Siamo particolarmente grati a Seth Darst per fornire proteine ​​RNAP e MFD e vettori di espressione. Siamo anche ringraziare Sergei Borukhov per la fornitura di Greb e Dan Zhang per il supporto tecnico. Questo lavoro è stato sostenuto da un finanziamento della National Institutes of Health (MOD) e da un Marie-Josee e Henry Kravis Fellowship presso l&#39;Università Rockefeller (RTP).

Questo metodo è stato utilizzato nella ricerca riportata in <a href="http://www.sciencemag.org/cgi/content-nw/full/327/5965/590/F3">Pomerantz e O&#39;Donnell, Science 327, 590-592 (2010)</a> . 1. Assemblaggio di un complesso RNAP fermato allungamento è stato eseguito come segue: 500 nM concentrazione finale di E. RNAP coli σ 70 Egli è stato mescolato con concentrazione del 5 nM finale di un modello di DNA biotinilato 3,6 kb che contiene il T7A1 promotore in 100 ml di tampone A (20 mM Tris-Cl (pH 7,5), 8 mM MgCl 2, 0.5 mM EDTA, 5 mM DTT, 10% glicerolo) per 10 minuti a 37 ° C. 100 mM di Apu e 40 mM ognuno di GTP, ATP e CTP sono stati aggiunti per altri 10 minuti a 37 ° C. 2. Immobilizzazione del complesso RNAP fermato allungamento su perline streptavidina è stata effettuata come segue: 200 ml di streptavidina sfere magnetiche patinata (Invitrogen) sono stati aggiunti alla reazione sopra per 10 minuti a temperatura ambiente. 3. Purificazione del complesso immobilizzato RNAP fermato allungamento è stato effettuato come segue: Le perle (da sopra) sono state lavate 5 volte con 0,9 ml di tampone A contenente 0,75 M di NaCl, 200 mg / ml di eparina, e 20 mg / ml ssDNA (Il surnatante è stato rimosso dopo ogni fase di lavaggio, di separazione magnetica.) Successivamente, la perline sono stati lavati 2 volte con 0,9 ml di tampone A. 4. Formazione di una forchetta replica a valle rispetto alla testa-on RNAP è stata eseguita come segue: Le perle (da sopra) sono stati risospesi in 100 ml di New England Biolabs buffer di 4 e 10 unità di Sap I (New England Biolabs) è stato aggiunto per 10 minuti a 37 ° C. Le perle sono stati lavati 3 volte con 0,9 ml di tampone A e poi risospeso in 50 ml di tampone T4 rapida reazione Legatura (New England Biolabs). 2 l di rapida ligasi T4 (New England Biolabs) è stato aggiunto insieme con 6 nM concentrazione finale di pre-ricotto DNA biforcuta (RP10, RP22, RP25) per 10 minuti a temperatura ambiente. Le perle sono stati lavati 3 volte con 0,9 ml di tampone A. 5. Assemblea dei replisoma e inizio della sintesi filone che porta al bivio replica è stata effettuata come segue: 448 pmol di DnaB (come esamero) è stata incubata con la 150 microlitri perle di tampone A (20 glicerolo mM Tris-Cl (pH 7,5), 8 mM MgCl 2, 0.5 mM EDTA, 5 mM DTT, 10%) per 30 s in 23 ° C. 4,9 pmol di Pol III * (Pol III HE meno β), 15 pmol di β, 2 mM ATP, e 60 mM ciascuno dei dGTP e dATP sono state aggiunte ad un volume di 200 l ed incubati per altri 5 minuti a 37 ° C. La replica è stata aperta in seguito l&#39;aggiunta di 10 mcg SSB e 24 mM ognuno di dATP e dTTP con [α-32 P] dTTP e [α-32 P] dCTP (attività specifica, 