We acknowledge Hannah Fox for help in the preparation of this manuscript. This work was supported by the NIH grant R01AI030612.

1. Cell Culture, Viral Infection, and EdC Labeling (Figure 1)
The following protocol involves working with viruses. Please refer to your institution&#39;s bio-safety protocols regarding safe handling of viruses and other biological agents. This protocol was approved by the Institutional Review Board of the University of Pittsburgh.
<ol>
	<li>Trypsinize a confluent 150 cm2 tissue culture flask of MRC-5 cells and transfer the cells to a 600 cm2</su...

<ol>
	<li>Knipe, D. M., Howley, P. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Fields virology. , (2013).</li><li>Engel, E. A., Song, R., Koyuncu, O. O., Enquist, L. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Investigating+the+biology+of+alpha+herpesviruses+with+MS-based+proteomics.">Investigating the biology of alpha herpesviruses with MS-based proteomics.</a> Proteomics. 15, 1943-1956 (2015).</li><li>Wagner, L. M., DeLuca, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temporal+association+of+herpes+simplex+virus+ICP4+with+cellular+complexes+functioning+at+multiple+steps+in+PolII+transcription.">Temporal association of herpes simplex virus ICP4 with cellular complexes functioning at multiple steps in PolII transcription.</a> PloS One. 8, e78242 (2013).</li><li>Taylor, T. J., Knipe, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomics+of+herpes+simplex+virus+replication+compartments:+association+of+cellular+DNA+replication,+repair,+recombination,+and+chromatin+remodeling+proteins+with+ICP8.">Proteomics of herpes simplex virus replication compartments: association of cellular DNA replication, repair, recombination, and chromatin remodeling proteins with ICP8.</a> J Virol. 78, 5856-5866 (2004).</li><li>Fontaine-Rodriguez, E. C., Taylor, T. J., Olesky, M., Knipe, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomics+of+herpes+simplex+virus+infected+cell+protein+27:+association+with+translation+initiation+factors.">Proteomics of herpes simplex virus infected cell protein 27: association with translation initiation factors.</a> Virology. 330, 487-492 (2004).</li><li>Greco, T. M., Diner, B. A., Cristea, I. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+Impact+of+Mass+Spectrometry-Based+Proteomics+on+Fundamental+Discoveries+in+Virology.">The Impact of Mass Spectrometry-Based Proteomics on Fundamental Discoveries in Virology.</a> Annu Rev Virol. 1, 581-604 (2014).</li><li>Conwell, S. E., White, A. E., Harper, J. W., Knipe, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Identification+of+TRIM27+as+a+novel+degradation+target+of+herpes+simplex+virus+1+ICP0.">Identification of TRIM27 as a novel degradation target of herpes simplex virus 1 ICP0.</a> J Virol. 89, 220-229 (2015).</li><li>Suk, H., Knipe, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Proteomic+analysis+of+the+herpes+simplex+virus+1+virion+protein+16+transactivator+protein+in+infected+cells.">Proteomic analysis of the herpes simplex virus 1 virion protein 16 transactivator protein in infected cells.</a> Proteomics. 15, 1957-1967 (2015).</li><li>Balasubramanian, N., Bai, P., Buchek, G., Korza, G., Weller, S. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Physical+interaction+between+the+herpes+simplex+virus+type+1+exonuclease,+UL12,+and+the+DNA+double-strand+break-sensing+MRN+complex.">Physical interaction between the herpes simplex virus type 1 exonuclease, UL12, and the DNA double-strand break-sensing MRN complex.</a> J Virol. 84, 12504-12514 (2010).</li><li>Sampath, P., Deluca, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Binding+of+ICP4,+TATA-binding+protein,+and+RNA+polymerase+II+to+herpes+simplex+virus+type+1+immediate-early,+early,+and+late+promoters+in+virus-infected+cells.">Binding of ICP4, TATA-binding protein, and RNA polymerase II to herpes simplex virus type 1 immediate-early, early, and late promoters in virus-infected cells.