Bead Bound Combinatorial Oligonucleoside Phosphorothioate And Phosphorodithioate Aptamer Libraries

Abstract

The present invention includes composition and methods for making and using a combinatorial library having two or more beads, wherein attached to each bead is a unique nucleic acid aptamer that have disposed thereon a unique sequence. The library aptamers may be attached covalently to the one or more beads, which may be polystyrene beads. The aptamers may include phosphorothioate, phosphorodithioate and/or methylphosphonate linkages and may be single or double stranded DNA, RNA or even PNAs.

1 - 81 . (canceled) 
     
     
         82 . A method for isolation of a target comprising the steps of:
 dispersing one or more probe beads comprising an aptamer library in a thixotropic agent;   contacting the probe beads with a target;   scanning for probe beads that generate a detectable signal from interaction between the one or more probe beads and the target; and   picking one or more probe beads based on the detectable signal.   
     
     
         83 . The method of  claim 82 , wherein the aptamer is further defined as comprising one or more modification to the phosphate backbone. 
     
     
         84 . The method of  claim 82 , wherein the aptamer is further defined as comprising one or more thio-modifications. 
     
     
         85 . The method of  claim 82 , wherein the aptamer is further defined as comprising one or more modification dithio-modifications. 
     
     
         86 . The method of  claim 82 , wherein the aptamer is further defined as comprising one or more modification selected from a thioaptamers (S-ODN) or a dithioaptamers (S 2 -ODN), wherein the thioaptamers (S-ODN) or the dithioaptamers (S 2 —ODN) are selected from the group rATP(αS 2 ), rUTP(αS 2 ), rGTP(αS 2 ), rCTP(αS 2 ), rATP(αS), dTTP(αS), dGTP(αS), dCTP(αS), dATP(αS 2 ), dTTP(αS 2 ), dGTP(αS 2 ) and dCTP(αS 2 ). 
     
     
         87 . The method of  claim 82 , further comprising the step of identifying the target using mass spectrometry. 
     
     
         88 . The method of  claim 82 , wherein each of the probe beads are further modified to comprise a calorimetric agent. 
     
     
         89 . The method of claim  1 , wherein each of the probe beads further comprises one or more fluorophors attached to the 5′ end, the 3′ end or internally within the aptamers. 
     
     
         99 . The method of  claim 82 , wherein the target is labeled with an enzyme, a dye, a radioisotope, an electron dense particle, a magnetic particle, a fluorescent agent, an antibody, a magnetic particle or a chromophore. 
     
     
         100 . The method of  claim 82 , wherein the target is detectable with an enzyme, a radioisotope, an electron dense particle, a magnetic particle, a fluorescent agent, an antibody, a magnetic particle or a chromophore. 
     
     
         101 . The method of  claim 82 , wherein the probe bead is acquired by a scanning robotic head and the target is extracted from the probe bead in situ. 
     
     
         102 . The method of  claim 82 , wherein the probe bead is acquired by a scanning robotic head and the target is extracted from the probe bead in situ by proteolysis and transferred to the inlet of an LC-MS, LC-MS/MS, MALDI-MS, MALDI-TOF/MS or MALDI-MS analysis by SELDI ionization. 
     
     
         103 . The method of  claim 82 , wherein the probe bead is further processed to remove the target bound to the aptamer bead and analyzing the target by binding a second detectable label to the target. 
     
     
         104 . The method of  claim 82 , wherein the thixotrophic agent comprises a polyacrylamide gel. 
     
     
         105 . The method of  claim 82 , wherein picking the one or more probes beads is semi-manually. 
     
     
         106 . The method of  claim 82 , wherein the target is one or more proteins. 
     
     
         107 . The method of  claim 82 , wherein the one or more probe beads are dispersed within the thixotropic agent by molecular printing. 
     
     
         108 . The method of  claim 82 , wherein the one or more probe beads are dispersed within the thixotropic agent using an ink-jet printer.