Compositions for multiplex imaging using labeled nucleic acid imaging agents

Abstract

The present application provides compositions for multiplex imaging using labeled nucleic acid imaging agents.

What is claimed is: 
     
         1 . A composition comprising
 (1) a label,   (2) a first nucleic acid domain, a second nucleic acid domain, and a third nucleic acid domain, wherein each nucleic acid domain is from 1 to 9 nucleotides long,   (3) a first linking moiety linking the first nucleic acid domain and the second nucleic acid domain and   (4) a second linking moiety linking the second nucleic acid domain and the third nucleic acid domain,   wherein both linking moieties are independently chosen from (a) an abasic site with an intact phosphodiester backbone, (b) a linker cleavable by a nucleic acid glycosylase, (c) non-natural nucleotides, or (d) a restriction site or a nicking site.   
     
     
         2 . The composition of  claim 1 , further comprising additional nucleic acid domains linked by additional linking moieties. 
     
     
         3 . The composition of  claim 1 , wherein at least one linking moiety is an abasic, apyrimidinic site with an intact phosphodiester backbone. 
     
     
         4 . The composition of  claim 1 , wherein at least one of the linking moieties is susceptible to cleavage by Endonuclease VIII. 
     
     
         5 . The composition of  claim 1 , wherein the nucleic acid domains comprise DNA. 
     
     
         6 . The composition of  claim 1 , wherein the nucleic acid domains comprise RNA. 
     
     
         7 . The composition of  claim 1 , wherein at least one of the linking moieties comprises at least one non-natural nucleotide. 
     
     
         8 . The composition of  claim 1 , wherein at least one of the linking moieties comprises 8-oxoguanine. 
     
     
         9 . The composition of  claim 1 , wherein at least one of the linking moieties comprise at least one uracil group. 
     
     
         10 . The composition of  claim 1 , wherein at least one of the linking moieties comprise 1 to 20 uracil groups. 
     
     
         11 . The composition of  claim 1 , wherein at least one of the linking moieties comprise at least one deoxyuridine (dU). 
     
     
         12 . The composition of  claim 1 , wherein at least one of the linking moieties comprise 1 to 20 dU. 
     
     
         13 . The composition of  claim 1 , wherein at least one of the linking moieties is susceptible to cleavage by uracil-DNA glycosylase. 
     
     
         14 . The composition of  claim 1 , wherein at least one of the linking moieties is susceptible to cleavage by uracil-DNA glycosylase and Endonuclease VIII. 
     
     
         15 . The composition of  claim 1 , wherein the at least one of the linking moieties comprises at least one abasic site susceptible to cleavage by Endonuclease VIII. 
     
     
         16 . The composition of  claim 1 , wherein at least one of the linking moieties comprise at least one dU and at least one abasic site susceptible to cleavage by uracil-DNA glycosylase, Endonuclease VIII, or both. 
     
     
         17 . The composition of  claim 1 , wherein the at least one of the linking moieties comprise less than or equal to 9 nucleotides other than dU. 
     
     
         18 . The composition of  claim 1 , wherein at least one of the linking moieties includes photocleavable non-natural nucleotides. 
     
     
         19 . The composition of  claim 1 , wherein at least one of the linking moieties includes a restriction site or a nicking site susceptible to cleavage by restriction endonuclease or nicking endonuclease. 
     
     
         20 . The composition of  claim 18 , wherein the nicking endonuclease is Cas9 nickase. 
     
     
         21 . The composition of  claim 1 , wherein at least one of the linking moieties is susceptible to cleavage by zinc finger nucleases, transcription activator-like effector nucleases (TALENs), and deoxyribozymes.