3.000-5.000 cpm / pmol) ad un volume finale di 250 microlitri. Reazioni sono state terminato dopo 10 minuti su l&#39;aggiunta di 12 ml di 500 mM EDTA. 6. Purificazione e concentrazione del radio-prodotti contrassegnati DNA è stata eseguita come segue: Le perle (da sopra) sono stati bolliti dopo la reazione è stata interrotta al fine di rimuovere il DNA dalle perline. Qualsiasi residuo di DNA che rimangono aderenti al perline è stato rimosso trattando le perle con proteinasi K in un volume di 10 ul per 30 minuti a 50 ° C. Le perle sono state poi bollito e il surnatante è stato rimosso dalla separazione magnetica. Il supernatante combinato contenente il DNA è stato purificato utilizzando il kit di pulizia Qiagen PCR. Purificato radio-marcato DNA dei prodotti sono stati poi analizzati in un gel alcalino di agarosio. Replica * in assenza di uno scontro RNAP fermato complesso allungamento è stata eseguita come sopra, però, σ 70 è stato omesso. Rappresentante dei risultati: Collisione del replisoma con una testa-on RNAP risultati di solito in due prodotti di 2,5 kb e 3,6 kb di lunghezza. Da 2,5 kb prodotto rappresenta la lunghezza del DNA dalla forcella al RNAP fermato ei risultati replisoma stallo sulla collisione con il RNAP. Il prodotto 3,6 kb rappresentare tutta la lunghezza del DNA e dei risultati sia da occupazione incompleta del promotore da parte RNAP o parziale replisoma lettura tramite del capo-on RNAP. Un buon risultato o accurata dimostra che circa il 50% full-length del DNA viene prodotto. Tuttavia, in alcuni casi meno occupazione del promotore da RNAP verifica e una più alta percentuale di full-length del DNA si osserva quanto una popolazione maggiore di replisomes non incontrano uno scontro RNAP. Replica in assenza di un RNAP fermato in un solo full-length del DNA (3,6 kb). <img src="/files/ftp_upload/1919/1919fig1.jpg" alt="Figura 1" /> Figura. 1 Il replisoma è impedita da una testa-on RNAP. (A) di setup sperimentale. A E. coli RNAP complesso allungamento fermato è stato montato su un DNA biotinilato contenente il promotore T7A1 come descritto in precedenza (9). In breve, un complesso allungamento fermato è stato formato da 20 bps a valle del promotore incubando oloenzima RNAP con il DNA biotinilato per 10 minuti seguita dall&#39;aggiunta di Apu, GTP, ATP e CTP per altri 10 min. Perline streptavidina sono stati aggiunti per altri 10 minuti poi le perle sono state lavate cinque volte ciascuna con 0,9 ml di tampone contenente 0.75M NaCl, 200 mg / ml di eparina, e 100 nM a singolo filamento di DNA per rimuovere instabile RNAP-DNA complessi e NTP in eccesso . Il DNA è stato poi digerito con Sapi, lavato, e legato ad una pre-ricotto DNA biforcuta. Le perle sono stati lavati di nuovo prima del montaggio del replisoma. Il promotore si trova a 2,5 kb dalla forcella ed è orientato alla trascrizione diretta verso la forcella. (B) DnaB è stata aggiunta poi la replisoma è stato assemblato e replica è stato avviato sia in presenza (corsia 2) o assenza (corsia 1) di un a testa alta RNAP.

