Paper-based synthetic gene networks

Abstract

Disclosed herein are shelf-stable compositions based on synthetic gene networks and/or cell-free systems that are lyophilized on a solid support. The compositions can be easily transported and stored for a period of time, and activation can be done by simply adding water. Methods of use are also disclosed herein, including, but are not limited to, sensing and a variety of logic functions. The invention permits straightforward, sterile and abiotic distribution of synthetic biology-based technology to clinical settings, food processing and industry, the military and consumer products.

1 . A shelf-stable composition comprising a cell-free system comprising components sufficient for a template-directed synthetic reaction, wherein said cell-free system is lyophilized on a porous substrate and is substantially free of water, and wherein said cell-free system is active for said template-directed synthetic reaction upon re-hydration. 
     
     
         2 . The shelf-stable composition of  claim 1 , further comprising a synthetic gene network. 
     
     
         3 . The shelf-stable composition of  claim 2 , wherein said synthetic gene network comprises nucleic acids. 
     
     
         4 . (canceled) 
     
     
         5 . The shelf-stable composition of  claim 1 , wherein said template-directed synthetic reaction is a transcription reaction, a translation reaction or a coupled transcription and translation reaction. 
     
     
         6 .- 7 . (canceled) 
     
     
         8 . The shelf-stable composition of  claim 1 , wherein said components: (i) are sufficient for a transcription reaction, and comprise promoter-containing DNA, RNA polymerase, ribonucleotides, and a buffer system; (ii) are sufficient for a translation reaction, and comprise ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system; or (iii) are sufficient for a coupled transcription and translation reaction, and comprise promoter-containing DNA, RNA polymerase, ribonucleotides, ribosomes, aminoacyl transfer RNAs, translation factors, and a buffer system. 
     
     
         9 .- 10 . (canceled) 
     
     
         11 . The shelf-stable composition of  claim 1 , wherein said porous substrate comprises paper, quartz microfiber, mixed esters of cellulose, porous aluminum oxide, or a patterned surface. 
     
     
         12 . The shelf-stable composition of  claim 1 , wherein said porous substrate is pre-treated with bovine serum albumin, polyethylene glycol, Tween-20, Triton-X, milk powder, casein, fish gelatin, or a combination thereof. 
     
     
         13 . The shelf-stable composition of  claim 1 , wherein said cell-free system comprises a whole cell extract or a recombinant protein transcription/translation system. 
     
     
         14 .- 15 . (canceled) 
     
     
         16 . The shelf-stable composition of  claim 2 , wherein said synthetic gene network functions as a sensor. 
     
     
         17 . (canceled) 
     
     
         18 . The shelf-stable composition of  claim 16 , wherein said sensor can detect the presence of an analyte in an aqueous sample and detection of said analyte produces an optical or electronic signal. 
     
     
         19 . (canceled) 
     
     
         20 . The shelf-stable composition of  claim 2 , wherein said synthetic gene network comprises a logic circuit. 
     
     
         21 . The shelf-stable composition of  claim 20 , wherein said logic circuit comprises an AND gate, a NOT gate, an OR gate, a NOR gate, a NAND gate, a XOR gate, a XAND gate, or a combination thereof. 
     
     
         22 . The shelf-stable composition of  claim 20 , wherein said logic circuit is activated upon contacting said shelf-stable composition with water and a composition comprising a trigger. 
     
     
         23 . The shelf-stable composition of  claim 22 , wherein said trigger is selected from the group consisting of a chemical element, a small molecule, a peptide, a protein, a nucleic acid, an extract, and a combination thereof. 
     
     
         24 .- 48 . (canceled) 
     
     
         49 . A method of detecting an analyte, comprising:
 (i) providing a composition of  claim 1 , wherein said composition comprises a nucleic acid-based sensor;   (ii) contacting said composition with a sample to be tested for said analyte in the presence of water; and   (iii) detecting a signal, wherein detection of said signal indicates the presence of said analyte.   
     
     
         50 . The method of  claim 49 , further comprising a step of contacting said composition with a barrier to water evaporation or enclosing said composition in an enclosure after step (ii). 
     
     
         51 .- 52 . (canceled) 
     
     
         53 . The method of  claim 49 , wherein said nucleic acid-based sensor comprises a reporter gene or a catalytic nucleic acid. 
     
     
         54 .- 64 . (canceled) 
     
     
         65 . A kit comprising a shelf-stable composition of  claim 1  and packaging materials therefor. 
     
     
         66 . (canceled) 
     
     
         67 . A method of activating a synthetic gene network lyophilized on a porous substrate, comprising:
 (i) providing a shelf-stable composition of  claim 1 , wherein said composition comprises said synthetic gene network; and   (ii) contacting the composition with a solution comprising water.   
     
     
         68 .- 72 . (canceled) 
     
     
         73 . A method of stabilizing a synthetic gene network, comprising lyophilizing said synthetic gene network. 
     
     
         74 .- 81 . (canceled)