Name: Author Spotlight: Exploring Cloning Techniques for Full-Length DNA Fragments
Uploaded: 2024-05-17T14:15:00
Description: The construction of gene expression vectors is an important component of laboratory work in experimental biology. With technical advancements like Gibson ...

This work was supported by the financial support of the doctoral research initiation funds provided by the China West Normal University (No. 20E059).

1. Preparation of the template of the PRRSV gene
<ol>
	<li>Thaw the virus stock in 1 mL of RNA extraction reagent (see Table of Materials).</li>
	<li>Add 0.2 mL of chloroform and mix thoroughly. Incubate for 3 min.</li>
	<li>Centrifuge the mixture for 15 min at 12,000 &#215; g at 4 &#176;C. 
	NOTE: The mixture is divided into three phases, namely, a colorless aqueous phase, an interphase, and a red phenol-chloroform phase.</li>
	<li>Pipet the colorless aqueous phase out a...

Cloning the Full-Length PRRSV Gene in the pVAX1 Expression Vector

<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=Enzymatic+assembly+of+DNA+molecules+up+to+several+hundred+kilobases.">Enzymatic assembly of DNA molecules up to several hundred kilobases.</a> Nat Methods. 6 (5), 343-345 (2009).</li><li>Cho, J. G., Dee, S. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Porcine+reproductive+and+respiratory+syndrome+virus.">Porcine reproductive and respiratory syndrome virus.</a> Theriogenology. 66 (3), 655-662 (2006).</li><li>Holtkamp, D. 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L., Lager, K. M., Vorwald, A. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Clinical+consequences+of+exposing+pregnant+gilts+to+strains+of+porcine+reproductive+and+respiratory+syndrome+(PRRS)+virus+isolated+from+field+cases+of+&amp;#34;atypical&amp;#34+PRRS.">Clinical consequences of exposing pregnant gilts to strains of porcine reproductive and respiratory syndrome (PRRS) virus isolated from field cases of &amp;#34;atypical&amp;#34 PRRS.</a> Am. J. Vet. Res. 59 (12), 1540-1544 (1998).</li><li>Dee, S. A., Joo, H. S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Prevention+of+the+spread+of+porcine+reproductive+and+respiratory+syndrome+virus+in+endemically+infected+pig+herds+by+nursery+depopulation.">Prevention of the spread of porcine reproductive and respiratory syndrome virus in endemically infected pig herds by nursery depopulation.</a> Vet Rec. 135 (1), 6-9 (1994).</li><li>Dee, S. A., Joo, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Strategies+to+control+PRRS:+a+summary+of+field+and+research+experiences.">Strategies to control PRRS: a summary of field and research experiences.</a> Vet Microbiol. 55 (1-4), 347-343 (1997).</li><li>Renukaradhya, G. J., Meng, X. J., Calvert, J. G., Roof, M., Lager, K. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Live+porcine+reproductive+and+respiratory+syndrome+virus+vaccines:+Current+status+and+future+direction.">Live porcine reproductive and respiratory syndrome virus vaccines: Current status and future direction.</a> Vaccine. 33 (33), 4069-4080 (2015).</li><li>Conzelmann, K. K., Visser, N., Woensel, P. V., Thiel, H. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+characterization+of+porcine+reproductive+and+respiratory+syndrome+virus,+a+member+of+the+arterivirus+group.">Molecular characterization of porcine reproductive and respiratory syndrome virus, a member of the arterivirus group.</a> Virology. 193 (1), 329-339 (1993).</li><li>Han, M. Y., Yoo, D. