This work was supported by LRIR 16RH3003J grant from the Air Force Office of Scientific Research, as well as the Synthetic Biology for Military Environments Applied Research for the Advancement of S&#38;T Priorities (ARAP) program of the U.S. Office of the Under Secretary of Defense for Research and Engineering.
The plasmid vector sequence for ThyRS (pSALv-RS-GFPa1, 3.4 kb) was generously provided by Dr. J. Gallivan. Silkworm cocoons from Bombyx mori were generously donated by Dr. D.L. Kaplan from Tufts University, MA.

1. Construction of plasmid vector.
<ol>
	<li>Construct a plasmid vector (pSALv-RS-GFPa1, 3.4 kb) by amplification of the coding sequence of a theophylline riboswitch (ThyRS) coupled with GFPa1 from pJ201:23976-RS-GFPa1 vector (designed and created by DNA2.0) and insertion into E. coli expression vector, pSAL13. Use forward (5&#39;-CGTGGTACCGGTGATACCAGCATCGTCTTGATG-3&#39;) and reverse (5&#39;-CGTGCTCAGCTTAAGCCAGCTCGTAG-3&#39;) primers to amplify the coding sequence of ThyRS coupled with ...

<ol>
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Selectively permeable hydrogel microcapsules loaded with various types of DNA-encoded sensor designs can be prepared following this protocol. One of the distinctive features of the LbL approach is the ability to tailor the complexity of microcapsules during the bottom-up assembly, which usually starts with the adsorption of molecular species on sacrificial templates. By carefully adjusting concentrations of the initial components, pH conditions, and the number of layers, microcapsules with different DNA loading parameter...

