<meta charset="utf8"></head><body>CMG-vermittelte DNA-Dewindung durch Wachstum des ssDNA-RPA-Trakts beobachtet

<ol>
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X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mechanism+of+eukaryotic+CMG+helicase+activation.">The mechanism of eukaryotic CMG helicase activation.</a> Nature. 555 (7695), 265-268 (2018).</li><li>Ilves, I., Petojevic, T., Pesavento, J. J., Botchan, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Activation+of+the+MCM2-7+helicase+by+association+with+Cdc45+and+GINS+proteins.">Activation of the MCM2-7 helicase by association with Cdc45 and GINS proteins.</a> Mol Cell. 37 (2), 247-258 (2010).</li><li>Dewar, J. M., Walter, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanisms+of+DNA+replication+termination.">Mechanisms of DNA replication termination.</a> Nat Rev Mol Cell Biol. 18 (8), 507-516 (2017).</li><li>Burnham, D. R., Kose, H. B., Hoyle, R. B., Yardimci, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+mechanism+of+DNA+unwinding+by+the+eukaryotic+replicative+helicase.">The mechanism of DNA unwinding by the eukaryotic replicative helicase.</a> Nat Commun. 10 (1), 2159 (2019).</li><li>Kose, H. B., Larsen, N. B., Duxin, J. P., Yardimci, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Dynamics+of+the+eukaryotic+replicative+helicase+at+lagging-strand+protein+barriers+support+the+steric+exclusion+model.">Dynamics of the eukaryotic replicative helicase at lagging-strand protein barriers support the steric exclusion model.</a> Cell Rep. 26 (8), 2113-2125.e6 (2019).</li><li>Kose, H. B., Xie, S., Cameron, G., Strycharska, M. S., Yardimci, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Duplex+DNA+engagement+and+RPA+oppositely+regulate+the+DNA-unwinding+rate+of+CMG+helicase.">Duplex DNA engagement and RPA oppositely regulate the DNA-unwinding rate of CMG helicase.</a> Nat Commun. 11 (1), 3713 (2020).</li><li>Tanner, N. A., Van Oijen, A. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Visualizing+DNA+replication+at+the+single-molecule+level.">Visualizing DNA replication at the single-molecule level.</a> Methods Enzymol. 475, 259-278 (2010).</li><li>Swoboda, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Enzymatic+oxygen+scavenging+for+photostability+without+ph+drop+in+single-molecule+experiments.">Enzymatic oxygen scavenging for photostability without ph drop in single-molecule experiments.</a> ACS Nano. 6 (7), 6364-6369 (2012).</li><li>Baris, Y., Taylor, M. R. G., Aria, V., Yeeles, J. T. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Fast+and+efficient+DNA+replication+with+purified+human+proteins.">Fast and efficient DNA replication with purified human proteins.</a> Nature. 606, 204-210 (2022).</li><li>Lewis, J. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tunability+of+DNA+polymerase+stability+during+eukaryotic+DNA+replication.">Tunability of DNA polymerase stability during eukaryotic DNA replication.</a> Mol Cell. 77 (1), 17-25.e5 (2020).</li><li>Li, Z., Xu, X. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Post-translational+modifications+of+the+mini-chromosome+maintenance+proteins+in+DNA+replication.">Post-translational modifications of the mini-chromosome maintenance proteins in DNA replication.</a> Genes. 10 (5), 331 (2019).</li><li>Lewis, J. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Mechanism+of+replication+origin+melting+nucleated+by+CMG+helicase+assembly.">Mechanism of replication origin melting nucleated by CMG helicase assembly.</a> Nature. 606 (7916), 1007-1014 (2022).</li><li>Zeman, M. K., Cimprich, K. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Causes+and+consequences+of+replication+stress.">Causes and consequences of replication stress.</a> Nat Cell Biol. 16 (1), 2-9 (2014).</li><li>Sparks, J. L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+CMG+helicase+bypasses+DNA-protein+cross-links+to+facilitate+their+repair.">The CMG helicase bypasses DNA-protein cross-links to facilitate their repair.</a> Cell. 176 (1-2), 167-181.e21 (2019).</li><li>Taylor, M. R. G., Yeeles, J. T. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+initial+response+of+a+eukaryotic+replisome+to+DNA+damage.">The initial response of a eukaryotic replisome to DNA damage.