The authors greatly acknowledge the support of the Biotechnology and Biological Sciences Research Council awards BB/V017551/1 (S.K., T.P.H.) and BB/W01095X/1 (A.L., T.P.H.), and the Engineering and Physical Sciences Research Council - Defence Science and Technology Laboratories award EP/N026683/1 (C.J.W., A.M.B., T.P.H.). Data supporting this publication are openly available at: 10.25405/data.ncl.22232452. For the purpose of open access, the author has applied a Creative Commons Attribution (CC BY) license to any Author Accepted Manuscript version arising.

1. Cell lysate buffer and media preparation
<ol>
	<li>Preparation of 2x YT+P agar and medium
	<ol>
		<li>Prepare 2x YT+P agar by measuring out 16 g/L tryptone, 10 g/L yeast extract, 5 g/L NaCl, 40 mL/L 1 M K2HPO4, 22 mL/L 1 M KH2PO4, and 15 g/L agar. For the 2x YT+P broth, follow the previous composition but omit the agar.</li>
		<li>Sterilize by autoclaving the 2x YT+P.</li>
	</ol>
	</li>
	<li>Preparation of the S30A buffer
	<ol>
		<li>Prepare the S30A buffe...

Embedding CFPS Reactions in a Variety of Hydrogel Matrices

<ol>
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Outlined here are two protocols for the incorporation of E. coli cell lysate-based CFPS reactions into agarose hydrogels. These methods allow for simultaneous gene expression throughout the material. The protocol can be adapted for other CFPS systems and has been successfully conducted with commercially available CFPS kits in addition to the laboratory-prepared cell lysates detailed here. Importantly, the protocol allows for gene expression in the absence of an external liquid phase. This means that the system i...