The field of synthetic biology offers unique opportunities to develop sensing capabilities by exploiting natural mechanisms evolved by microorganisms to monitor their environment and potential threats. Importantly, these sensing mechanisms are typically linked to a response that protects these microorganisms from harmful exposure, regulating gene expression to mitigate negative effects or prevent intake of toxic materials. There have been significant efforts to engineer these microorganisms to create whole-cell sensors taking advantage of these natural responses but re-directing them to recognize novel targets and/or to produce a measurable signal that can be measured for quantification purposes (typically fluorescence)1,2. Currently, concerns with the use of genetically modified microorganisms (GMOs), especially when releasing in the environment or the human body, due to leakage of whole cells or some of their genetic material, even if encapsulated in a polymer matrix, suggest that alternative ways to exploit these sensing approaches are needed3.
A powerful approach to exploit the benefits of microorganisms-based sensing without the concern for the deployment of GMOs is the use of in vitro transcription/translation (IVTT) systems. From a practical perspective, IVTT systems consist of a mixture containing most of the cell components in an active state that has been &#34;extracted&#34; from cells by different means, including sonication, bead-beating, or others4. The final product of this process is a biochemical reaction mixture already optimized to perform transcription and translation that can be used to test different sensors in an &#34;open vessel&#34; format, without the constraints associated with the use of whole cells (membrane diffusion, transformation efficiency, cell toxicity, etc.). Importantly, different sensor components can be quantitatively added, and their effect studied by different optical and spectrometric techniques, as we have demonstrated5. It has been noticed that the performance of IVTT systems can be inconsistent; however, recent studies have shown approaches to standardize their preparation and characterization, which is of great help when studying their performance in sensor design6. Recently, many examples of IVTT systems using to create paper-based assays through the lyophilization of their components in paper matrices have been demonstrated, including detection of heavy metal ions, drugs, quorum sensing elements, and others7,8,9. An exciting application space for IVTT-based sensors is their use in sensing applications in different types of environments, including soil, water, and the human body. In order to deploy these IVTT systems to these challenging environments, an encapsulation approach need to be implemented to contain the IVTT components and protect them from degradation.
The most common encapsulation approaches for IVTT systems include the use of lipid capsules, micelles, polymersomes, and other tightly enclosed microcontainers10,11,12. One disadvantage of this approach is the need to incorporate either passive or active mechanisms to transport materials in and out of the containers to allow communication with the external environment and provide sensing capabilities. To overcome some of these issues, the study here reports a method that provides a simple yet effective approach to encapsulate the encoding materials for different sensor designs to be expressed in IVTT systems. This approach is based on the use of Layer-by-Layer (LbL) deposition of a biopolymer in the presence of the plasmids of interest to create hollow microcapsules with high porosity, which allows the protected genetic material to interact with the different components of the IVTT of choice. The study demonstrated that encapsulated plasmids could direct transcription and translation when activated within this polymeric matrix, as shown with the response of a plasmid-encoded aptamer and a riboswitch to their corresponding targets. Additionally, this LbL coating protects the plasmids for months without any special storage conditions.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>(Z)-4-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-1-(2,2,2-trifluoroethyl)-1H-imidazol-5(4 H)-one (DFHBI-1T)</td>
			<td>Lucerna</td>
			<td>DFHBI-1T</td>
			<td></td>
		</tr>
		<tr>
			<td>5x T4 DNA Ligase Buffer</td>
			<td>ThermoFisher Scientific</td>
			<td>46300-018</td>
			<td></td>
		</tr>
		<tr>
			<td>6x Blue Gel Loading Dye</td>
			<td>New England BioLabs</td>
			<td>B7021S</td>
			<td></td>
		</tr>
		<tr>
			<td>96-well plates, black circular</td>
			<td>Corning</td>
			<td>3601</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Sigma-Aldrich</td>
			<td>A9539</td>
			<td>BioReagent, for molecular biology, low EEO</td>
		</tr>
		<tr>
			<td>Ampicillin sodium salt</td>
			<td>Sigma-Aldrich</td>
			<td>A0166</td>
			<td>powder or crystals, BioReagent, suitable for cell culture</td>
		</tr>
		<tr>
			<td>BlpI restriction enzymes</td>
			<td>New England BioLabs</td>
			<td>R0585S</td>
			<td></td>
		</tr>
		<tr>
