Name: tools to study the role of architectural protein hmgb1 in the processing of helix distorting, site-specific dna interstrand crosslinks
Uploaded: 2016-11-10T13:00:00
Description: Watch this Scientific Journal Video about Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks at JoVE.com

Gli autori desiderano ringraziare i membri del laboratorio Vasquez per le discussioni utili. Questo lavoro è stato sostenuto dal National Institutes of Health / National Cancer Institute [CA097175, CA093279 per KMV]; e la prevenzione del cancro e Research Institute del Texas [RP101501]. Il finanziamento per la carica di accesso aperto: National Institutes of Health / National Cancer Institute [CA093279 per KMV].

1. Preparazione di ICL TFO-dirette sui plasmidi Substrati <ol><li> Incubare quantità equimolari di plasmide pSupFG1 10,11 DNA (DNA plasmide 5 mg è un buon punto di partenza) con psoraleni coniugato TFO AG30 in 8 ml di triplex tampone di legame [50% glicerolo, 10 mM Tris (pH 7,6), 10 mM MgCl 2] e dH 2 O ad un volume finale di 40 microlitri in un tubo ambra. Mescolare accuratamente pipettando su e giù. Incubare la reazione a 37 ° C bagnomaria per 12 ore. </li><li> Riscaldare la lampa...

<ol>
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E., Ljungman, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Psoralen-induced+DNA+interstrand+cross-links+block+transcription+and+induce+p53+in+an+ataxia-telangiectasia+and+rad3-related-dependent+manner.">Psoralen-induced DNA interstrand cross-links block transcription and induce p53 in an ataxia-telangiectasia and rad3-related-dependent manner.</a> Mol Pharmacol. 75, 599-607 (2009).</li><li>Vare, 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=DNA+interstrand+crosslinks+induce+a+potent+replication+block+followed+by+formation+and+repair+of+double+strand+breaks+in+intact+mammalian+cells.">DNA interstrand crosslinks induce a potent replication block followed by formation and repair of double strand breaks in intact mammalian cells.</a> DNA repair. 11, 976-985 (2012).</li><li>Huang, Y., Li, L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=DNA+crosslinking+damage+and+cancer+-+a+tale+of+friend+and+foe.">DNA crosslinking damage and cancer - a tale of friend and foe.</a> Transl Cancer Res. 2, 144-154 (2013).</li><li>Mukherjee, A., Vasquez, 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=HMGB1+interacts+with+XPA+to+facilitate+the+processing+of+DNA+interstrand+crosslinks+in+human+cells.">HMGB1 interacts with XPA to facilitate the processing of DNA interstrand crosslinks in human cells.</a> Nucleic Acids Res. 44, 1151-1160 (2016).</li><li>Bidney, D. L., Reeck, G. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Purification+from+cultured+hepatoma+cells+of+two+nonhistone+chromatin+proteins+with+preferential+affinity+for+single-stranded+DNA:+apparent+analogy+with+calf+thymus+HMG+proteins.">Purification from cultured hepatoma cells of two nonhistone chromatin proteins with preferential affinity for single-stranded DNA: apparent analogy with calf thymus HMG proteins.</a> Biochem Biophys Res Commun. 85, 1211-1218 (1978).</li><li>Bianchi, M. E., Beltrame, M., Paonessa, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Specific+recognition+of+cruciform+DNA+by+nuclear+protein+HMG1.">Specific recognition of cruciform DNA by nuclear protein HMG1.</a> Science. 243, 1056-1059 (1989).</li><li>Jung, Y., Lippard, 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=Nature+of+full-length+HMGB1+binding+to+cisplatin-modified+DNA.">Nature of full-length HMGB1 binding to cisplatin-modified DNA.</a> Biochemistry. 42, 2664-2671 (2003).</li><li>Reddy, M. C., Christensen, J., Vasquez, 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=Interplay+between+human+high+mobility+group+protein+1+and+replication+protein+A+on+psoralen-cross-linked+DNA.">Interplay between human high mobility group protein 1 and replication protein A on psoralen-cross-linked DNA.</a> Biochemistry. 44, 4188-4195 (2005).</li><li>Das, D., Scovell, W. 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+binding+interaction+of+HMG-1+with+the+TATA-binding+protein/TATA+complex.">The binding interaction of HMG-1 with the TATA-binding protein/TATA complex.</a> J Biol Chem. 276, 32597-32605 (2001).</li><li>Little, A. J., Corbett, E., Ortega, F., Schatz, D. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cooperative+recruitment+of+HMGB1+during+V(D)J+recombination+through+interactions+with+RAG1+and+DNA.">Cooperative recruitment of HMGB1 during V(D)J recombination through interactions with RAG1 and DNA.</a> Nucleic Acids Res. 41, 3289-3301 (2013).</li><li>Lange, S. S., Mitchell, D. L., Vasquez, 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=High+mobility+group+protein+B1+enhances+DNA+repair+and+chromatin+modification+after+DNA+damage.">High mobility group protein B1 enhances DNA repair and chromatin modification after DNA damage.</a> Proc Natl Acad Sci U S A. 105, 10320-10325 (2008).</li><li>Lange, S. S., Reddy, M. C., Vasquez, K. 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La formazione efficiente ICLs TFO-diretti dipende da due fattori fondamentali: in primo luogo, i componenti corretta tampone (per esempio, MgCl 2) e il tempo di incubazione del TFO con il suo substrato DNA bersaglio (dipende l&#39;affinità di legame del TFO al suo obiettivo duplex, e le concentrazioni utilizzate); e in secondo luogo, la corretta dose di UVA (365 nm) irradiazione per formare legami crociati psoraleni efficiente. formazione triplex ottimale può essere ottenuto utilizzando HPLC o gel ...