</a> J Virol. 82, 2339-2349 (2008).</li><li>Amelio, A. L., McAnany, P. K., Bloom, D. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+chromatin+insulator-like+element+in+the+herpes+simplex+virus+type+1+latency-associated+transcript+region+binds+CCCTC-binding+factor+and+displays+enhancer-blocking+and+silencing+activities.">A chromatin insulator-like element in the herpes simplex virus type 1 latency-associated transcript region binds CCCTC-binding factor and displays enhancer-blocking and silencing activities.</a> J Virol. 80, 2358-2368 (2006).</li><li>Cliffe, A. R., Knipe, D. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Herpes+simplex+virus+ICP0+promotes+both+histone+removal+and+acetylation+on+viral+DNA+during+lytic+infection.">Herpes simplex virus ICP0 promotes both histone removal and acetylation on viral DNA during lytic infection.</a> J Virol. 82, 12030-12038 (2008).</li><li>Herrera, F. J., Triezenberg, S. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=VP16-dependent+association+of+chromatin-modifying+coactivators+and+underrepresentation+of+histones+at+immediate-early+gene+promoters+during+herpes+simplex+virus+infection.">VP16-dependent association of chromatin-modifying coactivators and underrepresentation of histones at immediate-early gene promoters during herpes simplex virus infection.</a> J Virol. 78, 9689-9696 (2004).</li><li>Kent, J. 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=During+lytic+infection+herpes+simplex+virus+type+1+is+associated+with+histones+bearing+modifications+that+correlate+with+active+transcription.">During lytic infection herpes simplex virus type 1 is associated with histones bearing modifications that correlate with active transcription.</a> J Virol. 78, 10178-10186 (2004).</li><li>Oh, J., Fraser, N. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Temporal+association+of+the+herpes+simplex+virus+genome+with+histone+proteins+during+a+lytic+infection.">Temporal association of the herpes simplex virus genome with histone proteins during a lytic infection.</a> J Virol. 82, 3530-3537 (2008).</li><li>Catez, F., 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=HSV-1+genome+subnuclear+positioning+and+associations+with+host-cell+PML-NBs+and+centromeres+regulate+LAT+locus+transcription+during+latency+in+neurons.">HSV-1 genome subnuclear positioning and associations with host-cell PML-NBs and centromeres regulate LAT locus transcription during latency in neurons.</a> PLoS Pathog. 8, e1002852 (2012).</li><li>Everett, R. D., Murray, J., Orr, A., Preston, C. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Herpes+simplex+virus+type+1+genomes+are+associated+with+ND10+nuclear+substructures+in+quiescently+infected+human+fibroblasts.">Herpes simplex virus type 1 genomes are associated with ND10 nuclear substructures in quiescently infected human fibroblasts.</a> J Virol. 81, 10991-11004 (2007).</li><li>Tang, Q., 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=Determination+of+minimum+herpes+simplex+virus+type+1+components+necessary+to+localize+transcriptionally+active+DNA+to+ND10.">Determination of minimum herpes simplex virus type 1 components necessary to localize transcriptionally active DNA to ND10.</a> J Virol. 77, 5821-5828 (2003).</li><li>Ishov, A. M., Maul, G. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+periphery+of+nuclear+domain+10+(ND10)+as+site+of+DNA+virus+deposition.">The periphery of nuclear domain 10 (ND10) as site of DNA virus deposition.</a> J Cell Biol. 134, 815-826 (1996).</li><li>Maroui, M. 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=Latency+Entry+of+Herpes+Simplex+Virus+1+Is+Determined+by+the+Interaction+of+Its+Genome+with+the+Nuclear+Environment.">Latency Entry of Herpes Simplex Virus 1 Is Determined by the Interaction of Its Genome with the Nuclear Environment.