			<td>Corning Disposable Vacuum Filter/Storage Systems</td>
			<td>FisherScientific</td>
			<td>09-761-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Dimethyl sulfoxide, DMSO</td>
			<td>Sigma-Aldrich</td>
			<td>472301</td>
			<td>ACS reagent, &#8805;99.9%</td>
		</tr>
		<tr>
			<td>DNA Plasmid, pET28c-F30-2x Broccoli (5.4 kb), BrocApt.</td>
			<td>Addgene</td>
			<td>Plasmid #66788</td>
			<td></td>
		</tr>
		<tr>
			<td>DyLightTM550 Antibody Labeling kit (Invitrogen)</td>
			<td>ThermoFisher Scientific</td>
			<td>84530</td>
			<td></td>
		</tr>
		<tr>
			<td>E. coli S30 extract system for circular DNA</td>
			<td>Promega</td>
			<td>L1020</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon Conical centrifuge tubes, 15 mL</td>
			<td>FisherScientific</td>
			<td>14-959-53A</td>
			<td></td>
		</tr>
		<tr>
			<td>Falcon Conical centrifuge tubes, 50 mL</td>
			<td></td>
			<td>14-432-22</td>
			<td></td>
		</tr>
		<tr>
			<td>Fisherbrand Microcentrifuge tubes, 1.5 mL</td>
			<td>FisherScientific</td>
			<td>05-408-129</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrofluoric acid, HF</td>
			<td>Sigma-Aldrich</td>
			<td>695068</td>
			<td>ACS reagent, 48%</td>
		</tr>
		<tr>
			<td>Kanamycin sulfate</td>
			<td>Sigma-Aldrich</td>
			<td>60615</td>
			<td>mixture of Kanamycin A (main component) and Kanamycin B and C</td>
		</tr>
		<tr>
			<td>KpnI restriction enzymes</td>
			<td>New England BioLabs</td>
			<td>R0142S</td>
			<td></td>
		</tr>
		<tr>
			<td>LB agar plate supplemented with 100 &#181;g/mL ampicillin</td>
			<td>Sigma-Aldrich</td>
			<td>L5667</td>
			<td>pre-poured agar plates with 100 &#181;g/mL ampicillin</td>
		</tr>
		<tr>
			<td>LB agar plate supplemented with 50 &#181;g/mL kanamycin</td>
			<td>Sigma-Aldrich</td>
			<td>L0543</td>
			<td>pre-poured agar plates with 50 &#181;g/mL kanamycin</td>
		</tr>
		<tr>
			<td>LB broth (Lennox grade)</td>
			<td>Sigma-Aldrich</td>
			<td>L3022</td>
			<td></td>
		</tr>
		<tr>
			<td>Lithium bromide, LiBr</td>
			<td>Sigma-Aldrich</td>
			<td>213225</td>
			<td>ReagentPlus, &#8805;99%</td>
		</tr>
		<tr>
			<td>Max Efficiency DH5-&#945; competent E. coli strain</td>
			<td>ThermoFisher Scientific</td>
			<td>18258012</td>
			<td></td>
		</tr>
		<tr>
			<td>Methanol</td>
			<td>MilliporeSigma</td>
			<td>322415</td>
			<td>anhydrous, 99.8%</td>
		</tr>
		<tr>
			<td>MilliQ-water</td>
			<td>EMD MilliPore</td>
			<td></td>
			<td>Milli-Q Reference Water Purification System</td>
		</tr>
		<tr>
			<td>MinElute PCR Purification Kit</td>
			<td>Qiagen</td>
			<td>28004</td>
			<td></td>
		</tr>
		<tr>
			<td>N-(3-Dimethylaminopropyl)-N&#8242;-ethylcarbodiimide hydrochloride, EDC</td>
			<td>Sigma-Aldrich</td>
			<td>E1769</td>
			<td></td>
		</tr>
		<tr>
			<td>PBS (phosphate buffered saline)</td>
			<td>ThermoFisher Scientific</td>
			<td>10010023</td>
			<td>1x PBS, pH 7.4</td>
		</tr>
		<tr>
			<td>Phusion High-Fidelity DNA Polymerase</td>
			<td>New England Biolabs</td>
			<td>M0530S</td>
			<td></td>
		</tr>
		<tr>
			<td>Polyethylenimine, branched</td>
			<td>Sigma-Aldrich</td>
			<td>408727</td>
			<td>average Mw ~25,000</td>
		</tr>
		<tr>
			<td>PURExpress In Vitro Protein Synthesis Kit</td>
			<td>New England BioLabs</td>
			<td>E6800S</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAEX II Gel Extraction Kit</td>
			<td>Qiagen</td>
			<td>20021</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAprep Spin Miniprep Kit</td>
			<td>Qiagen</td>
			<td>&#160;27104</td>
			<td></td>
		</tr>
		<tr>
			<td>Quick-Load 2-Log DNA Ladder (0.1-10.0 kb)</td>
			<td>New England BioLabs</td>
			<td>N0469S</td>
			<td></td>
		</tr>
		<tr>
			<td>SiO&#8322; silica microspheres, 4.0 &#181;m</td>
			<td>Polysciences, Inc.</td>
			<td>24331-15</td>
			<td>10% aqueous solution</td>
		</tr>
		<tr>
			<td>Slide-A-Lyzer G2 Dialysis Cassettes, 3.5K MWCO, 15 mL</td>
			<td>ThermoFisher Scientific</td>
			<td>87724</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium carbonate, Na&#8322;CO&#8323;</td>
			<td>Sigma-Aldrich</td>
			<td>222321</td>
			<td>ACS reagent, anhydrous, &#8805;99.5%, powder</td>
		</tr>
		<tr>
			<td>Spectrum Spectra/Por Float-A-Lyzer G2 Dialysis Devices</td>
			<td>FisherScientific</td>
			<td>08-607-008</td>
			<td>Spectrum G235058</td>
		</tr>
		<tr>
			<td>SYBR Safe DNA gel stain</td>
			<td>ThermoFisher Scientific</td>
			<td>S33102</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA Ligase (5 U/&#181;L)</td>
			<td>ThermoFisher Scientific</td>
			<td>EL0011</td>
			<td></td>
		</tr>
		<tr>
			<td>Theophylline</td>
			<td>Sigma-Aldrich</td>
			<td>T1633</td>
			<td>anhydrous, &#8805;99%, powder</td>
		</tr>
		<tr>
			<td>Tris Acetate-EDTA buffer (TAE buffer)</td>
			<td>Sigma-Aldrich</td>
			<td>T6025</td>
			<td>Contains 40 mM Tris-acetate and 1 mM EDTA, pH 8.3.</td>
		</tr>
		<tr>
			<td>UltraPure DNase/RNase-Free Distilled Water</td>
			<td>FisherScientific</td>
			<td>10-977-023</td>
			<td></td>
		</tr>
		<tr>
			<td>ZymoPURE II Plasmid MaxiPrep kit</td>
			<td>ZymoResearch</td>
			<td>D4202</td>
			<td></td>
		</tr>
	</tbody>
</table>

