The research programs in the Liang laboratory at Emory are supported by the US National Institute of General Medical Sciences (NIGMS), National Institutes of Health (NIH) under award number R01GM130950, and the Research Start-Up Fund at Emory University School of Medicine. The author acknowledges the members of the Liang laboratory for helpful support and critical discussion.

1. Molecular cloning
NOTE: Ligase Independent Cloning (LIC) was used to make an RSV bi-cistronic coexpression construct plasmid. LIC is a method developed in the early 1990s, which uses the 3&#8217;-5&#8217; Exo activity of the T4 DNA&#160; polymerase to create overhangs with complementarity between the vector and the DNA insert21,22. The constructs were made using the 2BT-10 vector DNA, which consists of a 10x His tag at the N-terminal of the Open Reading Frame (ORF) (Figure 1).
<ol>
	<li>Perform linearization of LIC vectors using SSPI digestion.
	<ol>
		<li>Combine 10 &#956;L of SSPI 10X buffer, 4 &#956;L of SSPI enzyme at a concentration of 5 U/&#956;L, the equivalent volume of 5 &#956;g of vector miniprep DNA, and sterile ddH2O to 100 &#956;L.</li>
		<li>Incubate the digest for 3 hours at 37 &#176;C.</li>
		<li>Run the digest on a 1.0% agarose gel for the extraction of vector DNA.</li>
		<li>Use a gel extraction kit to perform extraction and purification. Suspend the final volume of vector DNA in 30 &#956;L of ddH2O and store it at -20 &#176;C.</li>
	</ol>
	</li>
	<li>Prepare the DNA inserts for N1-391 and P1-126 using the N1-391 Forward Primer, N1-391 Reverse Primer, P1-126 Forward Primer, and P1-126 Reverse Primer (Table 1). 
	NOTE: There is sufficient overlap with the linearized vector to ensure a melting temperature of between 55 &#176;C and 60 &#176;C. For the reverse primer, there is sufficient overlap with the reverse complementary strand of the linearized vector for the same reason.
	<ol>
		<li>Perform PCR amplification of the DNA insert using the conditions in Table 2 and Table 3.</li>
		<li>Extract the amplified DNA insert. Run the PCR products from the previous step on a 1.0% agarose gel, then extract and purify the bands by gel extraction. Suspend the final volume of extracted DNA in 15 &#956;L of ddH2O.</li>
	</ol>
	</li>
	<li>T4 DNA polymerase treatment of vector and insert DNA (Table 4). 
	NOTE: Treatment must be performed separately for the vector DNA and the insert DNA.
	<ol>
		<li>Incubate the mixture for 40 minutes at room temperature. Then, heat-inactivate the polymerase at 75 &#176;C for 20 minutes. Store the reaction mixture at -20 &#176;C.</li>
	</ol>
	</li>
	<li>Anneal the LIC vector and the insert vector.
	<ol>
		<li>Set up a negative control with 2 &#956;L of LIC vector DNA and 2 &#956;L of sterile ddH2O.</li>
		<li>Combine &#160;2 &#956;L of insert DNA and 2 &#956;L of LIC vector DNA from the previous T4 DNA polymerase reactions in a 0.2 mL tube.</li>
		<li>Perform the annealing reaction at room temperature for 10 minutes.</li>
		<li>Quench the reaction with 1.3 &#956;L of EDTA at a concentration of 25 mM.</li>
		<li>Transform the reaction into 100 &#956;L of E. coli Top10 competent cells and plate them on an ampicillin selection plate23,24.</li>
	</ol>
	</li>
	<li>Identify the positive constructs.
	<ol>
		<li>Prepare the plasmid miniprep solution. This can be done through colony picking and inoculation in LB media. Usually, 3 colonies are sufficient.</li>
		<li>Incubate the mixture overnight at 37 &#176;C.</li>
		<li>Centrifuge the mixture at 4,560 x g for 10 minutes and discard the supernatant.</li>
		<li>Resuspend the pellets in 250 &#956;L of P1 buffer and prepare plasmid minipreps using a spin miniprep kit.</li>
		<li>Conduct a digestion analysis of the miniprep product using AseI or other restriction enzymes.</li>
		<li>Load samples on 0.8% agarose gel and run the digested plasmid. Analyze the gel under a UV lamp.</li>
		<li>Use a sequencing service to validate the sequence of the positive product.</li>
	</ol>
	</li>
	<li>Obtain the coexpression DNA insert.
	<ol>
		<li>Perform PCR to obtain N1-391 and P1-126 using the previously constructed 2BT-10 N1-391 and 2BT-10 P1-126 as templates.</li>
		<li>Perform the 1st PCR to obtain N1-391 from the 2BT-10 N1-391 construct using the PCR conditions in Table 2 and Table 3 with the N1-391 Forward primer and Reverse Primer &#160;5 &#769;-GTGAAGATCCTGGCTGATGCAATGCGGCGGCG 
		CGCCGCGATCGCGGATCC-3 &#769;.</li>
		<li>Perform the 2nd PCR to obtain P1-126 from the 2BT-10 P1-126 construct using the Forward primer: 5&#8217;-CCGCCGCATTGCATCAGCCAGGATCTTCACTGC 
		AGGACTCGAGTTCTAGA-3 &#769;and the P1-126 Reverse primer (use the PCR conditions in Table 2 and Table 3).</li>
		<li>Finally, perform overlap PCR on the mixed products of the previous 2 PCR reactions to merge N1-391 and P1-126. Use the &#160;N1-391 Forward primer and P1-126 Reverse primer. Use the PCR conditions in Table 5 and Table 6.</li>
	</ol>
	</li>
	<li>Join the vector and the DNA insert.
	<ol>
		<li>Treat the overlap PCR product with T4 DNA polymerase following the protocol in step 1.3.</li>
		<li>Anneal the LIC vector and PCR product following the protocol in step 1.4.</li>
		<li>Identify the positive constructs following the protocol in step 1.5.</li>
	</ol>
	</li>
</ol>
2. Protein expression and purification
NOTE: Use E. coli for the bi-cistronic construct of the coexpression of both N and P. Culture the cells at 37 &#176;C, but carry out the expression at a reduced temperature (16 &#176;C) overnight. Purify the protein complexes through a combination of cobalt column, ion exchange, and size exclusion chromatography (Figure 2).
<ol>
	<li>Use the E. coli BL21(DE3) strain for protein production. Grow 4 L cell cultures at 37 &#176;C in LB (Luria Broth) medium until OD600 reaches 0.6.</li>
	<li>Lower the temperature to 16 &#176;C. An hour later, induce the expression with 0.5 mM isopropyl 1-thio--D-galactopyranoside (IPTG) overnight.</li>
