ACB and JLF acknowledge funding support by the ANR SINAPUV grant (ANR-17-CE07-0046). JLF and JB acknowledge funding support by the ANR SynBioDiag grant (ANR-18-CE33-0015). MSA and JLF acknowledge funding support by the ANR iCFree grant (ANR-20-BiopNSE). JB acknowledges support from the ERC starting &#34;COMPUCELL&#34; (grant number 657579). The Centre de Biochimie Structurale acknowledges support from&#160;the French Infrastructure for Integrated Structural Biology (FRISBI) (ANR-10-INSB-05-01). MK acknowledges funding support from INRAe&#39;s MICA department, Universit&#233; Paris-Saclay, Ile-de-France (IdF) region&#39;s DIM-RFSI, and ANR DREAMY (ANR-21-CE48-003). This work was supported by funding through the European Research Council Consolidator Award (865973 to CLB).

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Effects of gap length and the presence of cell-free extracts.</a> European Journal of Biochemistry. 105 (1), 109-116 (1980).</li><li>Sitaraman, K., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+novel+cell-free+protein+synthesis+system.">A novel cell-free protein synthesis system.</a> Journal of Biotechnology. 110 (3), 257-263 (2004).</li><li>Marshall, R., Maxwell, C. S., Collins, S. P., Beisel, C. L., Noireaux, V. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Short+DNA+containing+&#967;+sites+enhances+DNA+stability+and+gene+expression+in+E.+coli+cell-free+transcription-translation+systems.">Short DNA containing &#967; sites enhances DNA stability and gene expression in E. coli cell-free transcription-translation systems.</a> Biotechnology and Bioengineering. 114 (9), 2137-2141 (2017).</li><li>Yim, S. S., Johns, N. I., Noireaux, V., Wang, H. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protecting+linear+DNA+templates+in+cell-free+expression+systems+from+diverse+bacteria.">Protecting linear DNA templates in cell-free expression systems from diverse bacteria.</a> ACS Synthetic Biology. 9 (10), 2851-2855 (2020).</li><li>Norouzi, M., Panfilov, S., Pardee, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=High-efficiency+protection+of+linear+DNA+in+cell-free+extracts+from+Escherichia+coli+and+Vibrio+natriegens.">High-efficiency protection of linear DNA in cell-free extracts from Escherichia coli and Vibrio natriegens.</a> ACS Synthetic Biology. 10 (7), 1615-1624 (2021).</li><li>Zhu, B., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Increasing+cell-free+gene+expression+yields+from+linear+templates+in+Escherichia+coli+and+Vibrio+natriegens+extracts+by+using+DNA-binding+proteins.">Increasing cell-free gene expression yields from linear templates in Escherichia coli and Vibrio natriegens extracts by using DNA-binding proteins.</a> Biotechnology and Bioengineering. 117 (12), 3849-3857 (2020).</li><li>Batista, A. 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Here, we show that cell lysate prepared from E. coli BL21 Rosetta2 with a genomic knockout for either recB or recBCD operon supports high protein expression from linear DNA templates. This protocol elaborates a step-by-step lysate calibration procedure specific for linear DNA templates (Figure 2), which is a critical step that leads to the high expression from &#963;70 promoters in linear DNA, reaching near-plasmid levels for equimolar DNA concentrations. This prot...