Triplex di formazione oligonucleotidi (TFOS) DNA legano duplex in modo specifico per la sequenza tramite incollaggio Hoogsteen-idrogeno per formare strutture a tripla elica 1-5. La tecnologia Triplex è stata usata per interrogare una varietà di meccanismi biomolecolari, come la trascrizione, il DNA riparazione dei danni, e gene targeting (rivisto in riferimenti 6-8). TFOS sono stati ampiamente utilizzati per indurre un danno site-specific su plasmidi reporter 9,10. Il nostro laboratorio e altri hanno utilizzato in precedenza un TFO, AG30, legato ad una molecola psoraleni per indurre site-specific legami crociati interstrand DNA (ICL) nel gene supF sul plasmide pSupFG1 5,10-12. ICL sono altamente citotossico come queste lesioni reticolazione covalente i due filamenti di DNA, e se non riparati, possono bloccare la trascrizione del gene e impedire il meccanismo di replicazione del DNA 13,14. A causa della loro potenziale citotossico, agenti ICL-induttori sono stati utilizzati come farmaci chemioterapici nel trattamentodi cancro e altre malattie 15. Tuttavia, la trasformazione e la riparazione di ICL in cellule umane non è ben compreso. Così, una migliore comprensione dei meccanismi coinvolti nella trasformazione di ICLs in cellule umane può contribuire a migliorare l&#39;efficacia dei regimi chemioterapici ICL-base. ICL TFO-indotte e dei loro intermedi di riparazione hanno il potenziale di causare notevoli distorsioni strutturali per l&#39;elica del DNA. Tali distorsioni sono obiettivi probabili per le proteine di architettura, che si legano al DNA distorto con maggiore affinità rispetto a B-forma canonica duplex DNA 16-20. Qui, abbiamo studiato l&#39;associazione di una proteina architettonica altamente abbondanti, HMGB1 con ICL in cellule umane tramite immunoprecipitazione della cromatina (ChIP) saggi su plasmidi psoraleni reticolato e identificato un ruolo per HMGB1 nel modulare la topologia del DNA plasmide psoralen-reticolato in umana lisati cellulari di cancro. HMGB1 è altamente abbondante e ubiquitariamente espresso non suatono proteina architettonica che si lega al DNA danneggiato e substrati di DNA in alternativa strutturati con affinità maggiore di B-forma canonica DNA 17-20. HMGB1 è coinvolta in numerosi processi metabolici del DNA, come la trascrizione, la replicazione del DNA, e la riparazione del DNA 16,21-23. Abbiamo precedentemente dimostrato che HMGB1 si lega al ICL TFO-diretti in vitro con alta affinità 20. Inoltre, abbiamo dimostrato che la mancanza di HMGB1 aumentato il trattamento mutageno di ICL TFO-diretti e HMGB1 identificato come una riparazione per escissione di nucleotidi (NER) co-fattore 23,24. Recentemente, abbiamo scoperto che HMGB1 è associata con ICL TFO-diretti nelle cellule umane e la sua assunzione di tali lesioni dipende dalla proteina NER, XPA 16. Superavvolgimento negativo del DNA ha dimostrato di promuovere la rimozione efficiente di lesioni del DNA da NER 25, e abbiamo scoperto che HMGB1 induce superavvolgimento negativo preferenzialmente su TFO-diretti plas ICL contenentisubstrati metà (relativi ai substrati non danneggiati plasmidi) 16, fornendo una migliore comprensione del ruolo potenziale (s) di HMGB1 come cofattore NER. Il trattamento dei ICLs non è pienamente compresa in cellule umane; in tal modo, le tecniche e le analisi sviluppate sulla base degli strumenti molecolari qui descritte potrebbe portare all&#39;identificazione di proteine ​​supplementari coinvolte nella riparazione ICL, che a loro volta possono servire come bersagli farmacologici che possono essere sfruttate per migliorare l&#39;efficacia dei regimi chemioterapici cancro. Qui, un approccio efficace per valutare l&#39;efficienza della formazione ICL TFO-diretto nel DNA plasmidico da denaturazione agarosio elettroforesi su gel è stato discusso. Inoltre, utilizzando i plasmidi contenenti le ICL TFO-diretti, le tecniche per determinare l&#39;associazione di HMGB1 con plasmidi ICL-danneggiati in un contesto cellulare utilizzando saggi ChIP modificati sono stati descritti. Inoltre, un metodo facile per studiare modifiche topologiche introdotte da the HMGB1 proteine ​​architettonico, in particolare su substrati plasmide ICL-danneggiati in lisati cellulari umane è stata determinata eseguendo saggi superavvolgimento tramite elettroforesi bidimensionale agarosio. Le tecniche descritte possono essere utilizzate per favorire la comprensione del coinvolgimento di riparazione del DNA e delle proteine ​​architetturali nel trattamento dei danni DNA mirate su plasmidi in cellule umane. Descriviamo protocolli dettagliati per la formazione di TFO-diretti ICLs psoraleni sito-specifici sul DNA plasmidico, e successiva ChIP plasmid e superavvolgimento saggi per identificare le proteine ​​che associano con le lesioni e proteine ​​che alterano la topologia DNA, rispettivamente. Questi test possono essere modificati per eseguire con altri agenti che danneggiano il DNA, TFOS, substrati plasmidi, e linee cellulari di mammiferi di interesse. Infatti, abbiamo dimostrato che non vi è almeno un potenziale unico e ad alta affinità sito TFO vincolante all&#39;interno di ogni gene annotata nel genoma umano 26. Comemai, per chiarezza, abbiamo descritto queste tecniche per l&#39;uso di un TFO specifica psoralen-coniugato (pAG30) su uno specifico plasmide mutazione giornalista (pSupFG1) in cellule umane U2OS abbiamo utilizzato in Mukherjee &amp; Vasquez 2016 16.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>5&#39;HMT Psoralen-AG30</td>