	<li>Centrifuge the cells at 4,104 x g for 25 min and then discard the supernatant.</li>
	<li>Resuspend the cell pellets in 200 mL of lysis buffer A (50 mM sodium phosphate, pH 7.4, 500 mM NaCl, 5 mM imidazole, 10% glycerol, and 0.2% NP40). Use 50 mL of lysis buffer to resuspend the cell pellets from 1 L of cell culture.</li>
	<li>Lyse the cells by sonication for 15 min, 3 seconds on, and 3 seconds off. Then centrifuge cells at 37,888 x g for 40 min. 
	NOTE: The protocol can be paused by freezing the cells before sonication in a -80 &#176;C freezer.</li>
	<li>Load the supernatant into a cobalt gravity column (diameter x length: 2.5 cm x 10 cm) with ~10mL of beads pre-equilibrated with 5-10 column volumes (CV) of lysis buffer.</li>
	<li>Wash the column with 5 CV of buffer B (50 mM Tris-HCl pH 7.4, 1 M NaCl, 10% glycerol, and 5 mM imidazole) and 5 CV of buffer C (50 mM Tris-HCl pH 7.4, 500 mM NaCl, 10% glycerol, and 5 mM imidazole).</li>
	<li>Elute the protein from the beads using 2 CV of buffer D (50 mM Tris-HCl pH 7.4, 500 mM NaCl, and 250 mM imidazole).</li>
	<li>Dilute the eluted protein 5x with QA buffer (50 mM Tris-HCl pH 8.0, 5% Glycerol) for the Q column.</li>
	<li>Wash the 5 mL of Q column with QA buffer to equilibrate the column, then load the diluted sample into the Q column using the peristaltic pump (e.g., Rabbit).</li>
	<li>Load the Q column into the HPLC machine along with QA buffer and QB buffer(50 mM Tris-HCl pH7.4, 1.5 M NaCl, 5% glycerol). Set up the flow rate as 1 mL/min.</li>
	<li>Run the &#8220;pump wash&#8221; program to wash the machine with QB buffer followed by QA buffer (1-2 CVs/each). Set the system flow to 3 mL/min.</li>
	<li>Set the UV1 to 280 nm and UV2 to 260 nm. Use a 96 deep-well plate to collect the fractions.</li>
	<li>Elute proteins using a stepwise gradient of elution agent (QB Buffer) applying 3-4 CV of each concentration, increasing the percentage by 5% each time starting at 0% QB. N0P&#160; protein complex will come out at 15% QB Buffer.</li>
	<li>Once all of the protein is eluted, wash the column with 100% QB Buffer (2 CV).</li>
	<li>Isolate the protein by gel filtration Superdex 200 Increase 10/300 GL column (diameter x length: 1.0 cm x 30 cm) and equilibrate with buffer E (20 mM HEPES pH 7.4 and 200 mM NaCl).</li>
	<li>Analyze protein-containing fractions by SDS-PAGE.</li>
</ol>
3.&#160;In vitro assembly of the virus-specific NC 
NOTE: The in vitro assembly of the RSV-specific NC (N:RNA) was performed by incubating the prepared N0P complex with RNA oligos. Then, SEC chromatography was used to separate the assembly complex from the N0P and excess RNA (Figure 2).
<ol>
	<li>Mix and incubate the purified N0P complex with RNA oligo with the molecular ratio of 1:1.5 at room temperature for 1 hour, usually 1 mL of the protein N0P with a&#160;concentration of 1 mg/mL is enough for the next step. Set up the control sample, which only contains the same amount of N0P protein.</li>
	<li>Pre-equilibrate the gel filtration Superdex 200 Increase 10/300 GL column with the buffer E (20 mM HEPES, pH 7.4, 200 mM NaCl).</li>
	<li>Centrifuge the sample with 21,130 x g for 15 min, remove any precipitation and load the supernatant to the SEC column.</li>
	<li>Compare the SEC chromatography images of N:RNA assembly sample and N0P control sample, combine the A260/A280 ratio to identify which peaks are the assembled N-RNA, N0P, and free RNA.</li>
	<li>Collect the peak fractions, run the SDS-PAGE gel, or make grids.</li>
	<li>For the assembly N-RNA complex, collect all the fractions of N-RNA peak, do the RNA extraction and run the Urea-PAGE gel to double-check the length of specific RNA, which is the same as mixed and incubated at the first step.</li>
</ol>
4. Making negative stain grids
NOTE: Negative stain electron microscopy (EM) is a method in which the molecules are adsorbed to a carbon film and then embedded in a layer of heavy metal atoms. Negative stain EM produces a high image contrast, making it easy to see and computationally align the particles. Another advantage is that the adsorption of the particles to a carbon film usually induces the molecules to adhere to the grid with few preferred orientations. When the molecules are in a similar orientation, it is easy to separate them into structurally distinct classes. Negative stain EM is thus the appropriate technique to guide sample preparation25,26 (Figure 3).
<ol>
	<li>Microwave or heat 5 mL of ddH2O in a small glass beaker&#160;using a Tungsten heater until it is boiling.&#160;</li>
	<li>Weigh 37.5 mg of uranyl formate and add to 5 mL of heated ddH2O to make a 0.75% uranyl formate staining solution. Stir under an aluminum foil covered beaker to protect from light.</li>
	<li>Add 4 &#956;L of 10 M NaOH to the staining solution and continue to stir for 15 min, protected from the light.</li>
	<li>Filter the solution through a 0.22 mm filter into a test tube.</li>
	<li>Use glow discharge to make the continuous carbon-coated EM grids hydrophilic27. 
	NOTE: The grids are placed inside a chamber connected to a power supply. When high voltage is applied, the gas within the chamber ionizes, and the negatively charged ions deposit on the carbon grids to make them hydrophilic.</li>
	<li>Cut and fold a parafilm strip. Pipet 2 drops of 40 &#956;L of the buffer on one side of the parafilm, and pipet another 2 drops of 40 &#956;L of staining solution to the other side.</li>
	<li>To make the EM carbon grids, apply 3 &#956;L of protein sample for 1 minute.</li>
	<li>Blot the grids against a blotting paper. 
	NOTE: The grids are washed 2x with buffer, and 1x with the 0.75% uranyl formate staining solution blotted after each step.</li>
	<li>Hold the grid surface in the second drop of 0.75% uranyl formate staining solution for 30 seconds.</li>
	<li>Blot the grid against a blotting paper to remove excess stain solution and allow the grid to air-dry.</li>
	<li>Store the grids in the grid box before imaging.</li>
</ol>