Cell-free protein synthesis (CFPS) systems are increasingly being used as a fast, simple, and efficient method for biosensor engineering, decentralized manufacturing, and prototyping of genetic circuits1. Due to their great potential, CFPS systems are used regularly in the field of synthetic biology. However, so far CFPS systems rely on circular plasmids that can limit the technology from reaching its full potential. Preparing plasmid DNA depends on many time-consuming steps during&#160;cloning and&#160;large amounts of DNA isolation. On the other hand, PCR amplification from a plasmid, or a synthesized DNA template, can be used to simply prepare CFPS templates within a few hours2,3. Therefore, application of linear DNA offers a promising solution for CFPS. However, linear DNA is rapidly degraded by exonucleases naturally present in cellular extracts4. There are solutions that address this problem, such as using the &#955;-phage GamS protein5 or DNA containing Chi sites6 as protective agents, or directly protecting the linear DNA by chemical modification of its ends2,7,8,9. All these methods require supplementations to the cell extract, which are costly and time-consuming. It has been known for a long time that the exonuclease V complex (RecBCD) degrades linear DNA in cell lysates4. Recently, we showed that linear DNA can be much better protected in lysates from cells knocked out for exonuclease genes (recBCD)10.
In this protocol, steps for the preparation of cell-free lysates from the E. coli BL21 Rosetta2 &#916;recBCD strain by sonication lysis are described in detail. Sonication lysis is a common and affordable technique employed by several labs11,12. The extracts produced from this strain do not need the addition of any extra component or DNA template modification to support expression from linear DNA templates. The method relies on the essential step of buffer optimization for cell extracts specifically for linear DNA expression from native E. coli promoters. It has been shown that this specific buffer optimization for linear DNA expression is the key for native &#963;70 promoters to yield high protein production without GamS protein or Chi DNA supplementation, even avoiding purification of the PCR products10. The optimal concentration of Mg-glu for linear DNA expression was found to be similar to that for plasmid DNA. However, the optimal concentration of K-glu showed a substantial difference between linear and plasmid DNA, likely due to a transcription-related mechanism10. The functionality of proteins expressed using this method has been demonstrated for several applications, such as rapid screening of toehold switches and activity assessment of enzyme variants10.
This protocol provides a simple, efficient, and cost-effective solution for using linear DNA templates in E. coli cell-free systems by simply using mutant &#916;recBCD cell extracts and specific calibration for linear DNA as template.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr >
			<td >2-YT Broth</td>
			<td >Invitrogen</td>
			<td >22712020</td>
			<td ></td>
		</tr>
		<tr >
			<td >1.5 mL Safe-Lock tubes</td>
			<td>Eppendorf</td>
			<td>30120086</td>
			<td>1.5 mL microtube</td>
		</tr>
		<tr >
			<td >384-well square-bottom microplate</td>
			<td>Thermo Scientific Nunc</td>
			<td>142761</td>
			<td ></td>
		</tr>
		<tr >
			<td >3PGA (D-(-)-3-Phosphoglyceric acid disodium)</td>
			<td>Sigma-Aldrich</td>
			<td>P8877</td>
			<td></td>
		</tr>
		<tr >
			<td >adhesive plate seal</td>
			<td>Thermo Scientific Nunc</td>
			<td>232701</td>
			<td ></td>
		</tr>
		<tr >
			<td >Agar</td>
			<td>Invitrogen</td>
			<td>30391023</td>
			<td></td>
		</tr>
		<tr >
			<td >ATP (Adenosine 5&#39;-triphosphate disodium salt hydrate)</td>
			<td>Sigma-Aldrich</td>
			<td>A8937</td>
			<td></td>
		</tr>
		<tr >
			<td >BL21 Rosetta2</td>
			<td>Merck Millipore</td>
			<td>71402</td>
			<td></td>
		</tr>
		<tr >
			<td >BL21 Rosetta2 &#916;recB</td>
			<td>Addgene</td>
			<td>176582</td>
			<td></td>
		</tr>
		<tr >
			<td >BL21 Rosetta2 &#916;recBCD</td>
			<td>Addgene</td>
			<td>176583</td>
			<td></td>
		</tr>
		<tr >
			<td >cAMP (Adenosine 3&#39; 5&#39;-cyclic monophosphate)</td>
			<td>Sigma-Aldrich&#160;</td>
			<td>A9501</td>
			<td></td>
		</tr>
		<tr >
