Methods for preparing analytes and related kits

Abstract

Provided herein are methods for preparing and treating an analyte (e.g., a macromolecule or a plurality of macromolecules, peptides, polypeptides, and proteins) for analysis. In some embodiments, the analyte is prepared and treated in a method that includes the use of bait and capture nucleic acids, solid supports, and reaction mixtures including the bait and capture nucleic acids. In some embodiments, the analyte is coupled to a solid support. Also provided are kits containing components for performing the provided methods for preparing the analytes. In some embodiments, the methods are for preparing an analyte for sequencing.

1 . A method for treating an analyte, comprising:
 attaching an analyte to a bait nucleic acid to generate a nucleic acid-analyte chimera;   bringing the nucleic acid-analyte chimera into proximity with a solid support by hybridizing the bait nucleic acid in the nucleic acid-analyte chimera to a capture nucleic acid attached to the solid support; and   covalently coupling the nucleic acid-analyte chimera to the solid support;   wherein a plurality of the nucleic acid-analyte chimeras is coupled on the solid support and any adjacently coupled nucleic acid-analyte chimeras are spaced apart from each other at an average distance of about 50 nm or greater.   
     
     
         2 . The method of  claim 1 , wherein the analyte is attached to the 3′ end of the bait nucleic acid or to the 5′ end of the bait nucleic acid. 
     
     
         3 . The method of  claim 1 , wherein the analyte is attached to an internal position of the bait nucleic acid. 
     
     
         4 . (canceled) 
     
     
         5 . The method of  claim 1 , further comprising attaching a barcode to the coupled nucleic acid-analyte chimera, wherein the barcode comprises a compartment barcode, a partition barcode, a sample barcode, a fraction barcode, or any combination thereof. 
     
     
         6 . (canceled) 
     
     
         7 . The method of  claim 1 , wherein the bait nucleic acid is covalently attached to the analyte to generate the nucleic acid-analyte chimera. 
     
     
         8 - 12 . (canceled) 
     
     
         13 . The method of  claim 1 , wherein the analyte is a polypeptide. 
     
     
         14 . The method of  claim 13 , wherein the polypeptide is obtained by fragmenting proteins from a biological sample. 
     
     
         15 . (canceled) 
     
     
         16 . The method of  claim 1 , wherein the bait nucleic acid and/or capture nucleic acid further comprises a universal priming site, wherein the universal priming site comprises a priming site for amplification, sequencing, or both. 
     
     
         17 . (canceled) 
     
     
         18 . The method of  claim 1 , further comprising:
 contacting the analyte with a binding agent capable of binding to the analyte, wherein the binding agent comprises a coding tag with identifying information regarding the binding agent; and   transferring the identifying information of the coding tag to the bait nucleic acid or capture nucleic acid.   
     
     
         19 . The method of  claim 18 , further comprising repeating one or more times:
 contacting the analyte with an additional binding agent capable of binding to the analyte, wherein the additional binding agent comprises a coding tag with identifying information regarding the additional binding agent; and   transferring the identifying information of the coding tag regarding the additional binding agent to the bait nucleic acid or capture nucleic acid.   
     
     
         20 . (canceled) 
     
     
         21 . A nucleic acid-analyte composition comprising a plurality of nucleic acid-analyte chimeras and a plurality of capture nucleic acids attached to a solid support, the nucleic acid-analyte composition generated by the steps of:
 attaching an analyte to a bait nucleic acid to generate a nucleic acid-analyte chimera;   bringing the nucleic acid-analyte chimera into proximity with the solid support by hybridizing the bait nucleic acid in the nucleic acid-analyte chimera to a capture nucleic acid attached to the solid support; and   covalently coupling the nucleic acid-analyte chimera to the solid support;   wherein the plurality of nucleic acid-analyte chimeras is coupled on the solid support and any adjacently coupled nucleic acid-analyte chimeras are spaced apart at an average distance of about 50 nm or greater.   
     
     
         22 . The nucleic acid-analyte composition of  claim 21 , wherein the analyte is attached to the 3′ end of the bait nucleic acid or to the 5′ end of the bait nucleic acid. 
     
     
         23 . (canceled) 
     
     
         24 . The nucleic acid-analyte composition of  claim 21 , wherein the capture nucleic acid, the nucleic acid-analyte chimera, and/or the bait nucleic acid further comprises a barcode. 
     
     
         25 - 26 . (canceled) 
     
     
         27 . The nucleic acid-analyte composition of  claim 21 , wherein the bait nucleic acid is covalently attached to the analyte to generate the nucleic acid-analyte chimera. 
     
     
         28 . (canceled) 
     
     
         29 . The nucleic acid-analyte composition of  claim 21 , wherein the capture nucleic acid comprises a nucleic acid hairpin. 
     
     
         30 - 33 . (canceled) 
     
     
         34 . The nucleic acid-analyte composition of  claim 21 , wherein the analyte is a polypeptide. 
     
     
         35 - 37 . (canceled) 
     
     
         38 . The nucleic acid-analyte composition of  claim 21 , wherein the bait nucleic acid and/or capture nucleic acid further comprises a universal priming site, wherein the universal priming site comprises a priming site for amplification, sequencing or both. 
     
     
         39 . (canceled) 
     
     
         40 . The nucleic acid-analyte composition of  claim 21 , wherein the solid support is a porous bead. 
     
     
         41 . A kit, comprising:
 (a) a plurality of bait nucleic acids, each of the bait nucleic acids is configured to be attached to an analyte;   (b) a solid support comprising a plurality of capture nucleic acids attached hereto, each of the capture nucleic acids comprising a sequence complementary to a corresponding bait nucleic acid of the plurality of bait nucleic acids and configured to attach the analyte to the solid support, wherein any adjacently capture nucleic acids are spaced apart on the solid support at an average distance of about 50 nm or greater.   
     
     
         42 . The kit of  claim 41 , wherein at least one of the bait nucleic acids is configured to allow the analyte to be attached to the 3′ end of the bait nucleic acid or to the 5′ end of the bait nucleic acid. 
     
     
         43 - 44 . (canceled) 
     
     
         45 . The kit of  claim 41 , further comprising a plurality of barcodes, wherein the barcodes are attached to the bait nucleic acid or the capture nucleic acid, or the barcodes are configured to be attached to the bait nucleic acid or the capture nucleic acid. 
     
     
         46 - 47 . (canceled) 
     
     
         48 . The kit of  claim 41 , wherein at least one of the bait nucleic acids comprises a reactive coupling moiety configured for attachment to the analyte or to at least one of the capture nucleic acids. 
     
     
         49 - 51 . (canceled) 
     
     
         52 . The kit of  claim 41 , wherein at least one of the capture nucleic acids comprises a nucleic acid hairpin. 
     
     
         53 - 57 . (canceled)