			<td>Midland Certified Reagent Co., Midland, TX</td>
			<td>Custom order</td>
			<td>HPLC (or gel) purified</td>
		</tr>
		<tr>
			<td>Simple ChIP Enzymatic Chromatin IP Kit</td>
			<td>Cell signaling Inc.</td>
			<td>9003</td>
			<td>Manufacturer suggested protocol is optimized for chromatin IP and not for plasmid IP. The control IgG and H3 antibodies as well as the Protein G beads and micrococcal nuclease are supplied by the manufacturer.</td>
		</tr>
		<tr>
			<td>GoTaq Green</td>
			<td>Promega</td>
			<td>M7122</td>
			<td>PCR master mix</td>
		</tr>
		<tr>
			<td>HMGB1 antibody</td>
			<td>Abcam</td>
			<td>Ab18256</td>
			<td></td>
		</tr>
		<tr>
			<td>Wizard Gel and PCR cleanup kit</td>
			<td>Promega</td>
			<td>A9281</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroquine-diphosphate salt</td>
			<td>Sigma</td>
			<td>C6628-50G</td>
			<td>For two-dimensional agarose gel electrophoresis</td>
		</tr>
		<tr>
			<td>EcoRI</td>
			<td>New England BioLabs</td>
			<td>R0101S</td>
			<td></td>
		</tr>
		<tr>
			<td>GenePORTER transfection reagent</td>
			<td>Genlantis</td>
			<td>T201015</td>
			<td></td>
		</tr>
		<tr>
			<td>Vaccinia Topoisomerase I</td>
			<td>Invitrogen</td>
			<td>38042-024</td>
			<td></td>
		</tr>
		<tr>
			<td>Blak-Ray long wave ultraviolet lamp</td>
			<td>Upland, CA</td>
			<td>B 100 AP</td>
			<td>UVA lamp</td>
		</tr>
		<tr>
			<td>EpiSonic Multi-Functional Bioprocessor 1100</td>
			<td>Epigentek</td>
			<td>EQC-1100</td>
			<td>Water bath sonicator</td>
		</tr>
		<tr>
			<td>Mylar filter</td>
			<td>GE Healthcare Life Sciences</td>
			<td>80112939</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Sigma-Aldrich</td>
			<td>A6111</td>
			<td></td>
		</tr>
		<tr>
			<td>BIO-RAD Chemidoc</td>
			<td>BIO-RAD</td>
			<td>XRS+ system</td>
			<td>DNA imaging system</td>
		</tr>
		<tr>
			<td>Glycine</td>
			<td>Fisher Scientific</td>
			<td>BP381-500</td>
			<td></td>
		</tr>
		<tr>
			<td>37% Formaldehyde</td>
			<td>Sigma-Aldrich</td>
			<td>F8775-25ML</td>
			<td>Used for crosslinking&#160;</td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>New England Biolabs</td>
			<td>P8107S</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM</td>
			<td>ThermoFisher</td>
			<td>11965092</td>
			<td>Cell culture media</td>
		</tr>
		<tr>
			<td>PBS</td>
			<td>ThermoFisher</td>
			<td>70013073</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Trypsin-EDTA</td>
			<td>ThermoFisher</td>
			<td>25200056</td>
			<td>Cell culture</td>
		</tr>
		<tr>
			<td>Bromocresol green</td>
			<td>Sigma-Aldrich</td>
			<td>114-359</td>
			<td>DNA loading dye</td>
		</tr>
		<tr>
			<td>Siliconized tubes</td>
			<td>Fisher Scientific&#160;</td>
			<td>02-681-320</td>
			<td>Low retention microfuge tube</td>
		</tr>
		<tr>
			<td>Tris base</td>
			<td>Fisher Scientific</td>
			<td>BP152-1</td>
			<td></td>
		</tr>
		<tr>
			<td>Boric Acid</td>
			<td>Fisher Scientific</td>
			<td>A74-1</td>
			<td></td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Fisher Scientific</td>
			<td>BP24731</td>
			<td></td>
		</tr>
		<tr>
			<td>Photometer</td>
			<td>InternationalLight Technologies</td>
			<td>ILT1400-A</td>
			<td>UVA dose measurement</td>
		</tr>
		<tr>
			<td>Cell lines</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Human U2OS osteosarcoma</td>
			<td>ATCC</td>
			<td>ATCC HTB-96</td>
			<td>Cultured according to supplier&#8217;s recommendation</td>
		</tr>
		<tr>
			<td>Human cervical adenocarcinoma HeLa</td>
			<td>ATCC</td>
			<td>ATCC-CCL-2</td>
			<td>Cultured according to supplier&#8217;s recommendation</td>
		</tr>
		<tr>
			<td>Proximal forward primer</td>
			<td>5&#8242;-gcc ccc ctg acg agc atc ac</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Proximal reverse primer</td>
			<td>5&#8242;-tag tta ccg gat aag gcg cag cgg</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Distal forward primer</td>
			<td>5&#8242;-aat acc gcg cca cat agc ag</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>Distal reverse primer</td>
			<td>5&#8242;-agt att caa cat ttc cgt gtc gcc</td>
			<td></td>
			<td></td>
		</tr>
	</tbody>
</table>