			<td >Chloramphenicol&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>C0378</td>
			<td></td>
		</tr>
		<tr >
			<td >CoA (Coenzyme A hydrate)</td>
			<td>Sigma-Aldrich</td>
			<td>C4282</td>
			<td></td>
		</tr>
		<tr >
			<td >Corning 15 mL PP Centrifuge Tubes, Rack Packed with CentriStar Cap, Sterile</td>
			<td>Corning</td>
			<td>430790</td>
			<td>15 mL tube</td>
		</tr>
		<tr >
			<td >Corning 50 mL PP Centrifuge Tubes, Conical Bottom with CentriStar Cap, Sterile</td>
			<td>Corning</td>
			<td>430828</td>
			<td>50 mL tube</td>
		</tr>
		<tr >
			<td >CTP (Cytidine 5&#39;-triphosphate, disodium salt hydrate)</td>
			<td>Alfa Aesar</td>
			<td>&#160;J62238</td>
			<td></td>
		</tr>
		<tr >
			<td >DpnI</td>
			<td>NEB</td>
			<td>R0176S</td>
			<td></td>
		</tr>
		<tr >
			<td >DTT (DL-Dithiothreitol)</td>
			<td>Sigma-Aldrich</td>
			<td>D0632</td>
			<td></td>
		</tr>
		<tr >
			<td >Folinic acid (solid folinic acid calcium salt)</td>
			<td>Sigma-Aldrich</td>
			<td>F7878</td>
			<td></td>
		</tr>
		<tr >
			<td >GTP (Guanosine 5&#697;-Triphosphate,&#160; Disodium Salt)</td>
			<td>Sigma-Aldrich</td>
			<td>371701</td>
			<td></td>
		</tr>
		<tr >
			<td >HEPES</td>
			<td>Sigma-Aldrich</td>
			<td>&#160;H3375</td>
			<td></td>
		</tr>
		<tr >
			<td >K phosphate dibasic (K2HPO4)</td>
			<td>Carl Roth</td>
			<td>231-834-5</td>
			<td></td>
		</tr>
		<tr >
			<td >K phosphate monobasic (H2KO4P)</td>
			<td>Sigma-Aldrich</td>
			<td>P5655</td>
			<td></td>
		</tr>
		<tr >
			<td >K-glutamate</td>
			<td>Alfa Aesar</td>
			<td>A17232</td>
			<td></td>
		</tr>
		<tr >
			<td >Mg-glutamate&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>49605</td>
			<td></td>
		</tr>
		<tr >
			<td >Millex-GP Syringe Filter Unit, 0.22 &#181;m, polyethersulfone</td>
			<td>Merck Millipore</td>
			<td>SLGP033RB</td>
			<td>membrane filter 0.22 &#181;m</td>
		</tr>
		<tr >
			<td >Monarch PCR &#38; DNA Cleanup Kit</td>
			<td>NEB</td>
			<td>T1030S</td>
			<td>PCR &#38; DNA cleanup Kit</td>
		</tr>
		<tr >
			<td >Monarch Plasmid Miniprep Kit</td>
			<td>NEB</td>
			<td>T1010S</td>
			<td>Plasmid Miniprep Kit</td>
		</tr>
		<tr >
			<td >NAD (B-nicotinamide adenine dinucleotide hydrate)&#160;</td>
			<td>Sigma-Aldrich&#160;</td>
			<td>N6522</td>
			<td></td>
		</tr>
		<tr >
			<td >NIST-traceable FITC standard</td>
			<td>Invitrogen</td>
			<td>F36915</td>
			<td>NIST-FITC</td>
		</tr>
		<tr >
			<td >NucleoBond Xtra Maxi kit</td>
			<td>Macherey-Nagel</td>
			<td>740414.1</td>
			<td>Plasmid Maxiprep Kit</td>
		</tr>
		<tr >
			<td >PEG 8000</td>
			<td>Sigma-Aldrich</td>
			<td>89510</td>
			<td></td>
		</tr>
		<tr >
			<td >plate reader</td>
			<td>Biotek&#160;</td>
			<td>Synergy HTX</td>
			<td ></td>
		</tr>
		<tr >
			<td >Purified Recombinant EGFP Protein</td>
			<td>Chromotek</td>
			<td>egfp-250</td>
			<td>recombinant eGFP</td>
		</tr>
		<tr >
			<td >Q5 High-Fidelity 2X Master Mix</td>
			<td>NEB</td>
			<td>M0492S</td>
			<td>DNA polymerase</td>
		</tr>
		<tr >
			<td >Q5 High-Fidelity 2X Master Mix</td>
			<td>New England Biolabs</td>
			<td>M0492L</td>
			<td>DNA polymerase</td>
		</tr>
		<tr >
			<td >Qubit dsDNA BR Assay Kit</td>
			<td>Thermo</td>
			<td>Q32850</td>
			<td>fluorometric assay with DNA-binding dye</td>
		</tr>
		<tr >
			<td >RTS Amino Acid Sampler</td>
			<td>biotechrabbit</td>
			<td>BR1401801</td>
			<td></td>
		</tr>
		<tr >
			<td >Spermidine</td>
			<td>Sigma-Aldrich</td>
			<td>85558</td>
			<td></td>
		</tr>
		<tr >
			<td >Sterile water</td>
			<td></td>
			<td></td>
			<td >Purified water from the Millipore RiOs 8 system, sterilized by autoclaving.</td>
		</tr>
		<tr >
			<td >Tris base</td>
			<td>Life Science products Cytiva</td>
			<td>17-1321-01&#160;</td>
			<td></td>
		</tr>
		<tr >
			<td >tRNA</td>
			<td>Roche</td>
			<td>10109550001</td>
			<td></td>
		</tr>
		<tr >
			<td >Ultrasonic processor Vibra cell VC-505</td>
			<td>SONICS</td>
			<td>VC505</td>
			<td>sonicator</td>
		</tr>
		<tr >
			<td >UTP Na3 (Uridine 5&#39;- triphosphate, trisodium salt hydrate)</td>
			<td>Acros Organics&#160;</td>
			<td>226310010</td>
			<td></td>
		</tr>
		<tr >
			<td >Water, nuclease-free</td>
			<td>Thermo</td>
			<td>R0581</td>
			<td>nuclease-free water</td>
		</tr>
	</tbody>
</table>