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G., 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=Crystal+structure+of+a+nucleocapsid-like+nucleoprotein-RNA+complex+of+respiratory+syncytial+virus.">Crystal structure of a nucleocapsid-like nucleoprotein-RNA complex of respiratory syncytial virus.</a> Science. 326 (5957), 1279-1283 (2009).</li><li>Galloux, M., 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=Characterization+of+a+viral+phosphoprotein+binding+site+on+the+surface+of+the+respiratory+syncytial+nucleoprotein.">Characterization of a viral phosphoprotein binding site on the surface of the respiratory syncytial nucleoprotein.</a> Journal of Virology. 86 (16), 8375-8387 (2012).</li><li>Milles, S., 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=Self-Assembly+of+Measles+Virus+Nucleocapsid-like+Particles:+Kinetics+and+RNA+Sequence+Dependence.">Self-Assembly of Measles Virus Nucleocapsid-like Particles: Kinetics and RNA Sequence Dependence.</a> Angewandte Chemie Interntional Edition English. 55 (32), 9356-9360 (2016).</li><li>Desfosses, A., 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=Assembly+and+cryo-EM+structures+of+RNA-specific+measles+virus+nucleocapsids+provide+mechanistic+insight+into+paramyxoviral+replication.">Assembly and cryo-EM structures of RNA-specific measles virus nucleocapsids provide mechanistic insight into paramyxoviral replication.</a> Proceedings of the National Academy of Sciences of the United States of America. 116 (10), 4256-4264 (2019).</li></ol>

The authors have nothing to disclose.

The known nucleocapsid-like particle (NCLP) structures of the nonsegmented negative-sense (NNS) RNA viruses show that the assembled NCLPs are the complex N with host cellular RNAs when overexpressed in bacterial or eukaryotic expression systems15,16,17,18,19. Previous studies have attempted to get the RNA free N with a variety of methods, such as the RNase A d...

