Nucleic acid aptamers

Abstract

Disclosed herein are compositions including an aptamer bound to a complex, wherein the complex comprises at least two polypeptides. Also disclosed are methods of quantifying a fraction of PD1 occupied by PDL1 or a fraction of PDL1 occupied by PD1 in a sample, and methods of isolating complexes using aptamers that are capable of binding to the complex.

What is claimed is: 
     
         1 . A composition comprising an aptamer bound to a complex, wherein the complex comprises at least two polypeptides. 
     
     
         2 . The composition according to  claim 1 , wherein the at least two peptides are selected from the group consisting of PD1 and PDL1, IL1bR and IL1b, IL3R and IL3, IL4R and IL4, IL5R and IL5, IL6R and IL6, IL7R and IL7, IL8R and IL8, IL9R and IL9, IL10R and IL10, IL11R and IL11, IL12R and IL12, IL13R and IL13, IL14R and IL14, IL15R and IL15, IL16R and IL16, IL17R and IL17, IL18R and IL18, IL19R and IL19, IL20R and IL20, IL21R and IL21, IL22R and IL22, IL23R and IL23, IL24R and IL24, IL25R and IL25, IL26R and IL26, IL27R and IL27, IL28R and IL28, IL29R and IL29, IL3OR and IL30, IL31R and IL31, IL32R and IL32, IL33R and IL33, IL34R and IL34, IL35R and IL35, CSFR and CSF, TNFR and TNF, EGFR and EGF, FGFR and FGF, PDGFR and PDGF, TGF-b RI/II and TGF-b, CD137 and CD137L, CD40 and CD4OL, and PD1 and PDL2. 
     
     
         3 . The composition according to  claim 1 , wherein the at least two peptides are PD1 and PDL 1. 
     
     
         4 . The composition according to  claim 1 , wherein the aptamer specifically binds to the complex. 
     
     
         5 . The composition according to  claim 1 , wherein the aptamer bound to the complex additionally comprises a tag. 
     
     
         6 . The composition according to  claim 5 , wherein the tag is selected from a molecule that can be detected using optical sensors, molecular size sensors, or isotopic sensors. The composition according to  claim 1 , wherein the aptamer is additionally bound to a substrate. 
     
     
         8 . The composition according to  claim 1 , wherein the aptamer is operably linked to a therapeutic moiety. 
     
     
         9 . The composition according to  claim 8 , wherein the therapeutic moiety is selected from nucleic acid-based therapeutics, chemotherapeutics, immunotherapeutics, and small molecule therapeutics. 
     
     
         10 . A cell comprising the aptamer bound to the complex according to  claim 1 . 
     
     
         11 . A method of quantifying a fraction of PD1 occupied by PDL1 or a fraction of PDL1 occupied by PD1 in a sample, the method comprising:
 contacting the sample with a first aptamer that specifically binds to a PD1-PDL1 complex,   contacting the sample with a second aptamer that specifically binds to the unoccupied PDL1, and   determining the amount of bound first aptamer and second aptamer.   
     
     
         12 . The method according to  claim 11 , wherein the contacting of the sample with the first aptamer and the second aptamer is done simultaneously. 
     
     
         13 . The method according to  claim 11 , wherein the first aptamer and the second aptamer additionally comprise tags. 
     
     
         14 . The method according to  claim 13 , wherein the tag on the first aptamer is distinct from the tag on the second aptamer. 
     
     
         15 . A method of isolating the cell according to  claim 10 , comprising:
 providing a sample comprising the cell,   contacting the cell with a substrate that binds to the aptamer; and   separating the cell bound to the substrate from the sample.   
     
     
         16 . A method of isolating a complex, comprising:
 providing an aptamer, wherein the aptamer is capable of binding to a complex comprising at least a first polypeptide and a second polypeptide, wherein the first polypeptide is PD1 and the second polypeptide is PDL1,   contacting the aptamer with a sample comprising the at least first polypeptide and second polypeptide to forma a bound complex; and   isolating the bound complex from the sample.   
     