</a> PLoS Pathog. 12, e1005834 (2016).</li><li>Sirbu, B. M., Couch, F. B., Cortez, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Monitoring+the+spatiotemporal+dynamics+of+proteins+at+replication+forks+and+in+assembled+chromatin+using+isolation+of+proteins+on+nascent+DNA.">Monitoring the spatiotemporal dynamics of proteins at replication forks and in assembled chromatin using isolation of proteins on nascent DNA.</a> Nat Protoc. 7, 594-605 (2012).</li><li>Leung, K. H., Abou El Hassan, M., Bremner, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+rapid+and+efficient+method+to+purify+proteins+at+replication+forks+under+native+conditions.">A rapid and efficient method to purify proteins at replication forks under native conditions.</a> BioTechniques. 55, 204-206 (2013).</li><li>Hobbs, W. E., DeLuca, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Perturbation+of+cell+cycle+progression+and+cellular+gene+expression+as+a+function+of+herpes+simplex+virus+ICP0.">Perturbation of cell cycle progression and cellular gene expression as a function of herpes simplex virus ICP0.</a> J Virol. 73, 8245-8255 (1999).</li><li>Lomonte, P., Everett, R. D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Herpes+simplex+virus+type+1+immediate-early+protein+Vmw110+inhibits+progression+of+cells+through+mitosis+and+from+G(1)+into+S+phase+of+the+cell+cycle.">Herpes simplex virus type 1 immediate-early protein Vmw110 inhibits progression of cells through mitosis and from G(1) into S phase of the cell cycle.</a> J Virol. 73, 9456-9467 (1999).</li><li>Dembowski, J. A., DeLuca, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selective+recruitment+of+nuclear+factors+to+productively+replicating+herpes+simplex+virus+genomes.">Selective recruitment of nuclear factors to productively replicating herpes simplex virus genomes.</a> PLoS Pathog. 11, e1004939 (2015).</li><li>Dembowski, J. A., Dremel, S. E., DeLuca, N. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication-Coupled+Recruitment+of+Viral+and+Cellular+Factors+to+Herpes+Simplex+Virus+Type+1+Replication+Forks+for+the+Maintenance+and+Expression+of+Viral+Genomes.">Replication-Coupled Recruitment of Viral and Cellular Factors to Herpes Simplex Virus Type 1 Replication Forks for the Maintenance and Expression of Viral Genomes.</a> PLoS Pathog. 13, e1006166 (2017).</li><li>Bjornberg, O., Nyman, P. O. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+dUTPases+from+herpes+simplex+virus+type+1+and+mouse+mammary+tumour+virus+are+less+specific+than+the+Escherichia+coli+enzyme.">The dUTPases from herpes simplex virus type 1 and mouse mammary tumour virus are less specific than the Escherichia coli enzyme.</a> J Gen Virol. 77 (Pt 12), 3107-3111 (1996).</li><li>Chiou, S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA-+and+protein-scission+activities+of+ascorbate+in+the+presence+of+copper+ion+and+a+copper-peptide+complex.">DNA- and protein-scission activities of ascorbate in the presence of copper ion and a copper-peptide complex.</a> J Biochem. 94, 1259-1267 (1983).</li><li>Kennedy, D. C., 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=Cellular+consequences+of+copper+complexes+used+to+catalyze+bioorthogonal+click+reactions.">Cellular consequences of copper complexes used to catalyze bioorthogonal click reactions.</a> J Am Chem Soc. 133, 17993-18001 (2011).</li><li>Snel, B., Lehmann, G., Bork, P., Huynen, M. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=STRING:+a+web-server+to+retrieve+and+display+the+repeatedly+occurring+neighbourhood+of+a+gene.">STRING: a web-server to retrieve and display the repeatedly occurring neighbourhood of a gene.</a> Nucleic Acids Res. 28, 3442-3444 (2000).</li></ol>