cell-free protein synthesis from exonuclease-deficient cellular extracts utilizing linear dna templates

Cell-free protein synthesis (CFPS) has recently become very popular in the field of synthetic biology due to its numerous advantages. Using linear DNA templates for CFPS will further enable the technology to reach its full potential, decreasing the experimental time by eliminating the steps of cloning, transformation, and plasmid extraction. Linear DNA can be rapidly and easily amplified by PCR to obtain high concentrations of the template, avoiding potential in vivo expression toxicity. However, linear DNA templates are rapidly degraded by exonucleases that are naturally present in the cell extracts. There are several strategies that have been proposed to tackle this problem, such as adding nuclease inhibitors or chemical modification of linear DNA ends for protection. All these strategies cost extra time and resources and are yet to obtain near-plasmid levels of protein expression. A detailed protocol for an alternative strategy is presented here for using linear DNA templates for CFPS. By using cell extracts from exonuclease-deficient knockout cells, linear DNA templates remain intact without requiring any end-modifications. We present the preparation steps of cell lysate from Escherichia coli BL21 Rosetta2 &#916;recBCD strain by sonication lysis and buffer calibration for Mg-glutamate (Mg-glu) and K-glutamate (K-glu) specifically for linear DNA. This method is able to achieve protein expression levels comparable to that from plasmid DNA in E. coli CFPS.

Representative results are shown here after calibration of the lysate for optimal Mg-glutamate and K-glutamate levels separately for linear and plasmid DNA (Figure 1). The Mg-glutamate optimal concentration is similar across &#916;recB and &#916;recBCD extracts at 8 mM (Figure 1B). However, the optimal K-glutamate concentration for plasmid DNA is 140&#160;mM, whereas the optimal K-glutamate concentration for linear DNA for the same extract is 2...

Watch this Scientific Journal Video about Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates at JoVE.com

Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates

Presented here is a protocol for the preparation and buffer calibration of cell extracts from exonuclease V knockout strains of Escherichia coli BL21 Rosetta2 (&#916;recBCD and &#916;recB). This is a fast, easy, and direct approach for expression in cell-free protein synthesis systems using linear DNA templates.

