coupled to the second body;   promoting interactions between a first active segment of the first body and a second active segment of the second body;   identifying a connection between the first body and the second body upon sequencing molecules derived from the first active segment and the second active segment;   associating the first body with the first target, and the second body with the second target; and   generating a map of relative positioning of the first target and the second target, based upon the connection between the first body and the second body.   
     
     
         16 . The method of  claim 15 , wherein the first body comprises:
 a first molecule comprising the first capture probe at a first terminal end of the first molecule, and   a second molecule comprising:
 a linker region configured to extend the second molecule into space beyond the first terminal end of the first molecule, and 
 a first particle identification segment unique to the first body, 
 wherein the first active segment is positioned at a second terminal end of the second molecule. 
   
     
     
         17 . The method of  claim 16 , wherein at least one of the first molecule and the second molecule further comprises a cleavable molecule responsive to cleavage by a photocleaving mechanism. 
     
     
         18 . The method of  claim 15 , wherein the set of targets comprise mRNA molecules of the sample, wherein the first capture probe is configured to capture a polyA sequence of the first target, and wherein the second capture probe is configured to capture a polyA sequence of the second target. 
     
     
         19 . The method of  claim 15 , wherein the first target and the second target are located within a cell. 
     
     
         20 . The method of  claim 15 , wherein the first active segment is configured to interact with the second active segment by hybridization