Nucleic acid-functionalized nanoparticles

Abstract

Provided herein are functionalized nanoparticle compositions and methods of using the same. The functionalized nanoparticles provided include a nuclease cleavage site and are, inter alia, useful for the formation of nanoparticle aggregates and detection of nuclease activity through nanoparticle aggregate formation.

1 . A functionalized nanoparticle comprising a nanoparticle core and a nanoparticle coating, wherein said nanoparticle coating comprises:
 a plurality of nucleic acid moieties bonded to said nanoparticle core, wherein each of said nucleic acid moieties comprises:   (i) a first linker binding said nucleic acid moiety to said nanoparticle core; and   (ii) a single-stranded nucleic acid sequence of about 50 or less nucleotides in length covalently attached to said first linker, wherein said single-stranded nucleic acid sequence comprises a nuclease cleavage site.   
     
     
         2 . The functionalized nanoparticle of  claim 1 , wherein said nanoparticle core is an inorganic nanoparticle core. 
     
     
         3 . The functionalized nanoparticle of  claim 1 , wherein said nanoparticle core is a metal nanoparticle core. 
     
     
         4 . The functionalized nanoparticle of  claim 3 , wherein said metal nanoparticle core comprises titanium, zirconium, gold, silver, platinum, cerium, arsenic, iron, aluminum or silicon. 
     
     
         5 . The functionalized nanoparticle of  claim 3 , wherein said metal nanoparticle core is a gold nanoparticle core. 
     
     
         6 . The functionalized nanoparticle of  claim 1 , wherein said first linker is a bond, —C(O)—, —C(O)O—, —O—, —S—, —NH—, —NR 1 —, —C(O)NR 2 —, —S(O) n —, —S(O)NR 3 —, —OP(O)(OR 4 )O—, substituted or unsubstituted alkylene, substituted or unsubstituted heteroalkylene, substituted or unsubstituted cycloalkylene, substituted or unsubstituted heterocycloalkylene, substituted or unsubstituted arylene, or substituted or unsubstituted heteroarylene, an amino acid sequence linker, or a nucleic acid sequence linker;
 R 1 , R 2 , R 3 , R 4 , are independently hydrogen, halogen, —N 3 , —NO 2 , —CF 3 , —CCl 3 , —CBr 3 , —CI 3 , —CN, —OH, —NH 2 , —COOH, —CONH 2 , —NO 2 , —SH, —SO 2 Cl, —SO 3 H, —SO 4 H, —SO 2 NH 2 , —NHNH 2 , —ONH 2 , —OCH 3 , —NHCNHNH 2 , substituted or unsubstituted alkyl, substituted or unsubstituted heteroalkyl, substituted or unsubstituted cycloalkyl, substituted or unsubstituted heterocycloalkyl, substituted or unsubstituted aryl, or substituted or unsubstituted heteroaryl; and 
 n is 1 or 2. 
 
     
     
         7 . The functionalized nanoparticle of  claim 1 , wherein said single-stranded nucleic acid sequence is about 11 nucleotides in length. 
     
     
         8 . The functionalized nanoparticle of  claim 1 , wherein said single-stranded nucleic acid sequence comprises a modified nucleotide. 
     
     
         9 . The functionalized nanoparticle of  claim 8 , wherein said modified nucleotide is a 2′O-methylated nucleotide. 
     
     
         10 . The functionalized nanoparticle of  claim 1 , wherein said nuclease cleavage site is a bacterial nuclease cleavage site. 
     
     
         11 . A plurality of functionalized nanoparticles, wherein each functionalized nanoparticle is a functionalized nanoparticle of  claim 1 . 
     
     
         12 . The plurality of functionalized nanoparticles of  claim 11 , wherein said nanoparticles are in a vessel. 
     
     
         13 . The plurality of functionalized nanoparticles of  claim 12 , wherein said vessel is in a spectrophotometry device. 
     
     
         14 . A method of forming a nanoparticle aggregate, said method comprising:
 (i) contacting a nuclease with said plurality of functionalized nanoparticles of  claim 11 ; and   (ii) allowing said nuclease to cleave said single-stranded nucleic acid sequence at said nuclease cleavage site of said plurality of functionalized nanoparticles, thereby forming a nanoparticle aggregate.   
     
     
         15 . The method of  claim 14 , further comprising detecting said nanoparticle aggregate. 
     
     
         16 . The method of  claim 15 , wherein said detecting comprises colorimetric detection of said nanoparticle aggregate. 
     
     
         17 . The method of  claim 14 , wherein said allowing of step (ii) comprises forming a plurality of cleaved functionalized nanoparticles comprising a cleaved single-stranded nucleic acid sequence. 
     
     
         18 . The method of  claim 17 , wherein said cleaved single-stranded nucleic acid sequence is less than about 20 nucleotides in length. 
     
     
         19 . The method of  claim 17 , wherein said cleaved single-stranded nucleic acid sequence is less than about 10 nucleotides in length. 
     
     
         20 . The method of  claim 17 , wherein said cleaved single-stranded nucleic acid sequence is about 5 nucleotides in length.