Synthetic biology integrates diverse engineering disciplines to design and engineer biologically based parts, devices, and systems that can perform functions that are not found in nature. Most synthetic biology approaches are still bound to living cells. By contrast, cell-free synthetic biology systems facilitate unprecedented levels of control and freedom in design, enabling increased flexibility and a shortened time for engineering biological systems while eliminating many of the constraints of traditional cell-based gene expression methods1,2,3. CFPS is being used in an increasing number of applications across numerous disciplines, including constructing artificial cells, prototyping genetic circuits, developing biosensors, and producing metabolites4,5,6. CFPS has also been particularly useful for producing recombinant proteins that cannot be readily expressed in living cells, such as aggregation-prone proteins, transmembrane proteins, and toxic proteins6,7,8.
CFPS is typically performed in liquid reactions. This, however, may restrict their deployment in some situations, as any liquid cell-free device must be contained within a reaction vessel. The rationale for the development of the methods presented here was to provide robust protocols for embedding cell-free synthetic biology devices into hydrogels, not as a protein production platform per se but, instead, to allow the use of hydrogels as a physical chassis for the deployment of cell-free devices beyond the laboratory. The use of hydrogels as CFPS chassis has several advantages. Hydrogels are polymeric materials that, despite a high water content (sometimes in excess of 98%), possess solid properties9,10,11. They have uses as pastes, lubricants, and adhesives and are present in products as diverse as contact lenses, wound dressings, marine adhesive tapes, soil improvers, and baby diapers9,11,12,13,14. Hydrogels are also under active investigation as drug delivery vehicles9,15,16,17. Hydrogels may also be biocompatible, biodegradable, and possess some stimuli responses of their own9,18,19,20. Therefore, the goal here is to create a synergy between molecular biology-derived functionality and materials science. To this end, efforts have been made to integrate cell-free synthetic biology with a range of materials, including collagen, laponite, polyacrylamide, fibrin, PEG-peptide, and agarose11,21,22, as well as to coat surfaces of glass, paper, and cloth11,23,24 with CFPS devices. The protocols presented here demonstrate two methods for embedding CFPS reactions in macro-scale (i.e., &#62;1 mm) hydrogel matrices, using agarose as the exemplar material. Agarose was chosen due to its high water absorption capacity, controlled self-gelling properties, and tuneable mechanical properties11,24,25,26. Agarose also supports functional CFPS, is cheaper than many other hydrogel alternatives, and is biodegradable, making it an attractive choice as an experimental model system. These methods have, however, been previously demonstrated as appropriate for embedding CFPS in a range of alternative hydrogels11. Considering the wide range of applications of hydrogels and the functionality of CFPS, the methods demonstrated here can provide a basis from which researchers are able to develop biologically enhanced hydrogel materials suited to their own ends.
In previous studies, microgel systems with a size range of 1 &#181;m to 400 &#181;m have been used to perform CFPS in hydrogels submerged in reaction buffer23,27,28,29,30,31. The requirement to submerge hydrogels within CFPS reaction buffers, however, limits opportunities for their deployment as materials in their own right. The protocols presented here allow CFPS reactions to occur within hydrogels without the need to submerge the gels in reaction buffers. Second, the use of macroscale gels (between 2 mm and 10 mm in size) allows the study of the physical interaction between hydrogels and cell-free gene expression. For example, with this technique, it is possible to study how the hydrogel matrix affects CFPS reactions11 and how CFPS reactions can impact the hydrogel matrix31. Larger sizes of hydrogels also allow for the development of novel, bio-programmable materials32. Finally, by embedding CFPS reactions into hydrogels, there is also a potential reduction in the requirement for plastic reaction vessels. For the deployment of cell-free sensors, this has clear advantages over devices dependent on plasticware. Taken together, embedding CFPS reactions in hydrogels provides several advantages for the deployment of cell-free devices beyond the laboratory.
The overall goal of the methods presented here is to allow the operation of CFPS reactions within hydrogel matrices. Two different methods are demonstrated for embedding cell-free protein production reactions in macro-scale hydrogel materials (Figure 1). In Method A, CFPS components are introduced to lyophilized agarose hydrogels to form an active system. In Method B, molten agarose is mixed with CFPS reaction components to form a complete CFPS hydrogel system, which is then lyophilized and stored until needed. These systems can be rehydrated with a volume of water or buffer and analyte to commence the reaction.
This study uses Escherichia coli cell lysate-based systems. These are some of the most popular experimental CFPS systems, as E. coli cell lysate preparation is simple, inexpensive, and achieves high protein yields. The cell lysate is complemented with the macromolecular components needed to perform transcription and translation, including ribosomes, tRNAs, aminoacyl-tRNA synthetases, and initiation, elongation, and termination factors. Specifically, this paper demonstrates the production of eGFP and mCherry in agarose hydrogels using E. coli cell lysates and monitors the appearance of fluorescence using a plate reader and confocal microscopy. Representative results for the microtiter plate reader can be seen in Whitfield et al.31, and the underlying data are publicly available33. Further, the expression of fluorescent proteins throughout the gels is confirmed using confocal microscopy. The two protocols demonstrated in this paper allow for the assembly and storage of CFPS-based genetic devices in materia with the ultimate goal of creating a suitable physical environment for the distribution of cell-free gene circuitry in a manner supportive of field deployment.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Material</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>3-PGA</td>