This protocol includes multiple steps which, if not followed carefully, can result in significantly reduced protein yield or contamination with cellular DNA. It is critical that stationary cells are used for all experiments to ensure that cellular DNA is not labeled and purified. This can be confirmed by the absence of cellular DNA polymerases in the protein sample because HSV-1 does not utilize cellular DNA polymerase for genome synthesis. During EdC labeling and nuclei harvesting steps, samples should be staggered to e...

Viruses have a limited capacity to carry out essential functions and therefore depend on host factors to facilitate critical aspects of infection including viral gene expression, replication, repair, recombination, and transport. The activities of these host factors are often augmented by virally encoded proteins. In addition, viruses must avoid detection and interference by cellular responses to viral infection. Therefore, virus host interactions dictate the outcome of infection. Of paramount importance is understanding how viruses alter the cellular environment to adapt the cellular machinery to facilitate viral processes. Of particular interest is identifying which factors and processes act on viral genomes throughout the infectious cycle.
Herpes simplex virus type 1 (HSV-1) is a double stranded DNA virus that infects a substantial proportion of the human population. Within the first hour of infection, the viral genome enters the nucleus, where an ordered cascade of viral gene expression ensues in coordination with viral DNA (vDNA) replication1. In the nucleus, genomes are subject to epigenetic regulation, undergo repair and recombination, and are packaged into capsids, such that the first progeny virions are produced within less than six hours. The comprehensive evaluation of viral genome associated proteins throughout the course of infection will lay the groundwork to investigate the molecular details of processes that act on viral genomes, and will provide insight into which viral and cellular factors are involved in various stages of infection.
Previous methods for the investigation of host factors involved in viral infection include affinity purification of viral proteins for the analysis of associated cellular proteins2,3,4,5,6,7,8,9. These assays have been instrumental for the identification of cellular factors involved in host antiviral responses, as well as viral chromatin modification, gene expression, and DNA repair. However, it is difficult to ascertain whether interactions depend on the association with vDNA, and proteomics only provide insight into interactions that occur as a function of a specific viral factor. Chromatin immunoprecipitation (ChIP) has been used to identify where specific viral and cellular proteins bind to viral genomes10,11,12,13,14,15 and fluorescent in situ hybridization (FISH) combined with immunocytochemistry has enabled the visualization of cellular factors that colocalize with vDNA16,17,18,19,20. These assays allow for spatial and temporal analysis. However, limitations include the need for highly specific antibodies, limited sensitivity, and the need for previous insight into virus host interactions. We therefore developed a method based on iPOND (isolation of proteins on nascent DNA)21 and aniPOND (accelerated native iPOND)22 to selectively label and purify vDNA from infected cells for the unbiased identification of viral genome associated proteins by mass spectrometry. iPOND has been instrumental for the investigation of cellular replication fork dynamics.
For the selective purification of viral genomes from infected cells, replicating vDNA is labeled with ethynyl modified nucleosides, 5-ethynyl-2&#180;-deoxyuridine (EdU) or 5-ethynyl-2&#180;-deoxycytidine (EdC) (Figure 1), followed by covalent conjugation to biotin azide via click chemistry to facilitate single step purification of viral genomes and associated proteins on streptavidin-coated beads (Figure 2B). Importantly, infections are carried out in stationary cells, which are not engaged in cellular DNA replication to enable specific labeling of vDNA. Furthermore, HSV-1 infection causes cell cycle arrest and inhibits cellular DNA replication23,24. Virus can be prelabeled before infection for the analysis of proteins associated with incoming viral genomes (Figure 1A) or labeled during DNA replication for the analysis of proteins associated with newly synthesized vDNA (Figure 1B)25. Furthermore, pulse chase analysis can be used to investigate the nature of proteins associated with viral replication forks (Figure 1C)26. In addition, ethynyl-modified vDNA can be covalently conjugated to a fluorophore for spatial investigation of protein dynamics (Figure 2A and Figure 3). Imaging allows for the direct visualization of vDNA and is a complimentary approach for the validation of vDNA-protein interactions, and can be adapted to track viral genomes throughout infection. We anticipate that these approaches could be further modified to study any aspect of herpesviral infection, including latency and reactivation, and to study other DNA viruses. Moreover, labeling with 5-ethynyl uridine (EU) could allow for the analysis of RNA viral genomes.

