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 - 61 . (canceled) 
     
     
         62 . A system for target identification comprising:
 a two-dimensional matrix for separation of two or more probe beads bound to a target;   a scanner that images a signal from the two or more probe beads bound to a target; and   a spot-picker that picks one or more probe beads bound to a target.   
     
     
         63 . The system of  claim 62 , wherein the spot-picker transfers one or more probe beads bound to a target to a chamber for further chemical manipulation. 
     
     
         64 . The system of  claim 62 , wherein the spot-picker transfers one or more probe beads bound to a target to a chamber for probe sequencing. 
     
     
         65 . The system of  claim 62 , wherein the spot-picker transfers one or more probe beads bound to a target to a chamber for target identification. 
     
     
         66 . The system of  claim 62 , wherein the spot-picker comprises a robotic spot picker. 
     
     
         67 . The system of  claim 62 , wherein the two-dimensional matrix comprises a gel, a polymer, a thixotropic agent, a glass or a silicon matrix. 
     
     
         68 . The system of  claim 62 , wherein the spot-picker transfers one or more probe beads bound targets to a probe bead-target separator; and
 a conduit to transfer separated targets into a liquid chromatograph.   
     
     
         69 . The system of  claim 62 , wherein the spot-picker transfers one or more probe beads bound targets to a bead-target separator; and
 one or more conduits connected to the bead-target separator to transfer separated targets to a liquid chromatograph and a mass spectrometer.   
     
     
         70 . The system of  claim 62 , wherein the spot-picker transfers one or more probe beads bound targets to a probe bead-target separator; and
 one or more conduits connected to the probe bead-target separator to transfer separated targets to a liquid chromatograph and a mass spectrometer, therein the mass spectrometer comprising a MALDI-MS.   
     
     
         71 . The system of  claim 62 , wherein the probe beads comprise an aptamer are defined further as comprising a thioaptamer and wherein one or more but less than all of the linkages comprising one or more of the following: rATP(αS), rUTP(αS), rGTP(αS), rCTP(αS), 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 ). 
     
     
         72 . The system of  claim 62 , wherein the probe bead is acquired by a scanning robotic head and the target is extracted from the probe bead in situ. 
     
     
         73 . The system of  claim 62 , 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 or an LC-MS/MS. 
     
     
         74 . The system of  claim 62 , wherein the probe bead is acquired by a scanning robotic head and the target is extracted from the probe bead in situ for MALDI-MS analysis, wherein the MALDI-MS analysis is selected from the group consisting of MALDI-TOF/MS, MALDI-TOF/TOF-MS and MALDI-Q-TOF-MS. 
     
     
         75 . The system of  claim 62 , wherein the probe bead is acquired by a scanning robotic head and the target is extracted from the probe bead in situ for LC-MS analysis. 
     
     
         76 . The system of  claim 62 , wherein the probe bead is acquired by a scanning robotic head and the target is extracted from the probe bead in situ for MALDI-MS analysis. 
     
     
         77 . The system of  claim 62 , wherein the probe bead is acquired by a scanning robotic head and the target is extracted from the probe bead in situ for MALDI-MS analysis by SELDI ionization. 
     
     
         78 . The system of  claim 62 , wherein the probe bead is further processed to remove the target bound to the aptamer bead and analyzing the target by MS, MS/MS, MALDI-TOF, MALDI-TOF-MS, direct sequencing. 
     
     
         79 . The system of  claim 62 , wherein the MALDI ionization step is a SELDI ionization. 
     
     
         80 . The system of  claim 62 , wherein a probe on the probe bead comprise an isolated and purified aptamer, a thioaptamer, a DNA, a RNA, a PNA, a peptide, an antibody, a cell, a cell fragment, a carbohydrate, a lipid and mixtures or combinations thereof. 
     
     
         81 . A system for aptamer selection comprising:
 a two-dimensional matrix for separation of two or more aptamer beads bound to a target;   a scanner that images a signal from the two or more aptamer beads bound to a target; and   a spot-picker that picks one or more aptamer beads bound to a target.