<ol>
	<li>Rudolph, C. J., Dhillon, P., Moore, T., Lloyd, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Avoiding+and+resolving+conflicts+between+DNA+replication+and+transcription.">Avoiding and resolving conflicts between DNA replication and transcription.</a> DNA Repair (Amst). 6, 981-98 (2007).</li><li>Vilette, D., Ehrlich, S. D., Michel, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription-induced+deletions+in+plasmid+vectors:+M13+DNA+replication+as+a+source+of+instability.">Transcription-induced deletions in plasmid vectors: M13 DNA replication as a source of instability.</a> Mol Gen Genet. 252, 398-398 (1996).</li><li>Trautinger, B. W., Jaktaji, R. P., Rusakova, E., Lloyd, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=RNA+polymerase+modulators+and+DNA+repair+activities+resolve+conflicts+between+DNA+replication+and+transcription.">RNA polymerase modulators and DNA repair activities resolve conflicts between DNA replication and transcription.</a> Mol Cell. 19, 247-247 (2005).</li><li>McGlynn, P., Lloyd, R. G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Modulation+of+RNA+Polymerase+by+(p)ppGpp+Reveals+a+RecG-Dependent+Mechanism+for+Replication+Fork+Progression.">Modulation of RNA Polymerase by (p)ppGpp Reveals a RecG-Dependent Mechanism for Replication Fork Progression.</a> Cell. 101, 35-35 (2000).</li><li>McGlynn, P., Guy, C. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+forks+blocked+by+protein-DNA+complexes+have+limited+stability+in+vitro.">Replication forks blocked by protein-DNA complexes have limited stability in vitro.</a> J Mol Biol. 381, 249-249 (2008).</li><li>Labib, K., Hodgson, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+fork+barriers:+pausing+for+a+break+or+stalling+for+time.">Replication fork barriers: pausing for a break or stalling for time.</a> EMBO Rep. 8, 346-346 (2007).</li><li>Bidnenko, V., Ehrlich, S. D., Michel, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+fork+collapse+at+replication+terminator+sequences.">Replication fork collapse at replication terminator sequences.</a> Embo J. 21, 3898-3898 (2002).</li><li>Pomerantz, R. T., O'Donnell, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replisome+mechanics:+insights+into+a+twin+DNA+polymerase+machine.">Replisome mechanics: insights into a twin DNA polymerase machine.</a> Trends Microbiol. 15, 156-156 (2007).</li><li>Pomerantz, R. T., O'Donnell, 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+replisome+uses+mRNA+as+a+primer+after+colliding+with+RNA+polymerase.">The replisome uses mRNA as a primer after colliding with RNA polymerase.</a> Nature. 456, 762-762 (2008).</li><li>Heller, R. C., Marians, K. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+fork+reactivation+downstream+of+a+blocked+nascent+leading+strand.">Replication fork reactivation downstream of a blocked nascent leading strand.</a> Nature. 439, 557-557 (2006).</li><li>Yuzhakov, A., Turner, J., O'Donnell, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replication+fork+reactivation+downstream+of+a+blocked+nascent+leading+strand.">Replication fork reactivation downstream of a blocked nascent leading strand.</a> Cell. 86, 557-557 (1996).</li><li>Hinkle, D. C., Ring, J., Chamberlin, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Replisome+assembly+reveals+the+basis+for+asymmetric+function+in+leading+and+lagging+strand+replication.">Replisome assembly reveals the basis for asymmetric function in leading and lagging strand replication.</a> J Mol Biol. 70, 197-197 (1972).</li><li>Kaplan, D. L., O'Donnell, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Studies+of+the+binding+of+Escherichia+coli+RNA+polymerase+to+DNA.+V.+T7+RNA+chain+initiation+by+enzyme-DNA+complexes.">Studies of the binding of Escherichia coli RNA polymerase to DNA. V. T7 RNA chain initiation by enzyme-DNA complexes.</a> Mol Cell. 15, 453-453 (2004).</li><li>Park, J. S., Marr, M. T., Roberts, J. W. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Twin+DNA+pumps+of+a+hexameric+helicase+provide+power+to+simultaneously+melt+two+duplexes.">Twin DNA pumps of a hexameric helicase provide power to simultaneously melt two duplexes.</a> Cell. 109, 757-757 (2002).</li><li>Hanawalt, P. C., Spivak, G. E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=coli+Transcription+repair+coupling+factor+(Mfd+protein)+rescues+arrested+complexes+by+promoting+forward+translocation.">coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation.</a> Nat Rev Mol Cell Biol. 9, 958-958 (2008).</li><li>Hanawalt, P. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription-coupled+DNA+repair:+two+decades+of+progress+and+surprises.">Transcription-coupled DNA repair: two decades of progress and surprises.</a> Science. 266, 1957-1957 (1994).</li><li>Selby, C. P., Sancar, A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transcription-coupled+repair+and+human+disease.">Transcription-coupled repair and human disease.</a> J Biol Chem. 270, 4882-4882 (1995).</li><li>Liu, B., Alberts, B. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+and+function+of+transcription-repair+coupling+factor.+I.+Structural+domains+and+binding+properties.+Head-on+collision+between+a+DNA+replication+apparatus+and+RNA+polymerase+transcription+complex.">Structure and function of transcription-repair coupling factor. I. Structural domains and binding properties. Head-on collision between a DNA replication apparatus and RNA polymerase transcription complex.</a> Science. 267, 1131-1131 (1995).</li><li>George, D. L., Witkin, E. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Slow+excision+repair+in+an+mfd+mutant+of+Escherichia+coli+B/r.">Slow excision repair in an mfd mutant of Escherichia coli B/r.</a> Mol Gen Genet. 133, 283-283 (1974).</li></ol>