Nonsegmented negative-sense (NNS) RNA viruses include many significant human pathogens, such as rabies, Ebola, and respiratory syncytial virus (RSV)1,2. RSV is the leading cause of respiratory illness such as bronchiolitis and pneumonia in young children and older adults worldwide3. Currently, no effective vaccines or antiviral therapies are available to prevent or treat RSV4. As part of the life cycle, the RSV genome serves as the template for replication by the RSV RNA dependent RNA polymerase to produce an antigenome, which in turn acts as the template to generate a progeny genome. Both genome and antigenome RNAs are entirely encapsidated by the nucleoprotein (N) to form the nucleocapsids (NCs)3. Because the NCs serve as the templates for both replication and transcription by the RSV polymerase, proper NC assembly is crucial for the polymerase to gain access to the templates for RNA synthesis5. Interestingly, based on the structural analyses of the NNS viral polymerases, it is hypothesized that several N proteins transiently dissociate from the NCs to allow the access of the polymerase and rebind to RNA after the RNA synthesis6,7,8,9,10,11,12. &#160;
Currently, the RSV RNA polymerization assay has been established using purified RSV polymerase on short naked RNA templates13,14. However, the activities of the RSV polymerase do not reach optimal, as observed in the non-processive and abortive products generated by the RSV polymerase when using naked RNA templates. The lack of NC with virus-specific RNA is a primary barrier for the further mechanistic understanding of the RSV RNA synthesis. Therefore, using an authentic RNA template becomes a critical need to advance the fundamental knowledge of RSV RNA synthesis. The known structures of the nucleocapsid-like particles (NCLPs) from RSV and other NNS RNA viruses reveal that the RNAs in the NCLPs are either random cellular RNAs or average viral genomic RNAs15,16,17,18,19. Together, the main hurdle is that N binds non-specifically to cellular RNAs to form NCLPs when N is overexpressed in the host cells.
To overcome this hurdle, we established a protocol to obtain RNA-free (N0) first and assemble N0 with authentic viral genomic RNA into NCLPs20. The principle of this protocol is to obtain a large quantity of recombinant RNA-free N (N0) by co-expressing N with a chaperone, the N-terminal domain of RSV phosphoprotein (PNTD). The purified N0P could be stimulated and assembled into NCLPs by adding RSV-specific RNA oligos, and during the assembly process, the chaperone PNTD is displaced upon the addition of RNA oligos.
Here, we detail a protocol for the generation and assembly of RSV RNA-specific NCs. In this protocol, we describe the molecular cloning, protein preparation, in vitro assembly, and validation of the complex assembly. We highlight the cloning strategy to generate bi-cistronic constructs for protein coexpression for molecular cloning. For protein preparation, we describe the procedures of cell culture, protein extraction, and the purification of the protein complex. Then we discuss the method for in vitro assembly of the RSV RNA-specific NCs. Finally, we use size exclusion chromatography (SEC) and negative stain electron microscopy (EM) to characterize and visualize the assembled NCLPs.

<table border="0" cellpadding="0" cellspacing="0" style="width:1293px;" width="1293">
	<colgroup>
		<col />
		<col />
		<col />
		<col />
	</colgroup>
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Agarose</td>
			<td style="width:302px;">SIgma</td>
			<td style="width:301px;">A9539-500G</td>
			<td style="width:319px;">making construct using LIC method</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Amicon Ultra-15 Centrifugal Filter Unit</td>
			<td>Millipore</td>
			<td>UFC901024</td>
			<td>concentrate the protein sample</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Ampicillin sodium</td>
			<td style="width:302px;">GOLD BIOTECHNOLOGY</td>
			<td style="width:301px;">5118.111317A</td>
			<td>antibiotic for cell culture</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">AseI</td>
			<td style="width:302px;">NEB</td>
			<td style="width:301px;">R0526S</td>
			<td>making construct using LIC method</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Cobalt (High Density) Agarose Beads</td>
			<td style="width:302px;">Gold Bio</td>
			<td>H-310-500</td>
			<td>For purification of His-tag protein</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Corning LSE Digital Dry Bath Heater</td>
			<td style="width:302px;">CORNING</td>
			<td style="width:301px;">6885-DB</td>
			<td>Heate the sample</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">dCTP</td>
			<td style="width:302px;">Invitrogen</td>
			<td style="width:301px;">10217016</td>
			<td>making construct using LIC method</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">dGTP</td>
			<td style="width:302px;">Invitrogen</td>
			<td style="width:301px;">10218014</td>
			<td>making construct using LIC method</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Glycerol</td>
			<td style="width:302px;">Sigma</td>
			<td style="width:301px;">G5516-4L</td>
			<td>making solution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">HEPES</td>
			<td style="width:302px;">Sigma</td>
			<td style="width:301px;">H3375-100G</td>
			<td>making solution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">HiTrap Q HP</td>
			<td style="width:302px;">Sigma</td>
			<td style="width:301px;">GE29-0513-25</td>
			<td>Protein purification</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Imidazole</td>
			<td style="width:302px;">Sigma</td>
			<td style="width:301px;">I5513-100G</td>
			<td>making solution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">IPTG (Isopropyl-beta-D-thiogalactopyranoside)</td>
			<td style="width:302px;">GOLD BIOTECHNOLOGY</td>
			<td style="width:301px;">1116.071717A</td>
			<td>induce the expression of protein</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Microcentrifuge Tubes</td>
			<td style="width:302px;">VWR</td>
			<td style="width:301px;">47730-598</td>
			<td>for PCR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Misonix Sonicator XL2020 Ultrasonic Liquid Processor</td>
			<td style="width:302px;">SpectraLab</td>
			<td style="width:301px;">MSX-XL-2020</td>
			<td>sonicator for lysing cell</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Negative stain grids</td>
			<td style="width:302px;">Electron Microscopy Sciences</td>
			<td style="width:301px;">CF400-Cu-TH</td>
			<td>For making negative stain grids</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">New Brunswick Innova 44/44R</td>
			<td style="width:302px;">eppendorf</td>
			<td style="width:301px;">M1282-0000</td>
			<td>Shaker for culturing the cell</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Nonidet P 40 Substitute</td>
			<td style="width:302px;">Sigma</td>
			<td style="width:301px;">74385-1L</td>
			<td>making solution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">OneTaq DNA Polymerase</td>
			<td style="width:302px;">NEB</td>
			<td style="width:301px;">M0480L</td>
			<td>PCR</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">QIAquick Gel Extraction Kit</td>
			<td style="width:302px;">QIAGEN</td>
			<td style="width:301px;">28706</td>
			<td>Purify DNA</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">SSPI-HF</td>
			<td style="width:302px;">NEB</td>
			<td style="width:301px;">R3132S</td>
			<td>making construct using LIC method</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Superose 6 Increase 10/300 GL</td>
			<td style="width:302px;">Sigma</td>
			<td>GE29-0915-96</td>
			<td>Protein purification</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">T4 DNA polymerase</td>
			<td style="width:302px;">Sigma</td>
			<td>70099-3</td>
			<td>making construct using LIC method</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Thermo Scientific Sorvall RC 6 Plus Centrifuge</td>
			<td style="width:302px;">Fisher Scientific</td>
			<td style="width:301px;">36-101-0816</td>
			<td>Centrifuge, highest speed 20,000 rpm</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Trizma hydrochloride</td>
			<td style="width:302px;">Sigma</td>
			<td style="width:301px;">T3253-250G</td>
			<td>making solution</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:371px;">Uranyl Formate</td>
			<td style="width:302px;">Electron Microscopy Sciences</td>
			<td style="width:301px;">22451</td>
			<td>making negative stain solution</td>
		</tr>
	</tbody>
</table>