<table border="0" cellpadding="0" cellspacing="0" width="1930">
	<tbody>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">MRC-5 cells</td>
			<td style="width:197px;">ATCC</td>
			<td style="width:101px;">CCL-171</td>
			<td style="width:1215px;"></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Fetal Bovine Serum (FBS)</td>
			<td style="width:197px;">Gibco</td>
			<td style="width:101px;">26140-179</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Dulbecco&#39;s Modified Eagle Medium (DMEM)</td>
			<td style="width:197px;">Gibco</td>
			<td style="width:101px;">12800-082</td>
			<td>substituted with 10% FBS, 2 mM L-glutamine, 12 mM&#160; (for growth in flasks) or 30 mM (for growth in dishes) sodium-bicarbinate</td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:419px;">600 cm2 tissue culture dish</td>
			<td style="width:197px;">Thermo Fisher Scientific</td>
			<td align="right" style="width:101px;">166508</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Tris Buffered Saline (TBS), pH 7.4</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>137 mM NaCl, 5 mM KCl, 491 mM MgCl, 680 mM CaCl, 25.1 mM Tricine</td>
		</tr>
		<tr height="24">
			<td height="24" style="height:24px;width:419px;">HSV-1 stock</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>stocks with titers greater than 1x109 PFU/mL work best</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Sephadex G-25&#160; column (PD-10 Desalting Column)</td>
			<td style="width:197px;">GE Healthcare</td>
			<td align="right" style="width:101px;">17085101</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Dimethyl sulfoxide (DMSO)</td>
			<td style="width:197px;">Fisher Scientific</td>
			<td style="width:101px;">D128-1</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">5&#180;-Ethynyl-2&#180;-deoxycytidine (EdC)</td>
			<td style="width:197px;">Sigma-Aldrich</td>
			<td style="width:101px;">T511307</td>
			<td>Dissolve in DMSO to prepare 40 mM stock, aliquot, and store at -20 &#176;C&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">2&#180;-deoxycytidine (deoxyC)</td>
			<td style="width:197px;">Sigma-Aldrich</td>
			<td style="width:101px;">D3897</td>
			<td>Dissolve in water to prepare 40 mM stock, aliquot, and store at -20 &#176;C&#160;</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:419px;">Nuclear Extraction Buffer (NEB)</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>prepare fresh (20 mM Hepes pH 7.2, 50 mM NaCl, 3 mM MgCl2, 300 mM Sucrose, 0.5% Igepal)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Cell scraper</td>
			<td style="width:197px;">Bellco glass</td>
			<td style="width:101px;">7731-22000</td>
			<td>Autoclave before use</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Trypan blue solution</td>
			<td style="width:197px;">Sigma-Aldrich</td>
			<td style="width:101px;">T8154</td>
			<td></td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:419px;">PBS, pH 7.2 (10x)</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>1.37 M NaCl, 27 mM KCl, 100 mM Na2HPO4, 18 mM KH2PO4 (dilute to 1x in sterile water before use)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Copper (II) sulfate pentahydrate (CuSO4-5H2O)</td>
			<td style="width:197px;">Fisher Scientific</td>
			<td style="width:101px;">C489</td>
			<td>Prepare 100 mM stock and store at 4 &#176;C for up to 1 month</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">(+) Sodium L-ascorbate</td>
			<td style="width:197px;">Sigma-Aldrich</td>
			<td style="width:101px;">A4034</td>
			<td>Freshly prepare 100 mM stock and store on ice until use</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Biotin azide</td>
			<td style="width:197px;">Invitrogen</td>
			<td style="width:101px;">B10184</td>
			<td>Prepare 10 mM stock in DMSO, aliquot, and store at -20 &#176;C for up to 1 year&#160;</td>
		</tr>
		<tr height="25">
			<td height="25" style="height:25px;width:419px;">Click Reaction Mix</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>prepare immediately before use by adding reagents in the indicated order (10 mL: 8.8 mL 1x PBS, 200 mL 100 mM CuSO4, 25mL 10 mM Biotin Azide, 1 mL 100 mM sodium ascorbate)&#160;&#160;</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">cOmplete Protease Inhibitor Cocktail</td>
			<td style="width:197px;">Roche</td>
			<td align="right" style="width:101px;">11697498001</td>
			<td>Dissolve in 1 mL water to prepare 50x stock, can store at 4 &#176;C for up to 1 week, or directly add 1 pill to 50 mL buffer</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">freezing buffer</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>prepare fresh (7 mL 100% glycerol, 3 mL NEB, 200 &#956;L 50x protease inhibitor)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Buffer B1</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>prepare fresh (25 mM NaCl, 2 mM EDTA, 50 mM Tris-HCl pH 8, 1% Igepal, 1x protease inhibitor)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Buffer B2</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>prepare fresh (150 mM NaCl, 2 mM EDTA, 50 mM Tris-HCl pH 8, 0.5% Igepal, 1x protease inhibitor)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Buffer B3</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>prepare fresh (150 mM NaCl, 2 mM EDTA, 50 mM Tris-HCl pH 8, 1x protease inhibitor)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;">Vibra Cell Ultra Sonic Processer equipped with a 3 mm microtip probe</td>
			<td style="width:197px;">Sonics</td>
			<td style="width:101px;">VCX 130</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Cell strainer</td>
			<td style="width:197px;">Falcon</td>
			<td align="right" style="width:101px;">352360</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Dynabeads MyOne Streptavidin T1</td>
			<td style="width:197px;">Life Technologies</td>
			<td align="right" style="width:101px;">65601</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">DynaMag-2 Magnet</td>