			<td>Santa Cruz Biotechnology</td>
			<td>sc-214793B</td>
			<td></td>
		</tr>
		<tr>
			<td>Acetic Acid</td>
			<td>Sigma-Aldrich</td>
			<td>A6283</td>
			<td></td>
		</tr>
		<tr>
			<td>Agar</td>
			<td>Thermo Fisher Scientific</td>
			<td>A10752.22</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Severn Biotech</td>
			<td>30-15-50</td>
			<td></td>
		</tr>
		<tr>
			<td>Amino Acid Sampler Kit</td>
			<td>VWR</td>
			<td>BTRABR1401801</td>
			<td></td>
		</tr>
		<tr>
			<td>ATP</td>
			<td>Sigma-Aldrich</td>
			<td>A8937-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>cAMP</td>
			<td>Sigma-Aldrich</td>
			<td>A9501-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>Coenzyme A (CoA)</td>
			<td>Sigma-Aldrich</td>
			<td>C4282-100MG</td>
			<td></td>
		</tr>
		<tr>
			<td>CTP</td>
			<td>Alfa Aesar</td>
			<td>J14121.MC</td>
			<td></td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Thermo Fisher Scientific</td>
			<td>R0862</td>
			<td></td>
		</tr>
		<tr>
			<td>Folinic Acid</td>
			<td>Sigma-Aldrich</td>
			<td>F7878-100MG</td>
			<td></td>
		</tr>
		<tr>
			<td>GTP</td>
			<td>Carbosynth</td>
			<td>NG01208</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma-Aldrich</td>
			<td>H4034-25G</td>
			<td></td>
		</tr>
		<tr>
			<td>K-glutamate</td>
			<td>Sigma-Aldrich</td>
			<td>G1149-100G</td>
			<td></td>
		</tr>
		<tr>
			<td>Lysozyme</td>
			<td>Sigma-Aldrich</td>
			<td>L6876-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>Mg-glutamate</td>
			<td>Sigma-Aldrich</td>
			<td>49605-250G</td>
			<td></td>
		</tr>
		<tr>
			<td>NAD</td>
			<td>Sigma-Aldrich</td>
			<td>N6522-250MG</td>
			<td></td>
		</tr>
		<tr>
			<td>PEG-8000</td>
			<td>Promega</td>
			<td>V3011</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Hydroxide (KOH)</td>
			<td>Sigma-Aldrich</td>
			<td>757551-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Phosphate Dibasic (K2HPO4)</td>
			<td>Sigma-Aldrich</td>
			<td>P3786-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Phosphate Monobasic (KH2PO4)</td>
			<td>Sigma-Aldrich</td>
			<td>RDD037-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Protease Inhibitor cocktail</td>
			<td>Sigma-Aldrich</td>
			<td>P2714-1BTL</td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit Protein concentration kit</td>
			<td>Thermo Fisher Scientific</td>
			<td>A50668</td>
			<td></td>
		</tr>
		<tr>
			<td>Rossetta 2 DE 3 E.coli</td>
			<td>Sigma-Aldrich</td>
			<td>71397-3</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium Chloride (NaCl)</td>
			<td>Sigma-Aldrich</td>
			<td>S9888-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Spermidine</td>
			<td>Sigma-Aldrich</td>
			<td>85558-1G</td>
			<td></td>
		</tr>
		<tr>
			<td>Tryptone</td>
			<td>Thermo Fisher Scientific</td>
			<td>211705</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris</td>
			<td>Sigma-Aldrich</td>
			<td>GE17-1321-01</td>
			<td></td>
		</tr>
		<tr>
			<td>tRNA</td>
			<td>Sigma-Aldrich</td>
			<td>10109541001</td>
			<td></td>
		</tr>
		<tr>
			<td>UTP</td>
			<td>Alfa Aesar</td>
			<td>J23160.MC</td>
			<td></td>
		</tr>
		<tr>
			<td>Yeast Extract</td>
			<td>Sigma-Aldrich</td>
			<td>Y1625-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>Equipment</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>1.5 mL microcentrifuge tubes</td>
			<td>Sigma-Aldrich</td>
			<td>HS4323-500EA</td>
			<td></td>
		</tr>
		<tr>
			<td>10K MWCO dialysis cassettes</td>
			<td>Thermo Fisher Scientific</td>
			<td>66381</td>
			<td></td>
		</tr>
		<tr>
			<td>15 mL centrifuge tube</td>
			<td>Sarstedt</td>
			<td>62.554.502</td>
			<td></td>
		</tr>
		<tr>
			<td>50 mL centrifuge bottles</td>
			<td>Sarstedt</td>
			<td>62.547.254</td>
			<td></td>
		</tr>
		<tr>
			<td>500 mL centrifuge bottles</td>
			<td>Thermo Fisher Scientific</td>
			<td>3120-9500</td>
			<td></td>
		</tr>
		<tr>
			<td>Alpha 1-2 LD Plus freeze-dryer</td>
			<td>Christ</td>
			<td>part no. 101521, 101522, 101527</td>
			<td></td>
		</tr>
		<tr>
			<td>Benchtop Centrifuge</td>
			<td>Thermo Fisher Scientific</td>
			<td>H-X3R</td>
			<td></td>
		</tr>
		<tr>
			<td>Black 384 well microtitre plates</td>
			<td>Fischer Scientific</td>
			<td>66</td>
			<td></td>
		</tr>
		<tr>
			<td>Cuvettes</td>
			<td>Thermo Fisher Scientific</td>
			<td>222S</td>
			<td></td>
		</tr>
		<tr>
			<td>Elga Purelab Chorus</td>
			<td>Elga</td>
			<td>#####</td>
			<td></td>
		</tr>
		<tr>
			<td>Eppendorf Microcentrifuge 5425R</td>
			<td>Eppendorf</td>
			<td>EP00532</td>
			<td></td>
		</tr>
		<tr>
			<td>High Speed Centrifuge</td>
			<td>Beckman Coulter</td>
			<td>B34183</td>
			<td></td>
		</tr>
		<tr>
			<td>JMP license</td>
			<td>SAS Institute</td>
			<td>15</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnetic Stirrer</td>
			<td>Fischer Scientific</td>
			<td>15353518</td>
			<td></td>
		</tr>
		<tr>
			<td>Parafilm</td>
			<td>Amcor</td>
			<td>PM-966</td>
			<td></td>
		</tr>
		<tr>
			<td>Photospectrometer (Biophotometer)</td>
			<td>Eppendorf</td>
			<td>16713</td>
			<td></td>
		</tr>
		<tr>
			<td>Pipettes and tips</td>
			<td>Gilson</td>
			<td>#####</td>
			<td></td>
		</tr>
		<tr>
			<td>Precision Balance</td>
			<td>Sartorius</td>
			<td>16384738</td>
			<td></td>
		</tr>
		<tr>
			<td>Qubit 2.0 Fluorometer</td>
			<td>Thermo Fisher Scientific</td>
			<td>Q32866</td>
			<td></td>
		</tr>
		<tr>
			<td>Shaking Incubator</td>
			<td>Thermo Fisher Scientific</td>
			<td>SHKE8000</td>
			<td></td>
		</tr>
		<tr>
			<td>Sonic Dismembrator (Sonicator)</td>
			<td>Thermo Fisher Scientific</td>
			<td>12893543</td>
			<td></td>
		</tr>
		<tr>
			<td>Static Incubator</td>
			<td>Sanyo</td>
			<td>MIR-162</td>
			<td></td>
		</tr>
		<tr>
			<td>Syringe and needles</td>
			<td>Thermo Fisher Scientific</td>
			<td>66490</td>
			<td></td>
		</tr>
		<tr>
			<td>Thermo max Q8000 (Shaking Incubator)</td>
			<td>Thermo Fisher Scientific</td>
			<td>SHKE8000</td>
			<td></td>
		</tr>
		<tr>
			<td>Varioskan Lux platereader</td>
			<td>Thermo Fisher Scientific</td>
			<td>VLBL00GD1</td>
			<td></td>
		</tr>
		<tr>
			<td>Vortex Genie 2</td>
			<td>Cole-parmer</td>
			<td>OU-04724-05</td>
			<td></td>
		</tr>
		<tr>
			<td>VWR PHenomenal pH 1100 L, ph/mv/&#176;c meter</td>
			<td>VWR</td>
			<td>662-1657</td>
			<td></td>
		</tr>
	</tbody>
</table>