Cell-free protein synthesis (CFPS) has recently become very popular in the field of synthetic biology due to its numerous advantages. Using linear DNA ...

cell-free-protein-synthesis-from-exonuclease-deficient-cellular

Research

JoVE Journal

Bioengineering

3.5K Views.  Université Paris-Saclay. Presented here is a protocol for the preparation and buffer calibration of cell extracts from exonuclease V knockout strains of Escherichia coli BL21 Rosetta2 (ΔrecBCD and ΔrecB). This is a fast, easy, and direct approach for expression in cell-free protein synthesis systems using linear DNA templates.

Video: Cell-Free Protein Synthesis from Exonuclease-Deficient Cellular Extracts Utilizing Linear DNA Templates

Combinatorial Synthesis of and High-throughput Protein Release from Polymer Film and Nanoparticle Libraries

Polyanhydrides are a class of biomaterials with excellent biocompatibility and drug delivery capabilities. While they have been studied extensively with conventional one-sample-at-a-time synthesis techniques, a more recent high-throughput approach has been developed enabling the synthesis and testing of large libraries of polyanhydrides1. This will facilitate more efficient optimization and design process of these biomaterials for drug and vaccine delivery applications. The method in this work describes the combinatorial synthesis of biodegradable polyanhydride film and nanoparticle libraries and the high-throughput detection of protein release from these libraries. In this robotically operated method (Figure 1), linear actuators and syringe pumps are controlled by LabVIEW, which enables a hands-free automated protocol, eliminating user error. Furthermore, this method enables the rapid fabrication of micro-scale polymer libraries, reducing the batch size while resulting in the creation of multivariant polymer systems. This combinatorial approach to polymer synthesis facilitates the synthesis of up to 15 different polymers in an equivalent amount of time it would take to synthesize one polymer conventionally. In addition, the combinatorial polymer library can be fabricated into blank or protein-loaded geometries including films or nanoparticles upon dissolution of the polymer library in a solvent and precipitation into a non-solvent (for nanoparticles) or by vacuum drying (for films). Upon loading a fluorochrome-conjugated protein into the polymer libraries, protein release kinetics can be assessed at high-throughput using a fluorescence-based detection method (Figures 2 and 3) as described previously1. This combinatorial platform has been validated with conventional methods2 and the polyanhydride film and nanoparticle libraries have been characterized with 1H NMR and FTIR. The libraries have been screened for protein release kinetics, stability and antigenicity; in vitro cellular toxicity, cytokine production, surface marker expression, adhesion, proliferation and differentiation; and in vivo biodistribution and mucoadhesion1-11. The combinatorial method developed herein enables high-throughput polymer synthesis and fabrication of protein-loaded nanoparticle and film libraries, which can, in turn, be screened in vitro and in vivo for optimization of biomaterial performance.

This method describes the combinatorial synthesis of biodegradable polyanhydride film and nanoparticle libraries and the high-throughput detection of protein release from these libraries.

Polyanhydrides are a class of biomaterials with excellent biocompatibility and drug delivery capabilities. While they have been studied extensively with ...

Synthesis of an Intein-mediated Artificial Protein Hydrogel

We present the synthesis of a highly stable protein hydrogel mediated by a split-intein-catalyzed protein trans-splicing reaction. The building blocks of this hydrogel are two protein block-copolymers each containing a subunit of a trimeric protein that serves as a crosslinker and one half of a split intein. A highly hydrophilic random coil is inserted into one of the block-copolymers for water retention. Mixing of the two protein block copolymers triggers an intein trans-splicing reaction, yielding a polypeptide unit with crosslinkers at either end that rapidly self-assembles into a hydrogel. This hydrogel is very stable under both acidic and basic conditions, at temperatures up to 50 &#176;C, and in organic solvents. The hydrogel rapidly reforms after shear-induced rupture. Incorporation of a &#34;docking station peptide&#34; into the hydrogel building block enables convenient incorporation of &#34;docking protein&#34;-tagged target proteins. The hydrogel is compatible with tissue culture growth media, supports the diffusion of 20 kDa molecules, and enables the immobilization of bioactive globular proteins. The application of the intein-mediated protein hydrogel as an organic-solvent-compatible biocatalyst was demonstrated by encapsulating the horseradish peroxidase enzyme and corroborating its activity.