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Engineering+the+PRRS+virus+genome:+Updates+and+perspectives.">Engineering the PRRS virus genome: Updates and perspectives.</a> Vet Microbiol. 174 (3), 279-295 (2014).</li><li>Bryksin, A. V., Matsumura, I. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Overlap+extension+PCR+cloning:+a+simple+and+reliable+way+to+create+recombinant+plasmids.">Overlap extension PCR cloning: a simple and reliable way to create recombinant plasmids.</a> Biotechniques. 48 (6), 463-465 (2010).</li><li>Wang, 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=Restriction-based+multiple-fragment+assembly+strategy+to+avoid+random+mutation+during+long+cDNA+cloning.">Restriction-based multiple-fragment assembly strategy to avoid random mutation during long cDNA cloning.</a> J Cancer. 6 (7), 632-635 (2015).</li><li>Zhang, Z. D., 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=The+economic+impact+of+porcine+reproductive+and+respiratory+syndrome+outbreak+in+four+Chinese+farms:+Based+on+cost+and+revenue+analysis.">The economic impact of porcine reproductive and respiratory syndrome outbreak in four Chinese farms: Based on cost and revenue analysis.</a> Front Vet Sci. 9, 1024720 (2022).</li><li>Chen, N. H., 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=High+genetic+diversity+of+Chinese+porcine+reproductive+and+respiratory+syndrome+viruses+from+2016+to+2019.">High genetic diversity of Chinese porcine reproductive and respiratory syndrome viruses from 2016 to 2019.</a> Res Vet Sci. 131, 38-42 (2020).</li><li>Wang, X. 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=Salidroside,+a+phenyl+ethanol+glycoside+from+Rhodiola+crenulata,+orchestrates+hypoxic+mitochondrial+dynamics+homeostasis+by+stimulating+Sirt1/p53/Drp1+signaling.">Salidroside, a phenyl ethanol glycoside from Rhodiola crenulata, orchestrates hypoxic mitochondrial dynamics homeostasis by stimulating Sirt1/p53/Drp1 signaling.</a> J Ethnopharmacol. 293, 115278 (2022).</li><li>Hou, Y., 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=Salidroside+intensifies+mitochondrial+function+of+CoCl2-damaged+HT22+cells+by+stimulating+PI3K-AKT-MAPK+signaling+pathway.">Salidroside intensifies mitochondrial function of CoCl2-damaged HT22 cells by stimulating PI3K-AKT-MAPK signaling pathway.</a> Phytomedicine. 109, 154568 (2023).</li><li>Zhang, S. R., 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=Generation+of+an+infectious+clone+of+HuN4-F112,+an+attenuated+live+vaccine+strain+of+porcine+reproductive+and+respiratory+syndrome+virus+high+copy+plasmid.">Generation of an infectious clone of HuN4-F112, an attenuated live vaccine strain of porcine reproductive and respiratory syndrome virus high copy plasmid.</a> Virol J. 8, 410 (2011).</li><li>Ni, Y. Y., Huang, Y. W., Cao, D. J., Opriessnig, T., Meng, X. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Establishment+of+a+DNA-launched+infectious+clone+for+a+highly+pneumovirulent+strain+of+type+2+porcine+reproductive+and+respiratory+syndrome+virus:+identification+and+in+vitro+and+in+vivo+characterization+of+a+large+spontaneous+deletion+in+the+nsp2+region.">Establishment of a DNA-launched infectious clone for a highly pneumovirulent strain of type 2 porcine reproductive and respiratory syndrome virus: identification and in vitro and in vivo characterization of a large spontaneous deletion in the nsp2 region.</a> Virus Res. 160 (1-2), 264-273 (2011).</li></ol>