preparation of multifunctional silk-based microcapsules loaded with dna plasmids encoding rna aptamers and riboswitches

We introduce a protocol for the preparation of DNA-laden silk fibroin microcapsules via the Layer-by-Layer (LbL) assembly method on sacrificial spherical cores. Following adsorption of a prime layer and DNA plasmids, the formation of robust microcapsules was facilitated by inducing &#946;-sheets in silk secondary structure during acute dehydration of a single silk layer. Hence, the layering occurred via multiple hydrogen bonding and hydrophobic interactions. Upon adsorption of multilayered shells, the core-shell structures can be further functionalized with gold nanoparticles (AuNPs) and/or antibodies (IgG) to be used for remote sensing and/or targeted delivery. Adjusting several key parameters during sequential deposition of key macromolecules on silica cores such as the presence of a polymer primer, the concentration of DNA and silk protein, as well as a number of adsorbed layers resulted in biocompatible, DNA-laden microcapsules with variable permeability and DNA loadings. Upon dissolution of silica cores, the protocol demonstrated the formation of hollow and robust microcapsules with DNA plasmids immobilized to the inner surface of the capsule membrane. Creating a selectively permeable biocompatible membrane between the DNA plasmids and the external environment preserved the DNA during long-term storage and played an important role in the improved output response from spatially confined plasmids. The activity of DNA templates and their accessibility were tested during in vitro transcription and translation reactions (cell-free systems). DNA plasmids encoding RNA light-up aptamers and riboswitches were successfully activated with corresponding analytes, as was visualized during localization of fluorescently labeled RNA transcripts or GFPa1 protein in the shell membranes.

Here, the study addresses the functionality of DNA templates encoding different sensor designs (two types of RNA-regulated transcription/translation elements) after encapsulation in silk protein capsules. Microcapsules were prepared via templated Layer-by-Layer (LbL) assembly of the key components: A prime layer, DNA plasmids encoding sensor designs, and silk fibroin biopolymer (Figure 2). Deposition of macromolecules in a layered fashion allows controlling the permeability of the capsule me...

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Preparation of Multifunctional Silk-Based Microcapsules Loaded with DNA Plasmids Encoding RNA Aptamers and Riboswitches

The protocol describes the formation of robust and biocompatible DNA-laden microcapsules as multiplexed in vitro biosensors capable of tracking several ligands.

We introduce a protocol for the preparation of DNA-laden silk fibroin microcapsules via the Layer-by-Layer (LbL) assembly method on sacrificial spherical ...