We present the synthesis of a split-intein-mediated protein hydrogel. The building blocks of this hydrogel are two protein copolymers each containing a subunit of a trimeric protein that serves as a crosslinker and one half of a split intein. Mixing of the two protein copolymers triggers an intein trans-splicing reaction, yielding a polypeptide unit that self-assembles into a hydrogel. This hydrogel is highly pH- and temperature-stable, compatible with organic solvents, and easily incorporates functional globular proteins.

We present the synthesis of a highly stable protein hydrogel mediated by a split-intein-catalyzed protein trans-splicing reaction. The building blocks of ...

The Encapsulation of Cell-free Transcription and Translation Machinery in Vesicles for the Construction of Cellular Mimics

As interest shifts from individual molecules to systems of molecules, an increasing number of laboratories have sought to build from the bottom up cellular mimics that better represent the complexity of cellular life. To date there are a number of paths that could be taken to build compartmentalized cellular mimics, including the exploitation of water-in-oil emulsions, microfluidic devices, and vesicles. Each of the available options has specific advantages and disadvantages. For example, water-in-oil emulsions give high encapsulation efficiency but do not mimic well the permeability barrier of living cells. The primary advantage of the methods described herein is that they are all easy and cheap to implement. Transcription-translation machinery is encapsulated inside of phospholipid vesicles through a process that exploits common instrumentation, such as a centrifugal evaporator and an extruder. Reactions are monitored by fluorescence spectroscopy. The protocols can be adapted for recombinant protein expression, the construction of cellular mimics, the exploration of the minimum requirements for cellular life, or the assembly of genetic circuitry.

Herein we describe simple methods for the preparation of vesicles, the encapsulation of transcription and translation machinery, and the monitoring of protein production. The resulting cell-free systems can be used as a starting point from which to build increasingly complex cellular mimics.

As interest shifts from individual molecules to systems of molecules, an increasing number of laboratories have sought to build from the bottom up ...

Sealable Femtoliter Chamber Arrays for Cell-free Biology

Cell-free systems provide a flexible platform for probing specific networks of biological reactions isolated from the complex resource sharing (e.g., global gene expression, cell division) encountered within living cells. However, such systems, used in conventional macro-scale bulk reactors, often fail to exhibit the dynamic behaviors and efficiencies characteristic of their living micro-scale counterparts. Understanding the impact of internal cell structure and scale on reaction dynamics is crucial to understanding complex gene networks. Here we report a microfabricated device that confines cell-free reactions in cellular scale volumes while allowing flexible characterization of the enclosed molecular system. This multilayered poly(dimethylsiloxane) (PDMS) device contains femtoliter-scale reaction chambers on an elastomeric membrane which can be actuated (open and closed). When actuated, the chambers confine Cell-Free Protein Synthesis (CFPS) reactions expressing a fluorescent protein, allowing for the visualization of the reaction kinetics over time using time-lapse fluorescent microscopy. Here we demonstrate how this device may be used to measure the noise structure of CFPS reactions in a manner that is directly analogous to those used to characterize cellular systems, thereby enabling the use of noise biology techniques used in cellular systems to characterize CFPS gene circuits and their interactions with the cell-free environment.

A microfabricated device with sealable femtoliter-volume reaction chambers is described. This report includes a protocol for sealing cell-free protein synthesis reactants inside these chambers for the purpose of understanding the role of crowding and confinement in gene expression.

Cell-free systems provide a flexible platform for probing specific networks of biological reactions isolated from the complex resource sharing (e.g., ...