tools to study the role of architectural protein hmgb1 in the processing of helix distorting, site-specific dna interstrand crosslinks

casella di gruppo ad alta mobilità 1 proteine ​​(HMGB1) è una proteina di architettura non-istone che è coinvolto nella regolazione di molte funzioni importanti nel genoma, come la trascrizione, la replicazione del DNA, e la riparazione del DNA. HMGB1 si lega al DNA strutturalmente distorto con maggiore affinità rispetto alla canonica B-DNA. Ad esempio, abbiamo scoperto che HMGB1 si lega al DNA interstrand legami crociati (ICL), che collegano covalentemente i due filamenti del DNA, causa la distorsione dell&#39;elica, e se non riparati può causare la morte delle cellule. A causa della loro potenziale citotossico, diversi agenti ICL-inducono sono attualmente utilizzati come agenti chemioterapici in clinica. Mentre gli agenti ICL-formatura mostrano preferenze per alcune sequenze di base (ad esempio, 5&#39;-TA-3 &#39;è il sito di reticolazione preferito per psoraleni), che in gran parte inducono danni al DNA in modo indiscriminato. Tuttavia, covalentemente accoppiando l&#39;agente ICL induce ad un oligonucleotide triplex-formatura (TFO), che si lega al DNA in una sequenza specificamodo, il danno al DNA mirato può essere raggiunto. Qui, usiamo un TFO covalente coniugata sulla &#39;fine a una 4&#39;-idrossimetil-4,5&#39; la 5 (HMT) psoralen, 8-trimethylpsoralen per generare un ICL site-specific su un plasmide mutazione giornalista da utilizzare come strumento di per studiare la modifica architettonica, trasformazione e riparazione delle lesioni del DNA complessi HMGB1 in cellule umane. Descriviamo tecniche sperimentali per preparare ICL TFO-dirette sui plasmidi reporter, e di interrogare l&#39;associazione di HMGB1 con le ICL TFO-orientate in un contesto cellulare utilizzando saggi di immunoprecipitazione della cromatina. Inoltre, descriviamo saggi superavvolgimento DNA per valutare specifica modifica architettonica del DNA danneggiato misurando la quantità di giri superelica introdotte sul plasmide psoralen-reticolato da HMGB1. Queste tecniche possono essere utilizzate per studiare i ruoli di altre proteine ​​coinvolte nella trasformazione e riparazione di ICL TFO-dirette o altri danni al DNA mirato in qualsiasi linea cellulare di interesse.

