Compositions, methods and uses for biosynthetic plasmid integrated capture elements

Abstract

Embodiments herein report compositions, systems and methods for making and using plasmid vectors and nanotube complexes. In certain embodiments, compositions, systems and methods herein include making plasmid vectors having aptamer inserts. In some embodiments, methods disclosed herein may be used to rapidly generate large quantities of plasmid vectors having aptamer inserts directed to a particular target agent. Other aspects concern plasmid constructs associated with organic semiconductors. Yet other aspects concern complexes of nanotubes associated with dsDNA aptamers and tracking molecules.

1 - 24 . (canceled) 
     
     
         25 . A plasmid complex composition comprising:
 a plasmid having one or more unselected aptamers inserted into the plasmid to make a random aptamer-plasmid complex, wherein the unselected aptamers are not yet selected to bind to a target; and   an organic semiconductor associated with the one or more plasmids, wherein the random aptamer-plasmid complex and the organic semiconductor forms random aptamer-plasmid-organic semiconductor complex.   
     
     
         26 . The composition of  claim 25 , further comprising the random aptamer-plasmid-organic semiconductor complex associated with nanoparticles or microbeads. 
     
     
         27 . The composition of  claim 26 , wherein the nanoparticles immobilize the random aptamer-plasmid-organic semiconductor complex. 
     
     
         28 . The composition of  claim 26 , wherein the nanoparticles or microbeads are selected from the group consisting of paramagnetic nanoparticles, quantum dots, nanostructures, colloidal gold, colloidal silver, iron nanoparticles, platinum nanoparticles, microspheres, or nanospheres. 
     
     
         29 . The composition of  claim 25 , wherein the organic semiconductor comprises DAT or DALM or other organic semiconductor. 
     
     
         30 . The composition of  claim 25 , wherein the target comprises a protein, peptide, polysaccharide, lipid, or nucleic acid. 
     
     
         31 . The composition of  claim 26 , wherein the random aptamer-plasmid-organic semiconductor complex is further immobilized on a solid substrate. 
     
     
         32 . The composition of  claim 25 , wherein the target comprises a virus, a yeast, a spore, a bacterium, a disorder-associated molecule, a disease-progression molecule, a disease marker or a combination thereof. 
     
     
         33 . A method for producing a plasmid complex directed to bind a target molecule comprising:
 inserting unselected aptamers into plasmids having one or more selectable markers to make a plasmid-random aptamer complex, wherein the unselected aptamers are not yet selected to bind a target;   introducing the plasmids to a host organism capable of producing organic semiconductors;   allowing the organic semiconductors to associate with the plasmids to form a plasmid-random aptamer-organic semiconductor complex;   obtaining one or more target molecules associated with nanoparticles to make target molecule-nanoparticle complexes;   introducing target molecule-nanoparticle complexes to the host organism having plasmid-random aptamer-organic semiconductor complex constructs or to extracted plasmid-random aptamer-organic semiconductor complex constructs;   isolating the plasmid-random aptamer-organic semiconductor complex constructs associated with the target molecule-nanoparticle complexes; and   separating specific plasmid-random aptamer-organic semiconductor complexes that bind to the target molecule to generate a selected aptamer plasmid organic semiconductor complex.   
     
     
         34 . The method of  claim 33 , further comprising:
 introducing the selected aptamer plasmid organic semiconductor complexes to a random aptamer-plasmid construct-free bacterial or mammalian culture to make selected aptamer-plasmid construct producing clones;   introducing the culture to a selection media wherein only the cultures taking up the selected aptamer-plasmid organic semiconductor complexes propogate, and cloning the selected aptamer-plasmid-organic semiconductor complexes.   
     
     
         35 . The method of  claim 34 , further comprising, growing the clones on media, wherein the media permits synthesis of organic semiconductors and wherein the organic semiconductor associates with the selected aptamer-plasmid-organic semiconductor complexes making an organic semiconductor selected aptamer-plasmid complex capable of associating with the target molecule. 
     
     
         36 . The method of  claim 33 , wherein target molecule comprises a protein, peptide, polysaccharide, lipid, or nucleic acid. 
     
     
         37 . The method of  claim 33 , further comprising immobilizing the organic semiconductor-specific aptamer-plasmid complex on a surface. 
     
     
         38 . A complex composition comprising:
 a dsDNA random aptamer associated with a fluorescent agent and a carbon nanotube to form a complex comprising a carbon nanotube-random dsDNA aptamer-fluorescent agent, wherein the dsDNA aptamer binds a target agent.   
     
     
         39 . The composition of  claim 38 , wherein the complex is associated with nanoparticles or microbeads. 
     
     
         40 . The composition of  claim 38 , wherein the nanoparticles immobilize the complex. 
     
     
         41 . The composition of  claim 38 , wherein the nanoparticles or microbeads are selected from the group consisting of paramagnetic nanoparticles, quantum dots, nanostructures, colloidal gold, colloidal silver, iron nanoparticles, platinum nanoparticles, microspheres, or nanospheres. 
     
     
         42 . The composition of  claim 38 , wherein the fluorescent agent comprises quantum dots or other fluorescent agent capable of being quenched by the carbon nanotube. 
     
     
         43 . The composition of  claim 38 , wherein the target agent comprises a protein, peptide, polysaccharide, lipid, or nucleic acid. 
     
     
         44 . The composition of  claim 38 , wherein the complex is further immobilized on a solid substrate. 
     
     
         45 . The composition of  claim 38 , wherein the carbon nanotube further comprises a cell compatible coating. 
     
     
         46 . The composition of  claim 45 , wherein the cell compatible coating comprises an organic semiconductor. 
     
     
         47 . A plasmid-complex composition comprising:
 a plasmid having one or more unselected aptamers inserted into the plasmid to make random aptamer-plasmid complexes, wherein the unselected aptamers are not yet selected to bind to a target; and   an organic semiconductor, DALM, associated with the one or more plasmids, wherein the random aptamer-plasmid complexes and DALM form random aptamer-plasmid-DALM complexes.   
     
     
         48 . The composition of  claim 47 , further comprising the random aptamer-plasmid-DALM complexes associated with nanoparticles. 
     
     
         49 . The composition of  claim 48 , wherein the nanoparticles immobilize the random aptamer-plasmid-organic semiconductor complexes. 
     
     
         50 . The composition of  claim 47 , wherein the nanoparticles comprise paramagnetic nanoparticles, iron nanoparticles, platinum nanoparticles or other paramagnetic nanoparticles. 
     
     
         51 . The composition of  claim 47 , wherein the random aptamer-plasmid-DALM complexes are selected to bind targets. 
     
     
         52 . The composition of  claim 47 , wherein the targets are one or more proteins or protein complexes. 
     
     
         53 . The composition of  claim 47 , wherein the random aptamer-plasmid-DALM complexes are further immobilized on a solid substrate. 
     
     
         54 . The composition of  claim 47 , wherein the targets comprise bacteria.