Multivalent binding composition for nucleic acid analysis

Abstract

Multivalent binding compositions including a particle-nucleotide conjugate having a plurality of copies of a nucleotide attached to the particle are described. The multivalent binding compositions allow one to localize detectable signals to active regions of biochemical interaction, e.g., sites of protein-protein interaction, protein-nucleic acid interaction, nucleic acid hybridization, or enzymatic reaction, and can be used to identify sites of base incorporation in elongating nucleic acid chains during polymerase reactions and to provide improved base discrimination for sequencing and array based applications.

What is claimed: 
     
         1 . A system comprising:
 a conjugated nucleotide composition comprising a polymer core and a plurality of nucleotide moieties attached thereto; and   a solid support comprising a surface having a plurality of primed nucleic acid sequences coupled thereto, wherein said plurality of said primed nucleic acid sequences are extendible in a primer extension reaction, and wherein at least two nucleotide moieties of said plurality of said nucleotide moieties are coupled to at least two primed nucleic acid sequences of said plurality of said primed nucleic acid sequences.   
     
     
         2 . The system of claim  0 , further comprising:
 (1) a fluid flow controller;   (2) a fluid dispensing system; or   (3) a combination of (2) and (3), wherein any one of (2) to (3) is configured to direct said conjugated nucleotide composition to said plurality of said primed nucleic acid sequences.   
     
     
         3 . The system of  claim 1 , wherein said solid support is a flow cell. 
     
     
         4 . The system of  claim 3 , wherein said surface is one or more interior surfaces of said flow cell. 
     
     
         5 . The system of  claim 4 , wherein said at least two primed nucleic acid sequences are coupled to at least a portion of at least two capture nucleic acid sequences coupled to said one or more interior surfaces of said flow cell. 
     
     
         6 . The system of  claim 4 , further comprising:
 an imaging module operably coupled to said flow cell; and   one or more processors programed to implement:
 (i) directing said conjugated nucleotide composition to said at least two primed nucleic acid sequences coupled to said one or more interior surfaces of said flow cell; 
 (ii) imaging, by said imaging module, said one or more interior surfaces of said flow cell to detect a signal from one or more detectable moieties of said conjugated nucleotide composition; and 
 (ii) detecting, by said imaging module, said one or more signals to identify at least two nucleotides of said at least two primed nucleic acid sequences that are bound to said at least two nucleotide moieties. 
   
     
     
         7 . The system of  claim 3 , further comprising:
 an imaging module operably coupled to said flow cell, and comprising:   (1) a light source;   (2) an optical component; and   (3) an image sensor.   
     
     
         8 . The system of  claim 1 , wherein said conjugated nucleotide composition comprises one or more detectable moieties. 
     
     
         9 . The system of  claim 8 , wherein said one or more detectable moieties is coupled to said polymer core. 
     
     
         10 . The system of  claim 9 , wherein said one or more detectable moieties comprises a plurality of detectable moieties. 
     
     
         11 . The system of  claim 1 , wherein a primed nucleic acid sequence of said plurality of said primed nucleic acid sequences comprises a blocked nucleotide at 3′ end thereof, wherein said blocked nucleotide comprises a blocking group. 
     
     
         12 . The system of  claim 11 , wherein said blocking group comprises a 3′-O-alkyl hydroxylamino group, a 3′-phosphorothioate group, a 3′-O-malonyl group, or a 3′-O-benzyl group. 
     
     
         13 . The system of  claim 1 , further comprising a concatemer comprising said at least two primed nucleic acid sequences, wherein said at least two primed nucleic acid sequences comprise the same sequence. 
     
     
         14 . The system of  claim 1 , further comprising a second conjugated nucleotide composition comprising a second polymer core and a second plurality of nucleotide moieties attached thereto, wherein said second plurality of nucleotide moieties comprises a nucleobase that is different nucleobase type than a nucleobase of said plurality of nucleotide moieties. 
     
     
         15 . A composition comprising:
 (a) a polymer core, wherein said polymer core is substantially spherical in shape; and   (b) a plurality of nucleotide moieties coupled to said polymer core, wherein a nucleotide moiety of said plurality of nucleotide moieties does not comprise a blocking group at a 3′ position of a sugar moiety of said nucleotide moiety.   
     
     
         16 . The composition of  claim 15 , wherein at least two nucleotide moieties of said plurality of said nucleotide moieties are coupled to at least two primed nucleic acid sequences coupled to a surface of a solid support. 
     
     
         17 . The composition of  claim 15 , wherein said plurality of nucleotide moieties is coupled to said polymer core covalently. 
     
     
         18 . The composition of  claim 15 , wherein the polymer core comprises a branched polymer, a dendrimer, a cross-linked polymer, or a combination thereof. 
     
     
         19 . The composition of  claim 15 , wherein said plurality of nucleotide moieties comprises at least three nucleotide moieties. 
     
     
         20 . The composition of  claim 15 , further comprising one or more detectable labels coupled to said polymer core. 
     
     
         21 . The composition of  claim 20 , wherein said one or more detectable moieties comprises a plurality of detectable moieties. 
     
     
         22 . The composition of  claim 15 , wherein the composition is isolated. 
     
     
         23 . A composition comprising:
 (a) a polymer core; and   (b) a plurality of nucleotide moieties coupled to said polymer core, wherein at least two nucleotide moieties of said plurality of said nucleotide moieties are coupled to at least two primed nucleic acid sequences coupled to a surface of a solid support, and wherein said at least two of said primed nucleic acid sequences are extendible in a primer extension reaction.   
     
     
         24 . The composition of  claim 23 , wherein said plurality of nucleotide moieties is coupled to said polymer core covalently. 
     
     
         25 . The composition of  claim 23 , wherein the polymer core comprises a branched polymer, a dendrimer, a cross-linked polymer, or a combination thereof. 
     
     
         26 . The composition of  claim 23 , wherein said plurality of nucleotide moieties comprises at least three nucleotide moieties. 
     
     
         27 . The composition of  claim 23 , further comprising a linker coupling said plurality of nucleotide moieties to said polymer core. 
     
     
         28 . The composition of  claim 23 , further comprising one or more detectable labels coupled to said polymer core. 
     
     
         29 . The composition of  claim 28 , wherein said one or more detectable labels comprises a plurality of detectable moieties. 
     
     
         30 . The composition of  claim 23 , wherein a nucleotide moiety of said plurality of nucleotide moieties comprises a blocking group at a 3′ position of a sugar moiety of said nucleotide moiety.