Lavare il complesso allungamento fermato legato ai talloni con sale alto è fondamentale al fine di rimuovere qualsiasi instabili o non specificamente molecole RNAP legato. RNAP ha un&#39;affinità molto elevata per le strutture di tipo iniettore-stampo di DNA. Quindi, è necessario rimuovere tale non specifici RNAP-DNA complessi al fine di eseguire la replica dal primer-template. Concentrando la radio prodotti contrassegnati con la purificazione del DNA Qiagen PCR kit è critica anche al fine di ottenere un elevato rapporto segnale sufficientemente radioattive che possono essere osservati nel gel.

<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">	
		
		<div>
		<table border="1">
		<thead>
		<tr>
		<th>Material Name</th>
		<th>Type</th>
		<th>Company</th>
		<th>Catalogue Number</th>
		<th>Comment</th>
		</tr>
		</thead>
		<tbody>
		
<tr>
<td>Dynabeads M-270</td>
<td>&nbsp;</td>
<td>Invitrogen</td>
<td>653.05</td>
<td>&nbsp;</td>
<tr>
<td>SapI</td>
<td>&nbsp;</td>
<td>NEB</td>
<td>R0569S</td>
<td>&nbsp;</td>
<tr>
<td>T4 Quick Ligase</td>
<td>&nbsp;</td>
<td>NEB</td>
<td>M2200S</td>
<td>&nbsp;</td>
<tr>
<td>PCR Purification Kit</td>
<td>&nbsp;</td>
<td>Qiagen</td>
<td>28104</td>
<td>&nbsp;</td>		</tbody>
		</table>
		</div>

direct restart of a replication fork stalled by a head-on rna polymerase

Gli studi in vivo suggeriscono che le forcelle replica vengono arrestati a causa di incontri con testa alta complessi trascrizione. Eppure, il destino del replisoma e RNA polimerasi (RNAP) a seguito di una collisione frontale è sconosciuta. Qui, troviamo che la E. coli bancarelle replisoma su collisione con uno scontro complesso di trascrizione, ma invece di crollare, la forcella di replicazione resta altamente stabile e riprende alla fine allungamento dopo lo spostamento del RNAP dal DNA. Troviamo anche che la trascrizione di riparazione fattore di accoppiamento, DM, promuove riavviare diretta della forcella a seguito della collisione, facilitando lo spostamento del RNAP. Questi risultati dimostrano la stabilità intrinseca dell&#39;apparato replica e un ruolo nuovo per la trascrizione accoppiati percorso riparazione nella promozione di replica passato un blocco RNAP.

Watch this Scientific Journal Video about Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase at JoVE.com

Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Il destino del replisoma a seguito di una collisione con un testa-a RNA polimerasi (RNAP) è sconosciuta. Troviamo che le bancarelle replisoma su collisione con uno scontro RNAP, ma riprende allungamento dopo lo spostamento del RNAP dal DNA. MFD promuove riavviare la replica, facilitando lo spostamento del RNAP dopo la collisione.

Riavviare diretta di una forchetta di replica in stallo da un Head-On polimerasi RNA

In vivo studies suggest that replication forks are arrested due to encounters with head-on transcription complexes. Yet, the fate of the replisome and RNA ...

direct-restart-replication-fork-stalled-head-on-rna

Research

JoVE Journal

Biology

13.5K Views.  Rockefeller University. Il destino del replisoma a seguito di una collisione con un testa-a RNA polimerasi (RNAP) è sconosciuta. Troviamo che le bancarelle replisoma su collisione con uno scontro RNAP, ma riprende allungamento dopo lo spostamento del RNAP dal DNA. MFD promuove riavviare la replica, facilitando lo spostamento del RNAP dopo la collisione.

Video: Direct Restart of a Replication Fork Stalled by a Head-On RNA Polymerase

Production of Replication-Defective Retrovirus by Transient Transfection of 293T cells