Formazione del ICL TFO-diretta è critica per la metodica plasmidi basati, che vengono utilizzati per interrogare i ruoli delle proteine ​​architettoniche nella lavorazione ICL in cellule umane. Denaturazione agarosio elettroforesi su gel è un modo facile per determinare l&#39;efficienza della formazione ICL TFO-diretto. I plasmidi che ospitano ICL TFO-diretti migrano con una mobilità più lenta attraverso la matrice gel (Figura 1A, corsia 3) se confrontato con i p...

Watch this Scientific Journal Video about Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks at JoVE.com

Tools to Study the Role of Architectural Protein HMGB1 in the Processing of Helix Distorting, Site-specific DNA Interstrand Crosslinks

Targeted DNA damage can be achieved by tethering a DNA damaging agent to a triplex-forming oligonucleotide (TFO). Using modified TFOs, DNA damage-specific protein association, and DNA topology modification can be studied in human cells by the utilization of modified chromatin immunoprecipitation assays and DNA supercoiling assays described herein.

Strumenti per studiare il ruolo di architettura HMGB1 proteine ​​nella lavorazione di Helix deformante, DNA specifiche per sito interstrand Crosslinks

High mobility group box 1 (HMGB1) protein is a non-histone architectural protein that is involved in regulating many important functions in the genome, ...