Synthesis of Infectious Bacteriophages in an E. coli-based Cell-free Expression System

A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel capabilities to perform basic and applied sciences in test tube reactions. Over the past decade, cell-free TXTL has become a powerful technique for a broad range of novel multidisciplinary research areas related to quantitative and synthetic biology. The new TXTL platforms are particularly useful to construct and interrogate biochemical systems through the execution of synthetic or natural gene circuits. In vitro TXTL has proven convenient to rapidly prototype regulatory elements and biological networks as well as to recapitulate molecular self-assembly mechanisms found in living systems. In this article, we describe how infectious bacteriophages, such as MS2 (RNA), &#934;&#935;174 (ssDNA), and T7 (dsDNA), are entirely synthesized from their genome in one-pot reactions using an all Escherichia coli, cell-free TXTL system. Synthesis of the three coliphages is quantified using the plaque assay. We show how the yield of synthesized phage depends on the biochemical settings of the reactions. Molecular crowding, emulated through a controlled concentration of PEG 8000, affects the amount of synthesized phages by orders of magnitudes. We also describe how to amplify the phages and how to purify their genomes. The set of protocols and results presented in this work should be of interest to multidisciplinary researchers involved in cell-free synthetic biology and bioengineering.

Synthesis of Infectious Bacteriophages in an E. coli-based Cell-free Expression System

A new generation of cell-free transcription-translation platforms has been engineered to construct biochemical systems in vitro through the execution of gene circuits. In this article, we describe how bacteriophages, such as MS2, &#934;&#935;174, and T7, are synthesized from their genome using an all E. coli cell-free TXTL system.

A new generation of cell-free transcription-translation (TXTL) systems, engineered to have a greater versatility and modularity, provide novel ...

Design and Synthesis of a Reconfigurable DNA Accordion Rack

DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to &#229;ngstr&#246;m resolution, show great potential in various fields of nanotechnology such as the molecular reactors, drug delivery, and nanoplasmonic systems. The reconfigurable DNA accordion rack, which can collectively manipulate a 2D or 3D nanoscale network of elements, in multiple stages in response to the DNA inputs, is described. The platform has potential to increase the number of elements that DNA nanomachines can control from a few elements to a network scale with multiple stages of reconfiguration.
In this protocol, we describe the entire experimental process of the reconfigurable DNA accordion rack of 6 by 6 meshes. The protocol includes a design rule and simulation procedure of the structures and a wet-lab experiment for synthesis and reconfiguration. In addition, analysis of the structure using TEM (transmission electron microscopy) and FRET (fluorescence resonance energy transfer) is included in the protocol. The novel design and simulation methods covered in this protocol will assist researchers to use the DNA accordion rack for further applications.

We describe the detailed protocol for design, simulation, wet-lab experiments, and analysis for a reconfigurable DNA accordion rack of 6 by 6 meshes.

DNA nanostructure-based mechanical systems or DNA nanomachines, which produce complex nanoscale motion in 2D and 3D in the nanometer to &#229;ngstr&#246;m ...

Cell-free Protein Expression Using the Rapidly Growing Bacterium Vibrio natriegens

The marine bacterium Vibrio natriegens has garnered considerable attention as an emerging microbial host for biotechnology due to its fast growth rate. A general protocol is described for the preparation of V. natriegens crude cell extracts using common laboratory equipment. This high yielding protocol has been specifically optimized for user accessibility and reduced cost. Cell-free protein synthesis (CFPS) can be carried out in small scale 10 &#956;L batch reactions in either a 96- or 384-well format and reproducibly yields concentrations of &#62; 260 &#956;g/mL super folder GFP (sfGFP) within 3 h. Overall, crude cell extract preparation and CFPS can be achieved in 1&#8722;2 full days by a single user. This protocol can be easily integrated into existing protein synthesis pipelines to facilitate advances in bio-production and synthetic biology applications.

Cell-free Protein Expression Using the Rapidly Growing Bacterium Vibrio natriegens

Cell-free expression systems are powerful and cost-efficient tools for the high-throughput synthesis and screening of important proteins. Here, we describe the preparation of cell-free protein expression system using Vibrio natriegens for the rapid protein production using plasmid DNA, linear DNA, and mRNA template.

The marine bacterium Vibrio natriegens has garnered considerable attention as an emerging microbial host for biotechnology due to its fast growth rate. A ...