Our lab studies human myeloproliferative diseases induced by such oncogenes as Bcr-Abl or growth factor receptor-derived oncogenes (ZNF198-FGFR1, Bcr-PDGFR&#945;, etc.). We are able to model and study a human-like disease in our mouse model, by transplanting bone marrow cells previously infected with a retrovirus expressing the oncogene of interest. Replication-defective retrovirus encoding a human oncogene and a marker (GFP, RFP, antibiotic resistance gene, etc.) is produced by a transient transfection protocol using 293T cells, a human renal epithelial cell line transformed by the adenovirus E1A gene product. 293 cells have the unusual property of being highly transfectable by calcium phosphate (CaPO4), with up to 50-80% transfection efficiency readily attainable. Here, we co-transfect 293 cells with a retroviral vector expressing the oncogene of interest and a plasmid that expresses the gag-pol-env packaging functions, such as the single-genome packaging constructs kat or pCL, in this case the EcoPak plasmid. The initial transfection is further improved by use of chloroquine. Stocks of ecotropic virus, collected as culture supernatant 48 hrs. post-transfection, can be stored at -80&deg;C and used for infection of cell-lines in view of transformation and in vitro studies, or primary cells such as mouse bone marrow cells, that can then be used for transplant in our mouse model.

This technique demonstrates an efficient way to prepare replication-defective retroviral stocks encoding a human oncogene, and subsequently used for induction of myeloproliferative disease in the mouse model.

Produzione di replica-difettoso da Retrovirus trasfezione transiente di cellule 293T

Our lab studies human myeloproliferative diseases induced by such oncogenes as Bcr-Abl or growth factor receptor-derived oncogenes (ZNF198-FGFR1, ...

Ricerca

Biologia

Visualizing Single-molecule DNA Replication with Fluorescence Microscopy

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA template is attached to a functionalized glass coverslip and replicated extensively after introduction of replication proteins and nucleotides (Figure 1). The growing product double-strand DNA (dsDNA) is extended with laminar flow and visualized by using an intercalating dye. Measuring the position of the growing DNA end in real time allows precise determination of replication rate (Figure 2). Furthermore, the length of completed DNA products reports on the processivity of replication. This experiment can be performed very easily and rapidly and requires only a fluorescence microscope with a reasonably sensitive camera.


This protocol demonstrates a simple single-molecule fluorescence microscopy technique for visualizing DNA replication by individual replisomes in real time.

Visualizzazione singola molecola di DNA replica con microscopia a fluorescenza

We describe a simple fluorescence microscopy-based real-time method for observing DNA replication at the single-molecule level. A circular, forked DNA ...

Direct Observation of Enzymes Replicating DNA Using a Single-molecule DNA Stretching Assay

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. Linearized &lambda; DNA is modified to have a biotin on the end of one strand, and a digoxigenin moiety on the other end of the same strand. The biotinylated end is attached to a functionalized glass coverslip and the digoxigeninated end to a small bead. The assembly of these DNA-bead tethers on the surface of a flow cell allows a laminar flow to be applied to exert a drag force on the bead. As a result, the DNA is stretched close to and parallel to the surface of the coverslip at a force that is determined by the flow rate (Figure 1). The length of the DNA is measured by monitoring the position of the bead. Length differences between single- and double-stranded DNA are utilized to obtain real-time information on the activity of the replication proteins at the fork. Measuring the position of the bead allows precise determination of the rates and processivities of DNA unwinding and polymerization (Figure 2).

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system.

Osservazione diretta del DNA Enzimi Replica utilizzando un singolo-molecola di DNA Stretching Assay

We describe a method for observing real time replication of individual DNA molecules mediated by proteins of the bacteriophage replication system. ...

Visualizing RNA Localization in Xenopus Oocytes

RNA localization is a conserved mechanism of establishing cell polarity. Vg1 mRNA localizes to the vegetal pole of Xenopus laevis oocytes and acts to spatially restrict gene expression of Vg1 protein. Tight control of Vg1 distribution in this manner is required for proper germ layer specification in the developing embryo. RNA sequence elements in the 3' UTR of the mRNA, the Vg1 localization element (VLE) are required and sufficient to direct transport. To study the recognition and transport of Vg1 mRNA in vivo, we have developed an imaging technique that allows extensive analysis of trans-factor directed transport mechanisms via a simple visual readout. 
To visualize RNA localization, we synthesize fluorescently labeled VLE RNA and microinject this transcript into individual oocytes. After oocyte culture to allow transport of the injected RNA, oocytes are fixed and dehydrated prior to imaging by confocal microscopy. Visualization of mRNA localization patterns provides a readout for monitoring the complete pathway of RNA transport and for identifying roles in directing RNA transport for cis-acting elements within the transcript and trans-acting factors that bind to the VLE (Lewis et al., 2008, Messitt et al., 2008). We have extended this technique through co-localization with additional RNAs and proteins (Gagnon and Mowry, 2009, Messitt et al., 2008), and in combination with disruption of motor proteins and the cytoskeleton (Messitt et al., 2008) to probe mechanisms underlying mRNA localization.