generation and assembly of virus-specific nucleocapsids of the respiratory syncytial virus

The use of an authentic RNA template is critical to advance the fundamental knowledge of viral RNA synthesis that can guide both mechanistic discovery and assay development in virology. The RNA template of nonsegmented negative-sense (NNS) RNA viruses, such as the respiratory syncytial virus (RSV), is not an RNA molecule alone but rather a nucleoprotein (N) encapsidated ribonucleoprotein complex. Despite the importance of the authentic RNA template, the generation and assembly of such a ribonucleoprotein complex remain sophisticated and require in-depth elucidation. The main challenge is that the overexpressed RSV N binds non-specifically to cellular RNAs to form random nucleocapsid-like particles (NCLPs). Here, we established a protocol to obtain RNA-free N (N0) first by co-expressing N with a chaperone phosphoprotein (P), then assembling N0 with RNA oligos with the RSV-specific RNA sequence to obtain virus-specific nucleocapsids (NCs). This protocol shows how to overcome the difficulty in the preparation of this traditionally challenging viral ribonucleoprotein complex.

Purification of RNA-free N0P protein 
With this protocol, a large-scale soluble heterodimeric RSV N0P complex can be obtained. The full length of N and N terminal part of P proteins were co-expressed with 10X His-Tag on the N protein in E. coli. N0P was purified using a cobalt column, ion exchange, and size exclusion chromatography. N0P contains both the full-length N and N terminal P but did not contain cellular RNA based on the UV absorbance A<s...

Watch this Scientific Journal Video about Generation and Assembly of Virus-Specific Nucleocapsids of the Respiratory Syncytial Virus at JoVE.com

Generation and Assembly of Virus-Specific Nucleocapsids of the Respiratory Syncytial Virus

For in-depth mechanistic analysis of the respiratory syncytial virus (RSV) RNA synthesis, we report a protocol of utilizing the chaperone phosphoprotein (P) for coexpression of the RNA-free nucleoprotein (N0) for subsequent in vitro assembly of the virus-specific nucleocapsids (NCs).

The use of an authentic RNA template is critical to advance the fundamental knowledge of viral RNA synthesis that can guide both mechanistic discovery and ...

generation-assembly-virus-specific-nucleocapsids-respiratory

Universidad de Cartagena UDEC

Research

JoVE Journal

Biochemistry

3.6K Views.  Emory University School of Medicine. For in-depth mechanistic analysis of the respiratory syncytial virus (RSV) RNA synthesis, we report a protocol of utilizing the chaperone phosphoprotein (P) for coexpression of the RNA-free nucleoprotein (N0) for subsequent in vitro assembly of the virus-specific nucleocapsids (NCs).

Video: Generation and Assembly of Virus-Specific Nucleocapsids of the Respiratory Syncytial Virus

Examining Proteasome Assembly with Recombinant Archaeal Proteasomes and Nondenaturing PAGE:  The Case for a Combined Approach

Proteasomes are found in all domains of life. They provide the major route of intracellular protein degradation in eukaryotes, though their assembly is not completely understood. All proteasomes contain a structurally conserved core particle (CP), or 20S proteasome, containing two heptameric&#160;&#946; subunit rings sandwiched between two heptameric&#160;&#945; subunit rings. Archaeal 20S proteasomes are compositionally simpler compared to their eukaryotic counterparts, yet they both share a common assembly mechanism. Consequently, archaeal 20S proteasomes continue to be important models for eukaryotic proteasome assembly. Specifically, recombinant expression of archaeal 20S proteasomes coupled with nondenaturing polyacrylamide gel electrophoresis (PAGE) has yielded many important insights into proteasome biogenesis. Here, we discuss a means to improve upon the usual strategy of coexpression of archaeal proteasome &#945; and &#946; subunits prior to nondenaturing PAGE. We demonstrate that although rapid and efficient, a coexpression approach alone can miss key assembly intermediates. In the case of the proteasome, coexpression may not allow detection of the half-proteasome, an intermediate containing one complete &#945;-ring and one complete &#946;-ring. However, this intermediate is readily detected via lysate mixing. We suggest that combining coexpression with lysate mixing yields an approach that is more thorough in analyzing assembly, yet remains labor nonintensive. This approach may be useful for the study of other recombinant multiprotein complexes.

