Compositions for Selection of Aptamers

Abstract

The present disclosure describes compositions and methods for rapid selection of both binding and functional oligonucleotides (DNA, RNA, or any natural or synthetic analog of these). In certain embodiments, provided herein are flow cells (e.g., flow cells for an Illumina sequencing instrument or a Polonator sequencing instrument) comprising within its flow chamber a plurality of immobilized aptamer clusters (e.g., from an aptamer library described herein) and, optionally, one or more target cells (e.g., cancer cells, immune cells, etc.) and/or a detectable indicator of cellular function (e.g., a fluorescent indicator of apoptosis, cell proliferation, gene or protein expression, etc.). In certain embodiments, provided herein are methods of using such an aptamer cluster-containing flow cell to identify functional aptamers from an aptamer library (e.g., in a sequencing instrument, such as an Illumina sequencing instrument).

What is claimed is: 
     
         1 . A composition comprising a plurality of aptamer clusters immobilized on a surface, wherein at least 10 2  distinct aptamer clusters are immobilized on the surface, and a target cell labeled with a reporter of cell function. 
     
     
         2 . The composition of  claim 1 , wherein each aptamer cluster: (1) is of a known sequence; and (2) is at a known position on the surface. 
     
     
         3 . The composition of  claim 1 , wherein the surface is a surface of a flow cell. 
     
     
         4 . The composition of  claim 1 , wherein the reporter of cell function is a fluorescent reporter of cell function. 
     
     
         5 . The composition of  claim 1 , wherein at least 10 8  distinct aptamers are immobilized on the surface and each aptamer cluster comprises 10 3  to 10 6  copies of an aptamer. 
     
     
         6 . The composition of  claim 1 , wherein the aptamers in the aptamer cluster comprise nucleic acid adapters binding the aptamers to the surface. 
     
     
         7 . The composition of  claim 1 , wherein the aptamer clusters are labeled with a fluorescent marker. 
     
     
         8 . The composition of  claim 1 , wherein the aptamer clusters are labeled with an element for allowing visibility under a light microscope. 
     
     
         9 . The composition of  claim 8 , wherein the element is a nanoparticle. 
     
     
         10 . The composition of  claim 1 , wherein the reporter of cell function is a fluorescent reporter of cell function. 
     
     
         11 . The composition of  claim 1 , wherein the cell function is cell death, caspase-3/7 activity, proliferation, gene expression, or cytokine expression. 
     
     
         12 . The composition of  claim 1 , wherein the target cell is a bacterial cell. 
     
     
         13 . The composition of  claim 12 , wherein the cell function is cell death. 
     
     
         14 . The composition of  claim 1 , wherein the target cell is a human cell. 
     
     
         15 . The composition of  claim 14 , wherein the human cell is a cancer cell. 
     
     
         16 . The composition of  claim 15 , wherein the cell function is cell death. 
     
     
         17 . The composition of  claim 16 , wherein the reporter of cell function is 7-AAD or Annexin V. 
     
     
         18 . The composition of  claim 17 , wherein the cell death is by apoptosis and the reporter of cell function is a fluorescent indicator of apoptosis. 
     
     
         19 . The composition of  claim 18 , wherein the fluorescent indicator of apoptosis is Annexin V or green fluorescent caspase 3/7 activity reporter dye. 
     
     
         20 . The composition of  claim 14 , wherein the human cell is an immune cell. 
     
     
         21 . The composition of  claim 20 , wherein the immune cell is a T cell, a B cell, a macrophage, a eosinophil, a NK cell or a dendritic cell. 
     
     
         22 . The composition of  claim 20 , wherein the cell function is cell proliferation, cell death, or gene expression. 
     
     
         23 . The composition of  claim 20 , wherein the cell function is cytokine expression.