Visualizing RNA Localization in Xenopus Oocytes

Visualization of in vivo RNA transport is accomplished by microinjection of fluorescently labeled RNA transcripts into Xenopus oocytes, followed by confocal microscopy.

Visualizzazione RNA localizzazione in Xenopus Gli oociti

RNA localization is a conserved mechanism of establishing cell polarity.  Vg1 mRNA localizes to the vegetal pole of Xenopus laevis oocytes and acts to ...

Direct Delivery of MIF Morpholinos Into the Zebrafish Otocyst by Injection and Electroporation Affects Inner Ear Development

In recent years, electroporation has become a popular technique for in vivo transfection of DNA, RNA, and morpholinos into various tissues, including the eye, brain, and somites of zebrafish. The advantage of electroporation over other methods of genetic manipulation is that specific tissues can be targeted, both spatially and temporally, for the introduction of macromolecules by the application of electrical current. Here we describe the use of electroporation for transfecting mif and mif-like morpholinos into the tissues of the developing inner ear of the zebrafish. In past studies, mif morpholino injected into embryos at the 1- to 8-cell stage resulted in widespread morphological changes in the nervous system and eye, as well as the ear. By targeting the tissues of the inner ear at later stages in development, we can determine the primary effects of MIF in the developing inner ear, as opposed to secondary effects that may result from the influence of other tissues. By using phalloidin and acetylated tubulin staining to study the morphology of neurons, neuronal processes, and hair cells associated with the posterior macula, we were able to assess the efficacy of electroporation as a method for targeted transfection in the zebrafish inner ear. The otic vesicles of 24hpf embryos were injected with morpholinos and electroporated and were then compared to embryos that had received no treatment or had been only injected or electroporated. Embryos that were injected and electroporated showed a decrease in hair cell numbers, decreased innervation by the statoacoustic ganglion (SAG) and fewer SAG neurons compared with control groups. Our results showed that direct delivery of morpholinos into otocysts at later stages avoids the non-specific nervous system and neural crest effects of morpholinos delivered at the 1-8 cell stage. It also allows examination of effects that are directed to the inner ear and not secondary effects on the ear from primary effects on the brain, neural crest or periotic mesenchyme.

A method to deliver morpholinos directly into the zebrafish otocyst at 24hpf has been developed. Using microinjection of morpholinos into the lumen of otic vesicle and electroporation to effect penetration, we were able to bypass the effect of morpholinos on the brain and obtain effects specific to the inner ear.

Consegna diretta di Morpholinos MIF Into the Otocyst Zebrafish di iniezione e di elettroporazione influenza lo sviluppo dell&#39;orecchio interno

In recent years, electroporation has become a popular technique for in vivo transfection of DNA, RNA, and morpholinos into various tissues, including the ...

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence (T7, T3, SP6) and the gene to be transcribed (Figure 1A). A typical transcription reaction consists of the template DNA, RNA polymerase, ribonucleotide triphosphates, RNase inhibitor and buffer containing Mg2+ ions.
Large amounts of high quality RNA are often required for a variety of applications. Use of in vitro transcription has been reported for RNA structure and function studies such as splicing1, RNAi experiments in mammalian cells2, antisense RNA amplification by the "Eberwine method"3, microarray analysis4 and for RNA vaccine studies5. The technique can also be used for producing radiolabeled and dye labeled probes6. Warren, et al. recently reported reprogramming of human cells by transfection with in vitro transcribed capped RNA7. The T7 High Yield RNA Synthesis Kit from New England Biolabs has been designed to synthesize up to 180 &mu;g RNA per 20 &mu;l reaction. RNA of length up to 10kb has been successfully transcribed using this kit. Linearized plasmid DNA, PCR products and synthetic DNA oligonucleotides can be used as templates for transcription as long as they have the T7 promoter sequence upstream of the gene to be transcribed.
Addition of a 5' end cap structure to the RNA is an important process in eukaryotes. It is essential for RNA stability8, efficient translation9, nuclear transport10 and splicing11. The process involves addition of a 7-methylguanosine cap at the 5' triphosphate end of the RNA. RNA capping can be carried out post-transcriptionally using capping enzymes or co-transcriptionally using cap analogs. In the enzymatic method, the mRNA is capped using the Vaccinia virus capping enzyme12,13. The enzyme adds on a 7-methylguanosine cap at the 5' end of the RNA using GTP and S-adenosyl methionine as donors (cap 0 structure). Both methods yield functionally active capped RNA suitable for transfection or other applications14 such as generating viral genomic RNA for reverse-genetic systems15 and crystallographic studies of cap binding proteins such as eIF4E16.
In the method described below, the T7 High Yield RNA Synthesis Kit from NEB is used to synthesize capped and uncapped RNA transcripts of Gaussia luciferase (GLuc) and Cypridina luciferase (CLuc). A portion of the uncapped GLuc RNA is capped using the Vaccinia Capping System (NEB). A linearized plasmid containing the GLuc or CLuc gene and T7 promoter is used as the template DNA. The transcribed RNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity. Capped CLuc RNA is used as the internal control to normalize GLuc expression.