This protocol uses both subunit coexpression and postlysis subunit mixing for a more thorough examination of recombinant proteasome assembly.

Proteasomes are found in all domains of life. They provide the major route of intracellular protein degradation in eukaryotes, though their assembly is ...

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

Mitochondria are essential organelles involved in numerous metabolic pathways in plants, most notably the production of adenosine triphosphate (ATP) from the oxidation of reduced compounds such as nicotinamide adenine dinucleotide (NADH) and flavin adenine dinucleotide (FADH2). The complete annotation of the Arabidopsis thaliana genome has established it as the most widely used plant model system, and thus the need to purify mitochondria from a variety of organs (leaf, root, or flower) is necessary to fully utilize the tools that are now available for Arabidopsis to study mitochondrial biology. Mitochondria are isolated by homogenization of the tissue using a variety of approaches, followed by a series of differential centrifugation steps producing a crude mitochondrial pellet that is further purified using continuous colloidal density gradient centrifugation. The colloidal density material is subsequently removed by multiple centrifugation steps. Starting from 100 g of fresh leaf tissue, 2 - 3 mg of mitochondria can be routinely obtained. Respiratory experiments on these mitochondria display typical rates of 100 - 250 nmol O2 min-1 mg total mitochondrial protein-1 (NADH-dependent rate) with the ability to use various substrates and inhibitors to determine which substrates are being oxidized and the capacity of the alternative and cytochrome terminal oxidases. This protocol describes an isolation method of mitochondria from Arabidopsis thaliana leaves using continuous colloidal density gradients and an efficient respiratory measurements of purified plant mitochondria.

Isolation and Respiratory Measurements of Mitochondria from Arabidopsis thaliana

As mitochondria are only a small percentage of the plant cell, they need to be purified for a range of studies. Mitochondria can be isolated from a variety of plant organs by homogenization, followed by differential and density gradient centrifugation to obtain a highly purified mitochondrial fraction.

Mitochondria are essential organelles involved in numerous metabolic pathways in plants, most notably the production of adenosine triphosphate (ATP) from ...

Generation of Native, Untagged Huntingtin Exon1 Monomer and Fibrils Using a SUMO Fusion Strategy

Huntington&#39;s Disease (HD) is an inherited fatal neurodegenerative disease caused by a CAG expansion (&#8805;36) in the first exon of the HD gene, resulting in the expression of the Huntingtin protein (Htt) or N-terminal fragments thereof with an expanded polyglutamine (polyQ) stretch.
The exon1 of the Huntingtin protein (Httex1) is the smallest Htt fragment that recapitulates many of the features of HD in cellular and animal models and is one of the most widely studied fragments of Htt. The small size of Httex1 makes it experimentally more amenable to biophysical characterization using standard and high-resolution techniques in comparison to longer fragments or full-length Htt. However, the high aggregation propensity of mutant Httex1 (mHttex1) with increased polyQ content (&#8805;42) has made it difficult to develop efficient expression and purification systems to produce these proteins in sufficient quantities and make them accessible to scientists from different disciplines without the use of fusion proteins or other strategies that alter the native sequence of the protein. We present here a robust and optimized method for the production of milligram quantities of native, tag-free Httex1 based on the transient fusion of small ubiquitin related modifier (SUMO). The simplicity and efficiency of the strategy will eliminate the need to use non-native sequences of Httex1, thus making this protein more accessible to researchers and improving the reproducibility of experiments across different laboratories. We believe that these advances will also facilitate future studies aimed at elucidating the structure-function relationship of Htt as well as developing novel diagnostic tools and therapies to treat or slow the progression of HD.

Here, we present a robust and optimized protocol for the production of milligram quantities of native, tag-free monomers and fibrils of the exon1 of the Huntingtin protein (Httex1) based on the transient fusion of small ubiquitin related modifier (SUMO).

Huntington&#39;s Disease (HD) is an inherited fatal neurodegenerative disease caused by a CAG expansion (&#8805;36) in the first exon of the HD gene, ...

Manipulating Living Cells to Construct Stable 3D Cellular Assembly Without Artificial Scaffold

Regenerative medicine and tissue engineering offer several advantages for the treatment of intractable diseases, and several studies have demonstrated the importance of 3-dimensional (3D) cellular assemblies in these fields. Artificial scaffolds have often been used to construct 3D cellular assemblies. However, the scaffolds used to construct cellular assemblies are sometimes toxic and may change the properties of the cells. Thus, it would be beneficial to establish a non-toxic method for facilitating cell-cell contact. In this paper, we introduce a novel method for constructing stable cellular assemblies by using optical tweezers with dextran. One of the advantages of this method is that it establishes stable cell-to-cell contact within a few minutes. This new method allows the construction of 3D cellular assemblies in a natural hydrophilic polymer and is expected to be useful for constructing next-generation 3D single-cell assemblies in the fields of regenerative medicine and tissue engineering.