The Gibson assembly technique is an in vitro recombination-based molecular cloning method for the assembly of DNA fragments8. This method enables the assembly of multiple DNA fragments into a circular plasmid in a single-tube isothermal reaction. However, one of the obstacles to the Gibson Assembly technique is the acquisition of long fragments from cDNA. The long fragments are difficult to accurately amplify for many reasons. For example, primers are easier to mismatch during long extend...

As an essential technique to construct DNA-based experimental tools for expression in prokaryotic and eukaryotic cells, molecular cloning is a very important component of experimental biology. Molecular cloning involves four processes: the acquisition of insert DNA, ligation of the insert into the appropriate vector, transformation of the recombinant vector into Escherichia coli (E. coli), and identification of the positive clones1. So far, multiple methods have been adopted for joining DNA molecules by using restriction enzymes2,3 and PCR-mediated recombination4,5,6. Homologous recombination, known as seamless cloning technology, is the group of cloning methods, which allows sequence-independent and scarless insertion of one or more fragments of DNA into a vector. This technology includes sequence- and ligation-independent cloning (SLIC), Seamless Ligation Cloning Extract (SLiCE), In-Fusion, and Gibson Assembly. It employs an exonuclease to degrade one strand of the insert and a vector to generate cohesive ends, and either in vivo repair or in vitro recombination to covalently join the insert to the vector by forming phosphodiester bonds. The ability to join a single insert to a vector at any sequence without any scars is very appealing. Furthermore, the technology has the ability to join 5-10 fragments in a predetermined order without sequence restrictions.
As one of many recombinant DNA techniques, the Gibson Assembly technique, currently the most effective cloning method7,8, is a robust and elegant exonuclease-based method to assemble one or multiple linearized DNA fragments seamlessly. The Gibson Assembly reaction is performed under isothermal conditions using a mixture of three enzymes,namely, 5&#39; exonuclease, high-fidelity polymerase, and a thermostable DNA ligase. Single-strand 3&#180; overhangs created by the 5&#39;-3&#39; exonuclease contribute to the annealing of fragments that share complementarity at one end. The high-fidelity polymerase effectively fills the gaps in the annealed single-strand regions by adding dNTPs, and the thermostable DNA ligase seals the nicks to form joint DNA molecules8. Hence, this technical method has been widely used for the construction of gene expression vectors.
Porcine reproductive and respiratory syndrome (PRRS) is a viral disease that leads to reproductive impairment and respiratory failure in pigs caused by PRRSV at any age9. The syndrome is manifested as fever, anorexia, pneumonia, lethargy, depression, and respiratory distress. Moreover, clinical signs, including red/blue discoloration of the ears, have been observed in some epidemics. As a member of the family arterivirus, PRRSV is widely transmitted to pork-producing countries by direct contact and exchange of fluids, including urine, colostrum, and saliva. Due to the spread of PRRSV in the United States, the total economic losses of the pork industry have been estimated to be approximately $664 million per year, based on the breeding scale of 5.8 million sows and 110 million pigs10,11. The Animal and Plant Health Inspection Service report shows that 49.8% of unvaccinated pigs show the presence of PRRSV in serum12 and low levels of PRRSV in infected pigs are excreted through saliva, nasal secretions, urine, and feces13. Multiple strategies have been implemented to control PRRSV propagation14,15,16. In addition to elimination procedures to create completely virus-negative populations or improving biosafety and management, administering vaccines is an effective means of controlling PRRS.
PRRSV is an enveloped, single-stranded, positive-sense RNA virus with a length of approximately 15 kilobases (kb). The PRRSV genome consists of at least 10 open reading frames (ORFs), a short 5&#39; untranslated region (5&#39; UTR), and a poly(A) tail at the 3&#39; terminus (Figure 1A)17. The genome of a negative-stranded RNA virus is non-infectious whereas the genome from positive-stranded RNA viruses is infectious. There are two main strategies for RNA and DNA transfection for generating virus progeny18. However, cloning the full-length fragment corresponding to the RNA genome is crucial for the construction of infectious clones. Due to the long and complex nature of the PRRSV genome, the full-length genome cannot be easily obtained through PCR at once. Additionally, although the artificial synthesis of PRRSV genes is an effective solution, the synthesis of long fragments is often expensive. Hence, to obtain the PRRSV full-length expression vector, we attempted to create it by the multiple inserts homologous recombination method19,20. Unfortunately, we were not able to obtain the full-length gene expression vector. Therefore, in this study, we added appropriate restriction sites to the reverse primer and successfully obtained the pVAX1-PRRSV expression vector by several rounds of homologous recombination reactions. Furthermore, this method can also achieve deletion or mutation of target genes and efficiently join a large number of DNA fragments to the expression vector.