In Vesiculo Synthesis of Peptide Membrane Precursors for Autonomous Vesicle Growth

Compartmentalization of biochemical reactions is a central aspect of synthetic cells. For this purpose, peptide-based reaction compartments serve as an attractive alternative to liposomes or fatty acid-based vesicles. Externally or within the vesicles, peptides can be easily expressed and simplify the synthesis of membrane precursors. Provided here is a protocol for the creation of vesicles with diameters of ~200 nm based on the amphiphilic elastin-like polypeptides (ELP) utilizing dehydration-rehydration from glass beads. Also presented are protocols for bacterial ELP expression and purification via inverse temperature cycling, as well as their covalent functionalization with fluorescent dyes. Furthermore, this report describes a protocol to enable the transcription of RNA aptamer dBroccoli inside ELP vesicles as a less complex example for a biochemical reaction. Finally, a protocol is provided, which allows in vesiculo expression of fluorescent proteins and the membrane peptide, whereas synthesis of the latter results in vesicle growth.

Presented here are protocols for the creation of peptide-based small unilamellar vesicles capable of growth. To facilitate in vesiculo production of the membrane peptide, these vesicles are equipped with a transcription-translation system and the peptide-encoding plasmid.

Compartmentalization of biochemical reactions is a central aspect of synthetic cells. For this purpose, peptide-based reaction compartments serve as an ...

Preparing Protein Producing Synthetic Cells using Cell Free Bacterial Extracts, Liposomes and Emulsion Transfer

The bottom-up assembly approach for construction of synthetic cells is an effective tool for isolating and investigating cellular processes in a cell mimicking environment. Furthermore, the development of cell-free expression systems has demonstrated the ability to reconstitute the protein production, transcription and translation processes (DNA&#8594;RNA&#8594;protein) in a controlled manner, harnessing synthetic biology. Here we describe a protocol for preparing a cell-free expression system, including the production of a potent bacterial lysate and encapsulating this lysate inside cholesterol-rich lipid-based giant unilamellar vesicles (GUVs) (i.e., stable liposomes), to form synthetic cells. The protocol describes the methods for preparing the components of the synthetic cells including the production of active bacterial lysates, followed by a detailed step-by-step preparation of the synthetic cells based on a water-in-oil emulsion transfer method. These facilitate the production of millions of synthetic cells in a simple and affordable manner with a high versatility for producing different types of proteins. The obtained synthetic cells can be used to investigate protein/RNA production and activity in an isolated environment, in directed evolution, and also as a controlled drug delivery platform for on-demand production of therapeutic proteins inside the body.

This protocol describes the method, materials, equipment and steps for bottom-up preparation of RNA and protein producing synthetic cells. The inner aqueous compartment of the synthetic cells contained the S30 bacterial lysate encapsulated within a lipid bilayer (i.e., stable liposomes), using a water-in-oil emulsion transfer method.

The bottom-up assembly approach for construction of synthetic cells is an effective tool for isolating and investigating cellular processes in a cell ...

OnePot PURE Cell-Free System

The defined PURE (protein synthesis using recombinant elements) transcription-translation system provides an appealing chassis for cell-free synthetic biology. Unfortunately, commercially available systems are costly, and their tunability is limited. In comparison, a home-made approach can be customized based on user needs. However, the preparation of home-made systems is time-consuming and arduous due to the need for ribosomes as well as 36 medium scale protein purifications. Streamlining protein purification by coculturing and co-purification allows for minimizing time and labor requirements. Here, we present an easy, adjustable, time- and cost-effective method to produce all PURE system components within 1 week, using standard laboratory equipment. Moreover, the performance of the OnePot PURE is comparable to commercially available systems. The OnePot PURE preparation method expands the accessibility of the PURE system to more laboratories due to its simplicity and cost-effectiveness.

We present a fast and cost-effective method to produce the recombinant PURE cell-free TX-TL system using standard laboratory equipment.

The defined PURE (protein synthesis using recombinant elements) transcription-translation system provides an appealing chassis for cell-free synthetic ...