We demonstrate a novel method for constructing a single-cell-based 3-dimensional (3D) assembly without an artificial scaffold.

Regenerative medicine and tissue engineering offer several advantages for the treatment of intractable diseases, and several studies have demonstrated the ...

How to Stabilize Protein: Stability Screens for Thermal Shift Assays and Nano Differential Scanning Fluorimetry in the Virus-X Project

The Horizon2020 Virus-X project was established in 2015 to explore the virosphere of selected extreme biotopes and discover novel viral proteins. To evaluate the potential biotechnical value of these proteins, the analysis of protein structures and functions is a central challenge in this program. The stability of protein sample is essential to provide meaningful assay results and increase the crystallizability of the targets. The thermal shift assay (TSA), a fluorescence-based technique, is established as a popular method for optimizing the conditions for protein stability in high-throughput. In TSAs, the employed fluorophores are extrinsic, environmentally-sensitive dyes. An alternative, similar technique is nano differential scanning fluorimetry (nanoDSF), which relies on protein native fluorescence. We present here a novel osmolyte screen, a 96-condition screen of organic additives designed to guide crystallization trials through preliminary TSA experiments. Together with previously-developed pH and salt screens, the set of three screens provides a comprehensive analysis of protein stability in a wide range of buffer systems and additives. The utility of the screens is demonstrated in the TSA and nanoDSF analysis of lysozyme and Protein X, a target protein of the Virus-X project.

A protocol is presented to rapidly test the thermal stability of proteins in a variety of conditions through thermal shift assays and nano differential scanning fluorimetry. Buffer systems, salts and additives, together comprising three unique stability screens, are assayed with proteins to identify suitable buffers for functional and structural studies.

The Horizon2020 Virus-X project was established in 2015 to explore the virosphere of selected extreme biotopes and discover novel viral proteins. To ...

Hybrid Clear/Blue Native Electrophoresis for the Separation and Analysis of Mitochondrial Respiratory Chain Supercomplexes

Complexes of the oxidative phosphorylation machinery form supramolecular protein arrangements named supercomplexes (SCs), which are believed to confer structural and functional advantages to mitochondria. SCs have been identified in many species, from yeast to mammal, and an increasing number of studies report disruption of their organization in genetic and acquired human diseases. As a result, an increasing number of laboratories are interested in analyzing SCs, which can be methodologically challenging. This article presents an optimized protocol that combines the advantages of Blue- and Clear-Native PAGE methods to resolve and analyze SCs in a time-effective manner. With this hybrid CN/BN-PAGE method, mitochondrial SCs extracted with optimal amounts of the mild detergent digitonin are exposed briefly to the anionic dye Coomassie Blue (CB) at the beginning of the electrophoresis, without exposure to other detergents. This short exposure to CB allows to separate and resolve SCs as effectively as with traditional BN-PAGE methods, while avoiding the negative impact of high CB levels on in-gel activity assays, and labile protein-protein interactions within SCs. With this protocol it is thus possible to combine precise and rapid in gel activity measurements with analytical techniques involving 2D electrophoresis, immuno-detection, and/or proteomics for advanced analysis of SCs.

Here we present a protocol to extract, resolve and identify mitochondrial supercomplexes which minimizes exposure to detergents and Coomassie Blue. This protocol offers an optimal balance between resolution, and preservation of enzyme activities, while minimizing the risk of losing labile protein-protein interactions.

Complexes of the oxidative phosphorylation machinery form supramolecular protein arrangements named supercomplexes (SCs), which are believed to confer ...

Real-Time, Semi-Automated Fluorescent Measurement of the Airway Surface Liquid pH of Primary Human Airway Epithelial Cells

In recent years, the importance of mucosal surface pH in the airways has been highlighted by its ability to regulate airway surface liquid (ASL) hydration, mucus viscosity and activity of antimicrobial peptides, key parameters involved in innate defense of the lungs. This is of primary relevance in the field of chronic respiratory diseases such as cystic fibrosis (CF) where these parameters are dysregulated. While different groups have studied ASL pH both in vivo and in vitro, their methods report a relatively wide range of ASL pH values and even contradictory findings regarding any pH differences between non-CF and CF cells. Furthermore, their protocols do not always provide enough details in order to ensure reproducibility, most are low throughput and require expensive equipment or specialized knowledge to implement, making them difficult to establish in most labs. Here we describe a semi-automated fluorescent plate reader assay that enables the real-time measurement of ASL pH under thin film conditions that more closely resemble the in vivo situation. This technique allows for stable measurements for many hours from multiple airway cultures simultaneously and, importantly, dynamic changes in ASL pH in response to agonists and inhibitors can be monitored. To achieve this, the ASL of fully differentiated primary human airway epithelial cells (hAECs) are stained overnight with a pH-sensitive dye in order to allow for the reabsorption of the excess fluid to ensure thin film conditions. After fluorescence is monitored in the presence or absence of agonists, pH calibration is performed in situ to correct for volume and dye concentration. The method described provides the required controls to make stable and reproducible ASL pH measurements, which ultimately could be used as a drug discovery platform for personalized medicine, as well as adapted to other epithelial tissues and experimental conditions, such as inflammatory and/or host-pathogen models.