			<td style="width:197px;">Life Technologies</td>
			<td style="width:101px;">12321D</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Mini-Tube Rotator</td>
			<td style="width:197px;">Fisher Scientific</td>
			<td style="width:101px;">260750F</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">2X Laemmli sample buffer</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>Mix 400 mg of SDS, 2 mL 100% glycerol, 1.25 mL of 1 M Tris (pH 6.8), and 10 mg of bromophenol blue in 8 mL water. Store at 4&#160; &#176;C for up to 6 months. Before use add 1 M DTT to a final concentration of 200 mM.</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">cap locks for 1.5 mL tube</td>
			<td style="width:197px;">Fisher Scientific</td>
			<td style="width:101px;">NC9679153</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Standard western blotting reagents</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">NOVEX Colloidal Blue Staining Kit</td>
			<td style="width:197px;">Invitrogen</td>
			<td style="width:101px;">LC6025</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">12-well tissue culture dish</td>
			<td style="width:197px;">Corning</td>
			<td align="right" style="width:101px;">3513</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Coverslips</td>
			<td style="width:197px;">Fisher Scientific</td>
			<td style="width:101px;">12-545-100</td>
			<td>Autoclave before use</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Microscope slides</td>
			<td style="width:197px;">Fisher Scientific</td>
			<td style="width:101px;">12-552-5</td>
			<td></td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:419px;">16% paraformaldehyde</td>
			<td style="width:197px;">Electron Microscopy Sciences</td>
			<td align="right" style="width:101px;">15710</td>
			<td>dilute to 3.7% in 1x PBS before use</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Bovine serum albumin (BSA)</td>
			<td style="width:197px;">Fisher Scientific</td>
			<td style="width:101px;">BP1605</td>
			<td>prepare 3% in 1x PBS</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Permeabilization buffer (0.5% Triton-X 100)</td>
			<td style="width:197px;">Sigma-Aldrich</td>
			<td style="width:101px;">T8787</td>
			<td>prepare 0.5% Triton-X 100 in 1x PBS</td>
		</tr>
		<tr height="42">
			<td height="42" style="height:42px;width:419px;">Click reaction cocktail - Click-iT EdU Alexa Fluor 488 Imaging Kit</td>
			<td style="width:197px;">Molecular Probes</td>
			<td style="width:101px;">C10337</td>
			<td>prepare according to manufactorer&#39;s protocol</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Hoechst 33342</td>
			<td style="width:197px;">Life Technologies</td>
			<td style="width:101px;">H1399</td>
			<td>prepare 10 mg/mL in water, can store at 4 &#176;C for up to 1 year</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">mouse anti-ICP8 primary antibody</td>
			<td style="width:197px;">Abcam</td>
			<td style="width:101px;">ab20194</td>
			<td>Use a 1:200 dilution in 1x PBS</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">mouse anti-UL42 primary antibody (2H4)</td>
			<td style="width:197px;">Abcam</td>
			<td style="width:101px;">ab19311</td>
			<td>Use a 1:200 dilution in 1x PBS</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Goat anti-mouse 594-conjugated secondary antibody</td>
			<td style="width:197px;">Life Technologies</td>
			<td style="width:101px;">a11005</td>
			<td>Use a 1:500 dilution in 1x PBS</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Immu-mount</td>
			<td style="width:197px;">Thermo Fisher Scientific</td>
			<td align="right" style="width:101px;">9990402</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">2x SDS-bicarb solution</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>2% SDS, 200 mM NaHCO3</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Phenol:chloroform:isoamyl alcohol</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>mix 25:24:1 at least 1 day before use, store at 4 &#176;C in the dark</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">chloroform:isoamyl alcohol</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>mix 24:1 at least 1 day before use, store at room temperature in the dark</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">10x Tris EDTA (TE), pH 8.0</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>100 mM Tris, 10 mM EDTA (dilute to 1x before use)</td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Qiaquick PCR purification kit</td>
			<td style="width:197px;">Qiagen</td>
			<td align="right" style="width:101px;">28104</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">3 M sodium acetate pH 5.2</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Qubit 2.0 Fluorometer</td>
			<td style="width:197px;">Invitrogen</td>
			<td style="width:101px;">Q32866</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Qubit dsDNA HS Assay Kit</td>
			<td style="width:197px;">Invitrogen</td>
			<td style="width:101px;">Q32851</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Qubit assay tubes</td>
			<td style="width:197px;">Invitrogen</td>
			<td style="width:101px;">Q32856</td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Fluorescence microscope equipped with imaging software</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Microcentrifuge for 1.5 mL tubes</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Tabletop centrifuge for 15 and 50 mL tubes</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Cell culture incubator</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Biosafety cabinet</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td></td>
		</tr>
		<tr height="21">
			<td height="21" style="height:21px;width:419px;">Heat blocks</td>
			<td style="width:197px;"></td>
			<td style="width:101px;"></td>
			<td>65 &#176;C and 95 &#176;C</td>
		</tr>
	</tbody>
</table>