</a> Mol Cell. 70 (6), 1067-1080.e12 (2018).</li><li>Amunugama, 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=Replication+fork+reversal+during+DNA+interstrand+crosslink+repair+requires+CMG+unloading.">Replication fork reversal during DNA interstrand crosslink repair requires CMG unloading.</a> Cell Rep. 23 (12), 3419-3428 (2018).</li><li>Wu, R. 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=TRAIP+is+a+master+regulator+of+DNA+interstrand+crosslink+repair.">TRAIP is a master regulator of DNA interstrand crosslink repair.</a> Nature. 567 (7747), 267-272 (2019).</li><li>Vrtis, K. B., Dewar, J. M., Chistol, G., Wu, R. A., Graham, T. G. W., Walter, J. C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-strand+DNA+breaks+cause+replisome+disassembly.">Single-strand DNA breaks cause replisome disassembly.</a> Mol Cell. 81 (6), 1309-1318.e6 (2021).</li></ol>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>2-Mercaptoethanol</td>
			<td>Sigma-Aldrich</td>
			<td>M3148-25ML</td>
			<td></td>
		</tr>
		<tr>
			<td>Acrylamide / Bis Solution 40%&#160;</td>
			<td>BioRad</td>
			<td>1610148</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose UltraPure&#160;</td>
			<td>Invitrogen</td>
			<td>16500-500</td>
			<td>Used to prepare Tris Buffer (pH 8)</td>
		</tr>
		<tr>
			<td>&#196;KTA Pure&#160;</td>
			<td>GE Healthcare</td>
			<td>-</td>
			<td>Used with Fraction Collector F9-C; protein purification system</td>
		</tr>
		<tr>
			<td>ANTI-FLAG M2 affinity gel</td>
			<td>Sigma-Aldrich</td>
			<td>A2220</td>
			<td></td>
		</tr>
		<tr>
			<td>APS 10%&#160;</td>
			<td>Sigma-Aldrich</td>
			<td>A3678-25G</td>
			<td></td>
		</tr>
		<tr>
			<td>ATP (200 mM)</td>
			<td>Sigma-Aldrich</td>
			<td>A7699-5G</td>
			<td></td>
		</tr>
		<tr>
			<td>ATP-g-s (100 mM)</td>
			<td>Sigma-Aldrich</td>
			<td>11162306001</td>
			<td></td>
		</tr>
		<tr>
			<td>Biotin-PEG coverslip</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Prepared as described: https://doi.org/10.1016/j.ymeth.2012.03.033</td>
		</tr>
		<tr>
			<td>Biotinylated anti-digoxigenin antibody&#160;</td>
			<td>Perkin Elmer</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Blu Tack</td>
			<td>Bostik</td>
			<td>N/A</td>
			<td>Adhesive putty</td>
		</tr>
		<tr>
			<td>Boric acid</td>
			<td>Thermo Fisher Scientific</td>
			<td>B/3800/53</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA; 33 mg/mL</td>
			<td>SIGMA-ALDRICH</td>
			<td>A3858-10G</td>
			<td>Diluted from the stock</td>
		</tr>
		<tr>
			<td>CaCl2</td>
			<td>Sigma-Aldrich</td>
			<td>C7902</td>
			<td></td>
		</tr>
		<tr>
			<td>CaptoHiRes Q (5/50)</td>
			<td>Cytiva</td>
			<td>29275878</td>
			<td>Connected to the AKTA protein purification system; high-resolution ion exchange chromatography column</td>
		</tr>
		<tr>
			<td>Casein (5% in water, 50 mg/mL)</td>
			<td>Sigma-Aldrich</td>
			<td>C4765-10ML</td>
			<td></td>
		</tr>
		<tr>
			<td>ChemiDoc system</td>
			<td>Bio-Rad</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Clips</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Cutting board</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Dialysis tubing (3.5 kDa)</td>
			<td>Fisher Scientific</td>
			<td>11425859</td>
			<td></td>
		</tr>
		<tr>
			<td>digoxigenin-11-dUTP</td>
			<td>Roche</td>
			<td>11209256910</td>
			<td></td>
		</tr>
		<tr>
			<td>DNA loading dye 6x&#160;</td>
			<td>NEB</td>
			<td>B7024S</td>
			<td></td>
		</tr>
		<tr>
			<td>dNTP 10 mM</td>
			<td>NEB</td>
			<td>N0447S</td>
			<td></td>
		</tr>
		<tr>
			<td>Double-sided tape (0.14 mm thick)</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Fluorochem Limited</td>
			<td>M02712-10G</td>
			<td></td>
		</tr>
		<tr>
			<td>DYKDDDDK peptide&#160;</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Synthetised by chemical biology STP of The Francis Crick Institute</td>
		</tr>
		<tr>
			<td>EDTA</td>
			<td>Thermo Fisher Scientific</td>
			<td>D/0700/68</td>
			<td></td>
		</tr>
		<tr>