We present a protocol to make dynamic measurements of the airway surface liquid pH under thin film conditions using a plate-reader.

In recent years, the importance of mucosal surface pH in the airways has been highlighted by its ability to regulate airway surface liquid (ASL) ...

Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Chromatin is a higher-order structure that packages eukaryotic DNA. Chromatin undergoes dynamic alterations according to the cell cycle phase and in response to environmental stimuli. These changes are essential for genomic integrity, epigenetic regulation, and DNA metabolic reactions such as replication, transcription, and repair. Chromatin assembly is crucial for chromatin dynamics and is catalyzed by histone chaperones. Despite extensive studies, the mechanisms by which histone chaperones enable chromatin assembly remains elusive. Moreover, the global features of nucleosomes organized by histone chaperones are poorly understood. To address these problems, this work describes a unique single-molecule imaging technique named DNA curtain, which facilitates the investigation of the molecular details of nucleosome assembly by histone chaperones. DNA curtain is a hybrid technique that combines lipid fluidity, microfluidics, and total internal reflection fluorescence microscopy (TIRFM) to provide a universal platform for real-time imaging of diverse protein-DNA interactions.Using DNA curtain, the histone chaperone function of Abo1, the Schizosaccharomyces pombe bromodomain-containing AAA+ ATPase, is investigated, and the molecular mechanism underlying histone assembly of Abo1 is revealed. DNA curtain provides a unique approach for studying chromatin dynamics.

DNA curtain, a high-throughput single-molecule imaging technique, provides a platform for real-time visualization of diverse protein-DNA interactions. The present protocol utilizes the DNA curtain technique to investigate the biological role and molecular mechanism of Abo1, a Schizosaccharomyces pombe bromodomain-containing AAA+ ATPase.

Chromatin is a higher-order structure that packages eukaryotic DNA. Chromatin undergoes dynamic alterations according to the cell cycle phase and in ...

Advancing High-Resolution Imaging of Virus Assemblies in Liquid and Ice

Interest in liquid-electron microscopy (liquid-EM) has skyrocketed in recent years as scientists can now observe real-time processes at the nanoscale. It is extremely desirable to pair high-resolution cryo-EM information with dynamic observations as many events occur at rapid timescales - in the millisecond range or faster. Improved knowledge of flexible structures can also assist in the design of novel reagents to combat emerging pathogens, such as SARS-CoV-2. More importantly, viewing biological materials in a fluid environment provides a unique glimpse of their performance in the human body. Presented here are newly developed methods to investigate the nanoscale properties of virus assemblies in liquid and vitreous ice. To accomplish this goal, well-defined samples were used as model systems. Side-by-side comparisons of sample preparation methods and representative structural information are presented. Sub-nanometer features are shown for structures resolved in the range of ~3.5-&#197;-10 &#197;. Other recent results that support this complementary framework include dynamic insights of vaccine candidates and antibody-based therapies imaged in liquid. Overall, these correlative applications advance our ability to visualize molecular dynamics, providing a unique context for their use in human health and disease.

Here protocols are described to prepare virus assemblies suitable for liquid-EM and cryo-EM analysis at the nanoscale using transmission electron microscopy.

Interest in liquid-electron microscopy (liquid-EM) has skyrocketed in recent years as scientists can now observe real-time processes at the nanoscale. It ...

Using Microfluidics and Fluorescence Microscopy to Study the Assembly Dynamics of Single Actin Filaments and Bundles

In order to decipher the complex molecular mechanisms that regulate the assembly and disassembly of actin filaments, it is a great asset to monitor individual reactions live in well-controlled conditions. To do so, live single-filament experiments have emerged over the past 20 years, mostly using total internal reflection fluorescence (TIRF) microscopy, and have provided a trove of key results. In 2011, in order to further expand the possibilities of these experiments and to avoid recurring problematic artifacts, we introduced simple microfluidics in these assays. This study details our basic protocol, where individual actin filaments are anchored by one end to the passivated coverslip surface, align with the flow, and can be successively exposed to different protein solutions. We also present the protocols for specific applications and explain how controlled mechanical forces can be applied, thanks to the viscous drag of the flowing solution. We highlight the technical caveats of these experiments and briefly present possible developments based on this technique. These protocols and explanations, along with today&#39;s availability of easy-to-use microfluidics equipment, should allow non-specialists to implement this assay in their labs.

We present protocols for simple actin filament microfluidic assays, in combination with fluorescence microscopy, that allow one to accurately monitor individual actin filaments in real-time while sequentially exposing them to different protein solutions.

In order to decipher the complex molecular mechanisms that regulate the assembly and disassembly of actin filaments, it is a great asset to monitor ...

Generation and Assembly of Virus-Specific Nucleocapsids of the Respiratory Syncytial Virus

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Deciphering Molecular Mechanism of Histone Assembly by DNA Curtain Technique

Advancing High-Resolution Imaging of Virus Assemblies in Liquid and Ice

Using Microfluidics and Fluorescence Microscopy to Study the Assembly Dynamics of Single Actin Filaments and Bundles