methods for embedding cell-free protein synthesis reactions in macro-scale hydrogels

Synthetic gene networks provide a platform for scientists and engineers to design and build novel systems with functionality encoded at a genetic level. While the dominant paradigm for the deployment of gene networks is within a cellular chassis, synthetic gene networks may also be deployed in cell-free environments. Promising applications of cell-free gene networks include biosensors, as these devices have been demonstrated against biotic (Ebola, Zika, and SARS-CoV-2 viruses) and abiotic (heavy metals, sulfides, pesticides, and other organic contaminants) targets. Cell-free systems are typically deployed in liquid form within a reaction vessel. Being able to embed such reactions in a physical matrix, however, may facilitate their broader application in a wider set of environments. To this end, methods for embedding cell-free protein synthesis (CFPS) reactions in a variety of hydrogel matrices have been developed. One of the key properties of hydrogels conducive to this work is the high-water reconstitution capacity of hydrogel materials. Additionally, hydrogels possess physical and chemical characteristics that are functionally beneficial. Hydrogels can be freeze-dried for storage and rehydrated for use later. Two step-by-step protocols for the inclusion and assay of CFPS reactions in hydrogels are presented. First, a CFPS system can be incorporated into a hydrogel via rehydration with a cell lysate. The system within the hydrogel can then be induced or expressed constitutively for complete protein expression through the hydrogel. Second, cell lysate can be introduced to a hydrogel at the point of polymerization, and the entire system can be freeze-dried and rehydrated at a later point with an aqueous solution containing the inducer for the expression system encoded within the hydrogel. These methods have the potential to allow for cell-free gene networks that confer sensory capabilities to hydrogel materials, with the potential for deployment beyond the laboratory.

Author Spotlight: A Novel Approach for Embedding Cell-Free Protein Synthesis Reactions in Hydrogels 

Methods for Embedding Cell-Free Protein Synthesis Reactions in Macro-Scale Hydrogels

We know living systems continuously integrate information from many different sources and that these signals trigger complex and subtle responses. Much of this information processing occurs at the molecular level. We're interested in operating these processes within materials, but without cells.The purpose is to give materials novel functionality. Challenges in this work are primarily associated with the cell-free protein synthesis reaction, rather than working with hydrogel. Cell reaction require high quality cell lysate as well as high quality and purity DNA to function well.This protocol allows researchers to embed molecular biology reactions into a physical biodegradable material that can be taken outside of the laboratory. Also, because the reaction output interacts directly with the material chassis, there is potential for the development of materials with novel sensing and response capabilities. In short-term, we see these methods as providing a novel route to the deployment of cell-free diagnostic devices.This protocol allows a number of devices to be created and spatially organized in a manner that is not possible for liquid reactions. Our future interests are twofold. First, we are interested in expanding the nature of the hydrogels we use to bring more material functionality to the work.Second, we are interested in increasing the complexity and performance of the gene networks we operate in gels, expanding the biological functionality of these systems.