The overall goal of the modified chromatin immunoprecipitation and DNA supercoiling experiments is to study the association and subsequent topological modifications induced by architectural proteins on site-specific DNA damage induced by chemotherapeutic or carcinogenic agents in human cells. This methodology will allow us to address key questions about DNA damage and repair which should facilitate discovery of new pharmacological targets for cancer therapy. Our technology allows us to direct site-specific DNA damage, and facilitates evaluation of critical DNA repair processes relevant to human cancer.To begin, 24 hours before transfection, plate 400, 000 mammalian cells per 60 millimeter dish in DMEM supplemented with 10%FBS without antibiotics. Incubate the cells at 37 degrees Celsius and 5%carbon dioxide overnight. In a 14-milliliter round bottom tube, combine 30 microliters of room temperature transfectionary agent with 500 microliters of 1X growth medium that has been warmed to 37 degrees Celsius.In a second tube, combine two micrograms of TFO-directed ICL-containing plasmids in 500 microliters of 1X growth medium. Incubate the tubes at room temperature for 10 minutes. Combine mix one with mix two, and pipette up and down to thoroughly mix.Then incubate the solution at room temperature for 25 to 30 minutes. Next, use warm PBS to wash the cells twice. Then, add the transfection mix in a drop-wise fashion, distributing the solution evenly throughout the plate of cells.Add one milliliter of growth medium to the plate, and bring the final volume to two milliliters. Mix well, and place the culture plates at 37 degrees Celsius and 5%carbon dioxide. Four hours later, replace the medium with three milliliters of growth medium with 10%FBS, and incubate an additional 16 hours.Following the incubation, add 80 microliters of fresh 37%formaldehyde per plate to the cells, and incubate at room temperature in the dark for 10 minutes. Quench the formaldehyde cross-linking by adding 300 microliters of chilled glycine per plate, and incubate for five minutes. Then remove the medium, and use chilled PBS to wash the plates twice.Next, after adding one millimeter of chilled PBS, collect the cells by scraping into a microcentrifuge tube on ice, keeping samples on ice at all times. Prepare cell pellets by centrifuging at 13, 400 times G, and four degrees Celsius for five minutes. Then, remove the supernatant, and place the pellets on ice.Use one milliliter of chilled Buffer A to homogeneously re-suspend the pellets, and incubate on ice for 10 minutes. Then, pellet the cells as before. Now, with one milliliter of chilled Buffer B, homogeneously re-suspend the pellets, and incubate on ice for 10 minutes with occasional mixing by inverting.Then pellet the cells as before. After re-suspending the cells again, in 200 microliters of chilled Buffer B, add two microliters of micrococcal nuclease, or MNase, and incubate the reaction at room temperature for 10 minutes. Then, stop the MNase reaction by placing the tubes on ice, and adding 40 millimolar EDTA.The level of digestion by micrococcal nuclease is very critical, because overdigestion may cause loss of signal, whereas underdigestion may cause a lot of nonspecific background. After pelleting the cells, re-suspend the pellets in 100 microliters of chromatin immunoprecipitation, or ChIP buffer, supplemented with protease inhibitor cocktail. Then, transfer the cell suspension to a thin-walled microcentrifuge tube.Sonicate the samples by floating them on a water bath sonicator for 20 seconds, followed by 20 seconds on ice. Repeat the sonication steps nine times to generate approximately 800 to 1, 200 base-pair fragments. To 20 microliters of the sonicated samples, add three microliters of five molar sodium chloride, and one microliter of RNase A.Vortex the tubes, and incubate them at 37 degrees Celsius for 30 minutes.Then, add two microliters of proteinase K, and incubate at 65 degrees Celsius for two hours. After purifying the samples, according to the text protocol, run them on 1%agarose gel, and visualize with ethidium bromide. In three separate, pre-chilled siliconized tubes, add 30 microliters of lysate, and 70 microliters of chilled 1X ChIP buffer with added protease inhibitors.Add one microgram of anti-IgG, anti-histone H3, or anti-HMGB1 antibodies to the respective tubes. Incubate overnight in a cold room with continuous rotation. In the cold room, after re-suspending Protein G beads, add four microliters of the beads to each reaction tube, and incubate in a cold room with rotation for another two to four hours.Place the tubes on a magnetic rack to pellet the beads, and remove the supernatant. Add 200 microliters of 1X ChIP buffer with protease inhibitor cocktail to the pellets, and wash in the cold with