In vitro Transcription and Capping of Gaussia Luciferase mRNA Followed by HeLa Cell Transfection

This method describes high yield in vitro synthesis of both capped and uncapped mRNA from a linearized plasmid containing the Gaussia luciferase (GLuc) gene. The RNA is purified and a fraction of the uncapped RNA is enzymatically capped using the Vaccinia virus capping enzyme. In the final step, the mRNA is transfected into HeLa cells and cell culture supernatants are assayed for luciferase activity.

Trascrizione in vitro e tappatura mRNA Luciferase Gaussia Seguito da cellule HeLa Transfection

In vitro transcription is the synthesis of RNA transcripts by RNA polymerase from a linear DNA template containing the corresponding promoter sequence ...

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

Marine elasmobranchs are valued animal models for biomedical and genomic studies as they are the most primitive vertebrates to have adaptive immunity and have unique mechanisms for osmoregulation 1-3. As the most primitive living jawed-vertebrates with paired appendages, elasmobranchs are an evolutionarily important model, especially for studies in evolution and development. Marine elasmobranchs have also been used to study aquatic toxicology and stress physiology in relationship to climate change 4. Thus, development and adaptation of methodologies is needed to facilitate and expand the use of these primitive vertebrates to multiple biological disciplines. Here I present the successful adaptation of RNA whole mount in situ hybridization and histological techniques to study gene expression and cell histology in elasmobranchs.
Monitoring gene expression is a hallmark tool of developmental biologists, and is widely used to investigate developmental processes 5. RNA whole mount in situ hybridization allows for the visualization and localization of specific gene transcripts in tissues of the developing embryo. The expression pattern of a gene's message can provide insight into what developmental processes and cell fate decisions a gene may control. By comparing the expression pattern of a gene at different developmental stages, insight can be gained into how the role of a gene changes during development.
While whole mount in situ's provides a means to localize gene expression to tissue, histological techniques allow for the identification of differentiated cell types and tissues. Histological stains have varied functions. General stains are used to highlight cell morphology, for example hematoxylin and eosin for general staining of nuclei and cytoplasm, respectively. Other stains can highlight specific cell types. For example, the alcian blue stain reported in this paper is a widely used cationic stain to identify mucosaccharides. Staining of the digestive tract with alcian blue can identify the distribution of goblet cells that produce mucosaccharides. Variations in mucosaccharide constituents on short peptides distinguish goblet cells by function within the digestive tract 6. By using RNA whole mount in situ's and histochemical methods concurrently, cell fate decisions can be linked to gene-specific expression.
Although RNA in situ's and histochemistry are widely used by researchers, their adaptation and use in marine elasmobranchs have met limited and varied success. Here I present protocols developed for elasmobranchs and used on a regular basis in my laboratory. Although further modification of the RNA in situ's hybridization method may be needed to adapt to different species, the protocols described here provide a strong starting point for researchers wanting to adapt the use of marine elasmobranchs to their scientific inquiries.

RNA In situ Hybridization in Whole Mount Embryos and Cell Histology Adapted for Marine Elasmobranchs

By combining methods for RNA whole mount in situ hybridization and histology, gene expression can be linked with cell fate decisions in the developing embryo. These methods have been adapted to marine elasmobranchs and facilitate the use of these animals as model organisms for biomedical, toxicology and comparative studies.

RNA<em&gt; In situ</emIbridazione&gt; in embrioni Mount interi e istologia Adattato per Elasmobranchi Marine

Marine  elasmobranchs are valued animal models for biomedical and genomic studies as  they are the most primitive vertebrates to have adaptive immunity ...