purification of viral dna for the identification of associated viral and cellular proteins

The goal of this protocol is to isolate herpes simplex virus type 1 (HSV-1) DNA from infected cells for the identification of associated viral and cellular proteins by mass spectrometry. Although proteins that interact with viral genomes play major roles in determining the outcome of infection, a comprehensive analysis of viral genome associated proteins was not previously feasible. Here we demonstrate a method that enables the direct purification of HSV-1 genomes from infected cells. Replicating viral DNA is selectively labeled with modified nucleotides that contain an alkyne functional group. Labeled DNA is then specifically and irreversibly tagged via the covalent attachment of biotin azide via a copper(I)-catalyzed azide-alkyne cycloaddition or click reaction. Biotin-tagged DNA is purified on streptavidin-coated beads and associated proteins are eluted and identified by mass spectrometry. This method enables the selective targeting and isolation of HSV-1 replication forks or whole genomes from complex biological environments. Furthermore, adaptation of this approach will allow for the investigation of various aspects of herpesviral infection, as well as the examination of the genomes of other DNA viruses.

The use of click chemistry for the purification of DNA from cells was first accomplished by the iPOND method21. The purpose of iPOND is to purify cellular replication forks for the identification of associated proteins. We have adapted this technique to specifically study vDNA protein interactions during infection. Manipulation of the approach to label viral genomes with EdC (Figure 1), combined with synchronized infections, has allowe...

Watch this Scientific Journal Video about Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins at JoVE.com

Purification of Viral DNA for the Identification of Associated Viral and Cellular Proteins

The goal of this protocol is to specifically tag and selectively isolate viral DNA from infected cells for the characterization of viral genome associated proteins.

The goal of this protocol is to isolate herpes simplex virus type 1 (HSV-1) DNA from infected cells for the identification of associated viral and ...