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>1 kb plus DNA Ladder</td>
			<td>Tiangen Biochemical Technology (Beijing) Co., Ltd</td>
			<td>MD113-02</td>
			<td></td>
		</tr>
		<tr>
			<td>2x Universal Green PCR Master Mix</td>
			<td>Rong Wei Gene Biotechnology Co., Ltd</td>
			<td>A303-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Sangon Biotech (Shanghai) Co., Ltd.</td>
			<td>9012-36-6</td>
			<td></td>
		</tr>
		<tr>
			<td>Benchtop Microcentrifuge</td>
			<td>Thermo Fisher Scientific&#160; Co., Ltd</td>
			<td>FRESCO17</td>
			<td></td>
		</tr>
		<tr>
			<td>Clean Bench</td>
			<td>Sujing Antai Air Technology&#160; Co., Ltd</td>
			<td>VD-650-U</td>
			<td></td>
		</tr>
		<tr>
			<td>DNA Electrophoresis Equipment</td>
			<td>Cleaver Scientific&#160; Co., Ltd</td>
			<td>170905117</td>
			<td></td>
		</tr>
		<tr>
			<td>DNA Loading Buffer (6x)</td>
			<td>Biosharp Biotechnology Co., Ltd</td>
			<td>BL532A</td>
			<td></td>
		</tr>
		<tr>
			<td>E. Z. N. A. Gel Extraction kit</td>
			<td>Omega Bio-Tek Co., Ltd</td>
			<td>D2500-01</td>
			<td></td>
		</tr>
		<tr>
			<td>E.Z.N.A. Plasmid DNA Mini Kit I</td>
			<td>Omega Bio-Tek Co., Ltd</td>
			<td>D6943-01</td>
			<td></td>
		</tr>
		<tr>
			<td>Electro-heating Standing-temperature Cultivator</td>
			<td>Shanghai Hengyi Scientific Instrument Co., Ltd</td>
			<td>DHP-9082</td>
			<td></td>
		</tr>
		<tr>
			<td>ExonArt Seamless Cloning and Assembly kit</td>
			<td>Rong Wei Gene Biotechnology Co., Ltd</td>
			<td>A101-02</td>
			<td></td>
		</tr>
		<tr>
			<td>ExonScript RT SuperMix with dsDNase</td>
			<td>Rong Wei Gene Biotechnology Co., Ltd</td>
			<td>A502-1</td>
			<td></td>
		</tr>
		<tr>
			<td>FastDigest Eco321 (EcoRV)</td>
			<td>Thermo Fisher Scientific&#160; Co., Ltd</td>
			<td>FD0303</td>
			<td></td>
		</tr>
		<tr>
			<td>FastDigest HindIII</td>
			<td>Thermo Fisher Scientific&#160; Co., Ltd</td>
			<td>FD0504</td>
			<td></td>
		</tr>
		<tr>
			<td>FastDigest NheI</td>
			<td>Thermo Fisher Scientific&#160; Co., Ltd</td>
			<td>FD0974</td>
			<td></td>
		</tr>
		<tr>
			<td>FastDigest NotI</td>
			<td>Thermo Fisher Scientific&#160; Co., Ltd</td>
			<td>FD0596</td>
			<td></td>
		</tr>
		<tr>
			<td>Gel Doc XR</td>
			<td>Bio-Rad Laboratories Co., Ltd</td>
			<td>721BR07925</td>
			<td></td>
		</tr>
		<tr>
			<td>Goldview Nucleic Acid Gel Stain</td>
			<td>Shanghai Yubo Biotechnology Co., Ltd</td>
			<td>YB10201ES03</td>
			<td></td>
		</tr>
		<tr>
			<td>Ice Maker Machine</td>
			<td>Shanghai Bilang Instrument Manufacturing Co., Ltd</td>
			<td>FMB100</td>
			<td></td>
		</tr>
		<tr>
			<td>Invitrogen Platinum SuperFi II DNA Polymerase</td>
			<td>Thermo Fisher Scientific&#160; Co., Ltd</td>
			<td>12361010</td>
			<td></td>
		</tr>
		<tr>
			<td>LB Agar Plate (Kanamycin)</td>
			<td>Sangon Biotech (Shanghai) Co., Ltd.</td>
			<td>B530113-0010</td>
			<td></td>
		</tr>
		<tr>
			<td>LB sterile liquid medium (Kanamycin)</td>
			<td>Sangon Biotech (Shanghai) Co., Ltd.</td>
			<td>B540113-0001</td>
			<td></td>
		</tr>
		<tr>
			<td>Micropipettors</td>
			<td>Thermo Fisher Scientific&#160; Co., Ltd</td>
			<td>&#8212;</td>
			<td></td>
		</tr>
		<tr>
			<td>Microwave Oven</td>
			<td>Panasonic Electric (China) Co., Ltd</td>
			<td>NN-GM333W</td>
			<td></td>
		</tr>
		<tr>
			<td>Orbital Shakers</td>
			<td>Shanghai Zhicheng Analytical Instrument Manufacturing Co., Ltd</td>
			<td>ZHWY-2102C</td>
			<td></td>
		</tr>
		<tr>
			<td>PRRSV virus</td>
			<td>Sichuan Agricultural University</td>
			<td>&#8212;</td>
			<td></td>
		</tr>
		<tr>
			<td>SnapGene</td>
			<td>GSL Biotech, LLC</td>
			<td>v5.1</td>
			<td>To design primers</td>
		</tr>
		<tr>
			<td>T100 PCR Gradient Thermal Cycler</td>
			<td>Bio-Rad Laboratories&#160; Co., Ltd</td>
			<td>T100 Thermal Cycler</td>
			<td></td>
		</tr>
		<tr>
			<td>TAE buffer</td>
			<td>Sangon Biotech (Shanghai) Co., Ltd.</td>
			<td>B040123-0010</td>
			<td></td>
		</tr>
		<tr>
			<td>TRIzol Reagent</td>
			<td>Thermo Fisher Scientific&#160; Co., Ltd</td>
			<td>15596026</td>
			<td>RNA extraction reagent</td>
		</tr>
	</tbody>
</table>