This protocol details two methods for embedding CFPS reactions into hydrogel matrices, with Figure 1 presenting a schematic overview of the two approaches. Both methods are amenable to freeze-drying and long-term storage. Method A is the most utilized methodology for two reasons. First, it has been shown to be the most applicable method for working with a range of hydrogel materials11.&#160;Second, Method A allows for the parallel testing of genetic constructs. Method...

Watch this Scientific Journal Video about A Novel Approach for Embedding Cell-Free Protein Synthesis Reactions in Hydrogels at JoVE.com

Here, we present two protocols for embedding cell-free protein synthesis reactions in macro-scale hydrogel matrices without the need for an external liquid phase.

Synthetic gene networks provide a platform for scientists and engineers to design and build novel systems with functionality encoded at a genetic level. ...

methods-for-embedding-cell-free-protein-synthesis-reactions-macro

Research

JoVE Journal

Biology

Cell-Free Protein Synthesis in Rehydrated Lyophilized Hydrogels

To begin, transfer the hydrogels to 1.5 milliliter micro centrifuge tubes, trimming the gels with a scalpel if necessary to make them fit in the wells. In another 1.5 milliliter micro centrifuge tube, combine 10 microliters of the cell-free extract with 25 microliters of two x cell-free protein synthesis buffer and four micrograms of plasmid DNA. Make up to a total volume of 50 microliters with double distilled water to prepare the cell-free protein synthesis solution.Pipette the solution onto the freeze dried hydrogels, and allow the gels to soak in the cell-free protein synthesis system for five to 10 minutes at room temperature. Transfer the gels to a black 384 well microtiter plate using a spatula. Then, transfer the microtiter plate to a plate reader, and use the plate reader settings shown on the screen for fluorescence detection and analysis.

Cell-Free Protein Synthesis in Deployable Hydrogels

In a 1.5 milliliter microcentrifuge tube on ice, combine 10 microliters of the cell-free extract with four micrograms of plasmid DNA and 25 microliters of 2X cell-free protein synthesis buffer. Make up to a total volume of 50 microliters with double-distilled water to prepare the cell-free protein synthesis solution. Weigh 0.75 grams of agarose and add it to 100 milliliters of double-distilled water buffer to prepare 0.75%agarose.Microwave the 0.75%agarose in 30-second bursts at high power and pipette 50 microliters of the molten agarose into 1.5-milliliter microcentrifuge tubes or into molds of a desired shape. Place the molten agarose on a heat block set to 50 degrees Celsius and allow the agarose to cool but not polymerize. Then, mix the molten agarose with the cell-free protein synthesis solution by pipetting and stirring with the pipette tip.Allow the gels to cool to room temperature and polymerize for approximately two minutes. Transfer the polymerized agarose to 1.5-milliliter microcentrifuge tubes with a spatula and flash freeze in liquid nitrogen. Place the flash-frozen hydrogels into minus 80 degrees Celsius storage for one hour.After that, remove the microcentrifuge tube lids. Cover the tubes with a wax film and pierce the film to allow the moisture to be dried off. Set the temperature of the freeze dryer to minus 20 degrees Celsius and pressure to 0.1 millibars and freeze-dry the cell-free protein synthesis devices for 18 hours or overnight.Rehydrate the freeze-dried devices for 30 minutes with 50 microliters of double-distilled water without excess liquid, and transfer the gels to a black 384-well microtiter plate using a spatula. Finally, place the microtiter plate on a plate reader and use the plate reader settings shown on the screen for fluorescence detection and analysis. The cell-free protein synthesis of eGFP and mCherry in a hydrogel using E.coli cell lysates is shown in this figure.0.75%agarose gels were prepared without DNA template with four micrograms of either eGFP or mCherry template or with four micrograms of both eGFP and mCherry template. An overlay of the two channels is also shown, and the overlay includes the differential interference contrast image. The results confirmed the co-expression of both mCherry and eGFP in agarose.

819 Views.  Newcastle University.  Here, we present two protocols for embedding cell-free protein synthesis reactions in macro-scale hydrogel matrices without the need for an external liquid phase.

Embedding CFPS Reactions in a Variety of Hydrogel Matrices

Summary