rotation for five minutes. Next, with high salt 1X ChIP buffer, perform an additional wash.Then, use 160 microliters of elution buffer to re-suspend the pellets, and incubate at 37 degrees Celsius with rotation for 30 minutes. Pellet the beads, and collect the supernatant in a fresh tube. Add six microliters of five molar sodium chloride, and two microliters of proteinase K, and incubate overnight at 65 degrees Celsius.After purifying the DNA, according to the text protocol, perform PCR reactions using primer sets to the region or regions of interest, and resolve the products on a 1%agarose gel, stained with ethidium bromide. Prior to use, thaw previously prepared DNA repair synthesis buffer on ice, and add 40 millimolar phosphocreatine, and 2.5 micrograms of creatine phosphokinase. After preparing 10X supercoiling buffer, according to the text protocol, use one microliter of vaccinia topoisomerase 1 with 1X supercoiling buffer in a 10 microliter reaction to linearize 300 nanograms of supercoiled plasmid, PCA FG1.To the relaxed plasmids, add 25 microliters of freshly-thawed HeLa cell extract, and DNA synthesis buffer. Mix well, then add one microliter of vaccinia topoisomerase 1 to the reaction, and incubate at 37 degrees Celsius for one hour. Terminate the reactions by adding 1%SDS, and 0.25 milligrams per milliliter of proteinase K, and incubate at 65 degrees Celsius for two hours.After casting a 1%agarose gel with 1X TPE buffer, add DNA-loading dye to the reactions, and load the samples directly onto the gel at least four lanes apart. Run the gel for eight to 10 hours at two volts per centimeter in 1X TBE for the first dimension at room temperature to resolve the topoisomers. Prepare two liters of 1X TBE with three micrograms per milliliter of chloroquine phosphate.Soak the gel in 200 milliliters of the solution, covered in aluminum foil for 20 minutes. To electrophorese the gel in the second dimension, turn the gel 90 degrees in a clockwise fashion, and run it for four to six hours at two volts per centimeter in chloroquine containing 1X TBE to resolve the positive and negative supercoils. The amount of chloroquine in the electrophoresis buffer, and in the gel, is very critical, as well as running the gel at a very low voltage for the second dimension is very critical to separate the positive and the negative supercoils.After staining and destaining the gel, according to the text protocol, use an imager to visualize the thermodistribution of the topoisomers. As seen in this gel, approximately 79%of the plasmids harboring TFO-directed ICLs migrate with a slower mobility through the agarose gel matrix when compared to the uncross-linked control plasmids. ChIP assays performed on lysates from human U2OS cells transfected with either control plasmid or plasmids containing TFO-directed ICLs show enrichment of HMGB1 at the P-ICL region compared to the control region when immunoprecipitated with anti-HMGB1 antibody.When HMGB1 was depleted from the cells via siRNA treatment, the P-ICL-specific enrichment was diminished. When the same samples were immunoprecipitated using an anti-IgG antibody, minimal PCR amplification was detected. Finally, in this figure, two-dimensional agarose gel electrophoresis demonstrates architectural modification of the TFO-directed ICL-containing plasmids as negative supercoiling by HMGB1 in HeLa cell extracts.Once mastered, this technique can be performed in approximately five days, if performed correctly. While attempting this procedure, it's very important to remember that all the washes should be done in the cold room, as room temperature washes may increase the background signal. Following this procedure, other methods, such as siRNA-mediated protein depletion, followed by mutation screening assays, can be performed in order to answer questions, such as, is the protein of interest involved in DNA repair?Or, does it significantly alter the mutation spectra during the process? This technique paved the way to study association between proteins and site-specific DNA damage. After watching this video, you should have a good idea of how to study the association of architectural proteins to target a DNA cross-links, and subsequently, determine the effect of such association on the topology of the DNA.Don't forget that working with ethidium bromide can be extremely hazardous, and therefore, proper protective gear should be always worn during performing this experiment.

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Strumenti per studiare il ruolo di architettura HMGB1 proteine ​​nella lavorazione di Helix deformante, DNA specifiche per sito interstrand Crosslinks

Strumenti per studiare il ruolo di architettura HMGB1 proteine nella lavorazione di Helix deformante, DNA specifiche per sito interstrand Crosslinks