The overall goal of this method is to purify Herpes Simplex virus type one DNA from infected cells for the proteomic analysis of viral genome associated proteins. This method provides key insights into the involvement of cellular factors and Herpes virus infection. The main advantage of this technique is that it can be adapted to directly purify different populations of viral DNA from infected cells, allowing for the analysis of multiple aspects of infection.Begin this procedure with culturing of MRC five cells as described in the text protocol. Then, dilute HSV-1 in cold tris-buffered saline or TBS. For the following steps, it is important to turn off the blower and the tissue culture hood to prevent cells from drying out.Use a pipette to transfer the growth medium from the MRC 5 cells to a sterile bottle to add back to the cells after infection. Infect the cells by adding seven milliliters of diluted virus to the cells. Rock the cells every 10 minutes for one hour at room temperature.Following absorption, aspirate the innoculum, rinse the cells with 50 milliliters of room temperature TBS and replace the original growth medium. Then, incubate the cells at 37 degrees celsius in the presence of 5%carbon dioxide. After the onset of viral DNA replication, around four hours post infection, label replicating viral DNA.To do so, dilute EdC in one milliliter of growth medium and add it to the cell culture medium of infected cells for two to four hours. To harvest nuclei, replace the growth medium with 20 milliliters of nuclei extraction buffer and incubate for 20 minutes at four degree celsius with occasional rocking. After incubation, scrape nuclei from the plate using a cell scraper and transfer them to a 50 milliliter conical tube on ice.Centrifuge for 10 minutes at 2, 500 x g and four degree celsius to pellet the nuclei. Following centrifugation, discard the supernatant. Gently dislodge the nuclear pellet in 10 milliliters of phosphate buffer saline or PBS and transfer it to a 50 milliliter conical tube.Then, centrifuge the sample as before. After completely removing the PBS, re-suspend the nuclear pellet in 10 milliliters of click reaction mix, by gently pipetting up and down five times with a 10 milliliter pipette. Rotate the sample for one hour at four degree celsius, before pelleting the nuclei as before.Completely remove the quick reaction mix, then, wash the pellet by gently re-suspending it in 10 milliliters of PBS and centrifuging again. Now, carefully re-suspend the nuclear pellet in one milliliter PBS and transfer the solution to a 1.5 milliliter microcentrifuge tube. Following centrifugation, completely remove the PBS and flash freeze the pellet in liquid nitrogen.At this point, the pellet can be stored at 80 degree celsius or the procedure can be continued. To lyse the nuclei and fragment the DNA, re-suspend the thawed nuclei in 500 microliters of Buffer B1 by pipetting up and down. Incubate the suspension on ice for 45 minutes.Then, sonicate the samples six times for 30 seconds each at 40%amplitude, using a three millimeter microtip probe. Place the samples on ice for at least 30 seconds between pulses. After sonication, samples should appear clear, not cloudy.Pellet the cell debris by centrifuging at 14, 000 x G for 10 minutes at four degrees celsius. The pellet size should decrease substantially, filter the supernatant through a 100 micron cell strainer and retain the flow through. Then, add 500 microliters of Buffer B2 to the filtered supernatant.To bind the biotinylated DNA to streptavidin coated beads, prepare the streptavidin magnetic beads by transferring 300 microliters of bead slurry to a 1.5 milliliter microcentrifuge tube. Prepare one tube of beads per sample. Wash the beads three times with milliliter of Buffer B2 by vortexing to re-suspend, applying to a magnet to separate the beads and aspirating the wash buffer.Then, add 900 microliters of the sample to the washed beads. The remainder of the sample will be used for input DNA and protein isolation. Rotate the suspension overnight at four degree celsius.The next day, place the samples into a magnetic microfuge tube rack and remove the supernatant. Gently re-suspend the beads in one milliliter of Buffer B2, before rotating at four degree celsius for five minutes. Remove the supernatant again using the magnetic microfuge tube rack.This time, gently re-suspend the beads in one milliliter Buffer B3 and rotate at four degree celsius for five minutes. After removing the supernatant from the bead mixture using the magnet, re-suspend the beads in 50 microliters of 2x Laemmli sample buffer to allude DNA protein complexes. Next, boil the samples at 95 degrees celsius for 15 minutes.Vortex a mix before quickly spinning the samples in a microfuge. Apply the samples to the magnet and transfer the allot to a new tube. Finally, flash freeze the samples and store them at 80 degrees celsius.Perform protein analysis as described in the text protocol. EdC labeling was carried out for zero, 20, 40 or 60 minutes followed by the purification of viral DNA and associated proteins. The eluted proteins were subject to coomassie blue staining and western blotting with the antibody specific for viral DNA binding proteins, ICP4 and UL42.The arrow indicates streptavidin that was stripped from the beads during elution which is present under all conditions. Proteins isolated by this method are then subject to mass spectrometry. The pie chart illustrates the number of proteins in each functional category that were found to be associated with Herpes Simplex virus type on genomes at six hours post infection.A closer look at protein-protein interactions amongst identified proteins was carried out using the string functional protein association network database. The results reveal sub-complexes of proteins that function together in the same biological process. After watching this video, you should have a good understanding of how to purify viral DNA from infected cells for the proteomic investigation of viral genome associated proteins.This technique can be completed in three to four days. While attempting this procedure, it is important to remember to take precautions to prevent DNAse or protease contamination of samples. In addition to this procedure, other methods like immunofluorescence can be performed to verify the nature of EdC labeled viral DNA.This technique has paved the way for researchers in the field of Herpes virology, to explore the functions of host proteins and viral infection.

purification-viral-dna-for-identification-associated-viral-cellular

Research

JoVE Journal

Immunology and Infection

13.3K Views.  University of Pittsburgh School of Medicine. The overall goal of this method is to purify Herpes Simplex virus type one DNA from infected cells for the proteomic analysis of viral genome associated proteins. This method provides key insights into the involvement of cellular factors and Herpes virus infection. The main advantage of this technique is that it can be adapted to directly purify different populations of viral DNA from infected cells, allowing for the analysis of multiple aspects of infection.Begin this procedure with c...