RNA Isolation from Mouse Pancreas: A Ribonuclease-rich Tissue

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge. As a primary function of the pancreas is to aid in digestion, mouse pancreas may contain as much a 75 mg of ribonuclease. We report modifications of standard phenol/guanidine thiocyanate lysis reagent protocols to isolate RNA from mouse pancreas. Guanidine thiocyanate is a strong protein denaturant and will effectively disrupt the activity of ribonuclease under most conditions. However, critical modifications to standard protocols are necessary to successfully isolate RNA from ribonuclease-rich tissues. Key steps include a high lysis reagent to tissue ratio, removal of undigested tissue prior to phase separation and inclusion of a ribonuclease inhibitor to the RNA solution. Using these and other modifications, we routinely isolate RNA with RNA Integrity Number (RIN) greater than 7. The isolated RNA is of suitable quality for routine gene expression analysis. Adaptation of this protocol to isolate RNA from ribonuclease rich tissues besides the pancreas should be readily achievable.

We report a procedure to isolate RNA with high integrity from the ribonuclease rich mouse pancreas.

Isolamento dell&#39;RNA da mouse Pancreas: Un Tessuto ricco Ribonucleasi

Isolation of high-quality RNA from ribonuclease-rich tissue such as mouse pancreas presents a challenge.  As a primary function of the pancreas is to aid ...

Development of a Quantitative Recombinase Polymerase Amplification Assay with an Internal Positive Control

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to quantify DNA sample concentration using a standard curve. In this manuscript, a detailed protocol for developing and implementing a real-time quantitative recombinase polymerase amplification assay (qRPA assay) is provided. Using HIV-1 DNA quantification as an example, the assembly of real-time RPA reactions, the design of an internal positive control (IPC) sequence, and co-amplification of the IPC and target of interest are all described. Instructions and data processing scripts for the construction of a standard curve using data from multiple experiments are provided, which may be used to predict the concentration of unknown samples or assess the performance of the assay. Finally, an alternative method for collecting real-time fluorescence data with a microscope and a stage heater as a step towards developing a point-of-care qRPA assay is described. The protocol and scripts provided may be used for the development of a qRPA assay for any DNA target of interest.

Provided is a protocol for developing a real-time recombinase polymerase amplification assay to quantify initial concentration of DNA samples using either a thermal cycler or a microscope and stage heater. Also described is the development of an internal positive control. Scripts are provided for processing raw real-time fluorescence data.

Sviluppo di un Quantitative ricombinasi Polymerase Amplificazione Assay con un controllo positivo interno

It was recently demonstrated that recombinase polymerase amplification (RPA), an isothermal amplification platform for pathogen detection, may be used to ...

Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System

Obstacles present on DNA, including tightly-bound proteins and various lesions, can severely inhibit the progression of the cell&#39;s replication machinery. The stalling of a replisome can lead to its dissociation from the chromosome, either in part or its entirety, leading to the collapse of the replication fork. The recovery from this collapse is a necessity for the cell to accurately complete chromosomal duplication and subsequently divide. Therefore, when the collapse occurs, the cell has evolved diverse mechanisms that take place to restore the DNA fork and allow replication to be completed with high fidelity. Previously, these replication repair pathways in bacteria have been studied using UV damage, which has the disadvantage of not being localized to a known site. This manuscript describes a system utilizing a Fluorescence Repressor Operator System (FROS) to create a site-specific protein block that can induce the stalling and collapse of replication forks in Escherichia coli. Protocols detail how the status of replication can be visualized in single living cells using fluorescence microscopy and DNA replication intermediates can be analyzed by 2-dimensional agarose gel electrophoresis. Temperature sensitive mutants of replisome components (e.g. DnaBts) can be incorporated into the system to induce a synchronous collapse of the replication forks. Furthermore, the roles of the recombination proteins and helicases that are involved in these processes can be studied using genetic knockouts within this system.

Inducing a Site Specific Replication Blockage in E. coli Using a Fluorescent Repressor Operator System

We describe here a system utilizing a site-specific, reversible in vivo protein block to stall and collapse replication forks in Escherichia coli. The establishment of the replication block is evaluated by fluorescence microscopy and neutral-neutral 2-dimensional agarose gel electrophoresis is used to visualize replication intermediates.