a seamless cloning approach for porcine reproductive and respiratory syndrome virus expression vector construction

The construction of gene expression vectors is an important component of laboratory work in experimental biology. With technical advancements like Gibson Assembly, vector construction becomes relatively simple and efficient. However, when the full-length genome of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) cannot be easily amplified by a single polymerase chain reaction (PCR) from cDNA, or it is difficult to acquire a full-length gene expression vector by homologous recombination of multiple inserts in vitro, the current Gibson Assembly technique fails to achieve this goal.
Consequently, we aimed to divide the PRRSV genome into several fragments and introduce appropriate restriction sites into the reverse primer for obtaining PCR-amplified fragments. After joining the previous DNA fragment into the vector by homologous recombination technology, the new vector acquired the restriction enzyme cleavage site. Thus, we can linearize the vector by using the newly added enzyme cleavage site and introduce the next DNA fragment downstream of the upstream DNA fragment.
The introduced restriction enzyme cleavage site at the 3&#39; end of the upstream DNA fragment will be eliminated, and a new cleavage site will be introduced into the 3&#39; end of the downstream DNA fragment. In this way, we can join DNA fragments to the vector one by one. This method is applicable to successfully construct the PRRSV expression vector and is an effective method for assembling a large number of fragments into the expression vector.

Author Spotlight: Exploring Cloning Techniques for Full-Length DNA Fragments

A Seamless Cloning Approach for Porcine Reproductive and Respiratory Syndrome Virus Expression Vector Construction

This protocol demonstrates the construction of a lengthy and intricate gene expression vector. When a full-length DNA fragment cannot be obtained by a single PCR from cDNA, or the full-length gene expression vector cannot be obtained by multiple-insert homologous recombination in vitro, this method is applicable. Currently, multiple-insert ligation cloning is used to obtain full-length DNA fragment for cloning into a suitable vector.This method can achieve deletion or mutation of target genes and efficiently join a large number of DNA fragments to the expression vector.

In this paper, we present an in vitro recombination system to assemble and repair overlapping DNA molecules using the reverse primer via continually introduced restriction sites (Figure 1B). This system is a simple and efficient procedure comprising the preparation of the linear vector and the insert fragments containing overhangs introduced by PCR with primers having appropriate 5&#39; extension sequences and restriction sites; an in vitro single isothermal reaction and th...

Here, we present a protocol to obtain the pVAX1-PRRSV expression vector by introducing suitable restriction sites at the 3' end of the inserts. We can linearize the vector and join DNA fragments to the vector one by one through homologous recombination technology.

The construction of gene expression vectors is an important component of laboratory work in experimental biology. With technical advancements like Gibson ...