The significance of this protocol is that it provides a means for keeping DNA-encoded sensors functional by immobilizing DNA plasmid templates into semipermeable biocompatible microcapsules. The proposed DNA immobilization technique is versatile. It allows the fabrication of multifunctional biosensors with different in vitro activation mechanisms.We envision these microcapsules, coupled with the proper sensing elements, could be used to study different biological processes, including the release of signaling molecules in different environments such as biofilms and organs. This technique can provide insights into the biological systems at the microscale, particularly how the immobilization of DNA and molecular crowding can affect the kinetics and mechanism of gene activation. Start with the deposition of the polyethyleneimine prime layer onto the sacrificial silica, or SiO2, microparticles by adding one milliliter of polyethyleneimine solution to 300 microliters of the microparticles in a two-milliliter microcentrifuge tube.Agitate the mixture on a ThermoMixer at 800 rotations per minute at ambient conditions. Collect the microparticles by centrifugation at 0.2 g for one minute at room temperature, and carefully remove the supernatant. After 15 minutes, wash the microparticles four times with one milliliter of DNase-and RNase-free deionized water by centrifugation at 0.2 g for one minute at room temperature, discarding the supernatant after each centrifugation.Next, adjust the concentration of DNA plasmids from 50 to 200 nanogram per microliters with DNase-and RNase-free distilled water, and use one milliliter of the prepared solutions to deposit the DNA on the polyethyleneimine-primed microparticles. Gently agitate the microparticle mixture on a ThermoMixer at four degrees Celsius and 800 rpm for 15 minutes, and then collect the microparticles by centrifugation at 0.2 g for one minute. Mark the tubes for DNA plasmids encoding theophylline riboswitch, coupled with GFPa1 as ThyRS-GFPa1, and DNA plasmids encoding Broccoli aptamer as BrocApt.Carefully remove the supernatant, and wash the microparticles four times with one milliliter of DNase-and RNase-free distilled water as previously demonstrated, discarding the supernatant after each centrifugation. To deposit the silk fibroin layer, add one milliliter of the reconstituted aqueous silk fibroin solution to the DNA-absorbed microparticles, and gently vortex agitate the mixture on the ThermoMixer at 750 rpm for 15 minutes at 10 degrees Celsius. Collect the microparticles by centrifugation, and then wash them once with one milliliter of DNase-and RNase-free distilled water, as explained before.Repeat the centrifugation, and discard the supernatant. Add 0.5 milliliters of DNase and RNase distilled water, and mix the microparticles by vortexing. Then, treat the microparticles with 0.5 milliliters of 100%methanol at 10 degrees Celsius for five minutes on a ThermoMixer.After collecting the microparticles by centrifugation, treat the particles with 100%methanol on the ThermoMixer at 750 rotations per minute for 10 minutes at 10 degrees Celsius for beta-sheet formation. Centrifuge the mixture at 0.2 g for one minute at four degrees Celsius to collect microparticles before washing the particles twice with one milliliter of DNase-and RNase-free distilled water as demonstrated before. Dissolve SiO2 cores of microparticles by adding 8%hydrofluoric acid solution to pelleted core shell microparticles.Transfer the dissolved particles solutions to dialysis devices, and dialyze them against deionized water in a beaker. Then, use a one-milliliter pipette to collect the silk microcapsules suspension from dialysis devices into new two-milliliter microcentrifuge tubes. Transfer 100 microliters of the microcapsule sample into a single well of eight-well chambered glass slides, and allow the capsules to sediment for 20 to 30 minutes prior to imaging using a confocal laser scanning microscope, or CLSM.Pipette 100 microliters of the suspension of capsules into each well of a chambered glass slide. To each well, sequentially add 300 microliters of the fluorophore solution of varying molecular weights from the lowest to the highest. Mix the mixture by pipetting up and down, and let the mixture incubate for one hour at room temperature until the diffusion of fluorophore solutions reaches equilibrium.Later, transfer the slide to a CLSM to image each well using a 100x oil immersion objective at an excitation wavelength of 488 nanometers. Identify the area of interest by adjusting the focal plane, and focus on the capsules that appear in the form of circles of the largest diameter. Perform in vitro transcription/translation reaction by sequentially adding the cell-free components to a sample of microcapsules and incubating the tube at 30 degrees Celsius for four hours.Check the fluorescence on a plate reader using excitation wavelength at 488 nanometers and emission for GFP/FITC filter at around 510 nanometers. Finally, image the silk microcapsules on the CLSM system using lasers at 488 and 561 nanometers. In the study, robust silk fibroin microcaps with a homogeneous size of around 4.5 micrometers and a shell thickness of approximately 500 nanometers were produced.The permeability of the hollow silk fibroin capsule shells was analyzed by following the molecular weight cutoff method. An increase in the concentration of a polyethyleneimine prime layer leads to increased colloidal stability of microcapsules with more permeable shells, while eliminating the prime layer causes aggregation of capsules with less permeable shell membranes. The GFPa1 expression kinetics during ThyRS activation revealed higher GFPa1 gene activation from DNA plasmids loaded into silk microcapsules than control non-encapsulated DNA.In the representative analysis, CLSM images of silk fibroin capsules loaded with 32 DNA copies per capsule before and after incubation in the in vitro transcription, translation system are displayed. The cross-sectional intensity profiles of the silk fibroin capsules demonstrated the expression of GFPa1. The transcription kinetics of 20 layered silk microcapsules loaded with 30 DNA copies per capsule was compared with control non-encapsulated DNA.The higher output signal from silk microcapsules than non-encapsulated DNA samples of equivalent concentrations confirmed the effectivity of silk microcapsules. Following this protocol, several high-resolution microscopy techniques can be applied to image DNA entanglement in the immobilized state and decoupled gene activation process in vitro. This technique can be applied to answer molecular-level dynamics in minimal artificial cells.Specifically, when coupled with proper gene elements, the microcapsules can be used to study cell-to-cell communication.

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Biology

1.3K vistas.  UES Inc.. The significance of this protocol is that it provides a means for keeping DNA-encoded sensors functional by immobilizing DNA plasmid templates into semipermeable biocompatible microcapsules. The proposed DNA immobilization technique is versatile. It allows the fabrication of multifunctional biosensors with different in vitro activation mechanisms.We envision these microcapsules, coupled with the proper sensing elements, could be used to study different biological processes, including t...