     
         17 . The method according to  claim 16 , wherein the aptamer is attached to a substrate. 
     
     
         18 . The method according to  claim 16 , wherein the at least first polypeptide and second polypeptide are located on the surface of a cell and the cell is isolated from the sample. 
     
     
         19 . The method according to  claim 18 , wherein the at least two polypeptides comprise a receptor and a ligand. 
     
     
         20 . A method of treating a disease in a mammal, comprising contacting the mammal with the composition according to  claim 8 . 
     
     
         21 . A pair of aptamers comprising:
 (a) a first aptamer that specifically binds to a complex, wherein the complex comprises at least two members, wherein each member is a polypeptide, and   (b) a second aptamer that specifically binds to at least one unbound member of the complex.   
     
     
         22 . The pair of aptamers according to  claim 30 , wherein the first aptamer comprises a first tag. 
     
     
         23 . The pair of aptamers according to  claim 31 , wherein the first tag is selected from a molecule that can be detected using optical sensors, molecular size sensors, or isotopic sensors. 
     
     
         24 . The pair of aptamers according to  claim 30 , wherein the second aptamer comprises a second tag. 
     
     
         25 . The pair of aptamers according to  claim 33 , wherein the second tag is selected from a molecule that can be detected using optical sensors, molecular size sensors, or isotopic sensors. 
     
     
         26 . The pair of aptamers according to  claim 30 , wherein the first aptamer comprises a first tag, and wherein the second aptamer comprises a second tag. 
     
     
         27 . The pair of aptamers according to  claim 35 , wherein the first tag is distinct from the second tag. 
     
     
         28 . A method of treating a disease in a mammal, wherein the disease is associated with an increased amount of bound members of a complex, as compared to unbound members of the complex in a sample from the mammal, the method comprising
 (a) contacting the sample with the pair of aptamers of  claim 21  to quantify an amount of the first aptamer that is bound to the complex and an amount of the second aptamer that is bound to unbound member of the complex to determine the amount of complexes in the sample as compared to the amount of unbound members of the complex to determine a relative amount of bound and unbound members of a complex, and   (b) administering an appropriate therapeutic agent to ameliorate the disease.   
     
     
         29 . The method according to  claim 28 , wherein the first aptamer specifically binds to the complex. 
     
     
         30 . The method according to  claim 28 , wherein the aptamer bound to the complex comprises a first tag. 
     
     
         31 . The method according to  claim 30 , wherein the first tag is selected from a molecule that can be detected using optical sensors, molecular size sensors, or isotopic sensors. 
     
     
         32 . The method according to  claim 28 , wherein the second aptamer specifically binds to at least one unbound member of the complex. 
     
     
         33 . The method according to  claim 32 , wherein the aptamer bound to at least one unbound member of the complex comprises a second tag. 
     
     
         34 . The method according to  claim 33 , wherein the second tag is selected from a molecule that can be detected using optical sensors, molecular size sensors, or isotopic sensors. 
     
     
         35 . The method according to  claim 28 , wherein the first aptamer specifically binds to the complex and comprises a first tag, and wherein the second aptamer specifically binds to the at least one unbound member of the complex and comprises a second tag. 
     
     
         36 . The method according to  claim 35 , wherein the first tag is distinct from the second tag. 
     
     
         37 . A method of treating a disease in a mammal,
 wherein the disease is associated with an increased amount of bound members of a complex, as compared to unbound members of the complex in a sample from the mammal,   wherein the complex comprises at least a first polypeptide and a second polypeptide, the method comprising:
 (a) quantifying an amount of a first aptamer that is bound to the complex and a second aptamer that is bound to unbound member of the complex to determine the amount of complexes in a sample as compared to the amount of unbound members of the complex to determine a relative amount of bound and unbound members of a complex, and 
 (b) administering an appropriate therapeutic agent to ameliorate the disease.