			<td>EGFP-RPA&#160;</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Purified as desribed in &#8216;Single Molecule Analysis&#8217;, Series Methods in Molecular Biology, Vol. 783 (2011), Peterman, E. J. G. and Wuite G. J. L. editors, Humana Press. Protein information: 2 mM, human, expressed in E. coli.</td>
		</tr>
		<tr>
			<td>EGTA</td>
			<td>Sigma-Aldrich</td>
			<td>03779-10G</td>
			<td></td>
		</tr>
		<tr>
			<td>Epoxy - 5 minute</td>
			<td>Devcon</td>
			<td>20845</td>
			<td></td>
		</tr>
		<tr>
			<td>Fujifilm FLA-5000&#160;</td>
			<td>Fujifilm</td>
			<td>&#160;FLA-5000&#160;</td>
			<td>Fluorescent image analyzer</td>
		</tr>
		<tr>
			<td>GelRed Nucleic Acid Stain; 10000x</td>
			<td>Cambridge Bioscience</td>
			<td>41003-BT</td>
			<td>Example of nucleic acid stain which is a safer alternative to ethidium bromide.&#160;</td>
		</tr>
		<tr>
			<td>Glass or quartz slide with holes for tubing&#160;</td>
			<td>Dremel Model 395</td>
			<td></td>
			<td>1 mm thick slide, cut to 2.4 cm x 1cm, two holes drilled 1.4 mm apart. The holes should be drilled to different sizes to accommodate different tubing at each end.</td>
		</tr>
		<tr>
			<td>Glycerol</td>
			<td>Fisher Scientific</td>
			<td>G/0650/17</td>
			<td></td>
		</tr>
		<tr>
			<td>Glycine HCl, pH 3.5</td>
			<td>Sigma-Aldrich</td>
			<td>G8898</td>
			<td></td>
		</tr>
		<tr>
			<td>Hamilton syringe, 1000 series GASTIGHT, PTFE luer lock 1010TLL, PTFE Luer lock (with slots), volume 10 mL</td>
			<td>Merck</td>
			<td>26211-U</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES pH 7.5</td>
			<td>Sigma-Aldrich</td>
			<td>H4034</td>
			<td></td>
		</tr>
		<tr>
			<td>I-CeuI</td>
			<td>NEB</td>
			<td>R0699L</td>
			<td></td>
		</tr>
		<tr>
			<td>KCl</td>
			<td>Fisher Scientific</td>
			<td>P/4280/53</td>
			<td></td>
		</tr>
		<tr>
			<td>Magnesium acetate</td>
			<td>Sigma-Aldrich</td>
			<td>M2545</td>
			<td></td>
		</tr>
		<tr>
			<td>Maxi GeBaFlex-tube Dialysis Kit; MWCO 14 kDa&#160;</td>
			<td>Generon</td>
			<td>D055</td>
			<td></td>
		</tr>
		<tr>
			<td>Metal spatula</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Metal tweezers</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sigma-Aldrich</td>
			<td>M2393</td>
			<td></td>
		</tr>
		<tr>
			<td>Millex-GP (Syringe filters) 0.22 &#181;m&#160;</td>
			<td>Merck</td>
			<td>SLGP033RS</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma-Aldrich</td>
			<td>S7653</td>
			<td></td>
		</tr>
		<tr>
			<td>Needle</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>NotI-HF</td>
			<td>NEB</td>
			<td>R3189L</td>
			<td></td>
		</tr>
		<tr>
			<td>NuPAGE 4%&#8211;12% Bis-Tris Protein Gels</td>
			<td>Thermo Fisher Scientific</td>
			<td>10247002;</td>
			<td></td>
		</tr>
		<tr>
			<td>NuPAGE MOPS SDS Running Buffer&#160;</td>
			<td>Thermo Fisher Scientific</td>
			<td>NP0001</td>
			<td></td>
		</tr>
		<tr>
			<td>Objective heater</td>
			<td>Okolab</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>PCR mix - 2x</td>
			<td></td>
			<td></td>
			<td>Prepared from Phusion DNA polymerase (20 &#181;L), 10 mM dNTPs (40 &#181;L), 5x Phusion HF buffer (400 &#181;L) and water (540 &#181;L).</td>
		</tr>
		<tr>
			<td>Peptide NH2-CHHHHHHHHHHLPETGG-COOH, labelled with LD655-MAL&#160;</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>peptide NH2-CHHHHHHHHHHLPETGG-COOH, labeled with LD655-MAL (Lumidyne Technologies) on the cysteine residue, was synthetised and purified by the peptide chemistry STP of The Francis Crick Institute</td>
		</tr>
		<tr>
			<td>pGC261 plasmid</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>https://doi.org/10.1016/j.cell.2018.10.053</td>
		</tr>
		<tr>
			<td>Phusion High-Fidelity DNA Polymerase</td>
			<td>NEB</td>
			<td>M0530L</td>
			<td></td>
		</tr>
		<tr>
			<td>Plastic tweezers</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Polyethylene tubing PE20 (inner diameter 0.015&#8221;, outer diameter 0.043&#8221;)</td>
			<td>Becton Dickinson</td>
			<td>427406</td>
			<td></td>
		</tr>
		<tr>
			<td>Polyethylene tubing PE60 (inner diameter 0.03&#8221;, outer diameter 0.048&#8221;)</td>
			<td>Becton Dickinson</td>
			<td>427416</td>
			<td></td>
		</tr>
		<tr>
			<td>Poly-Prep Chromatography Columns; 10 ml and 20 ml&#160;</td>
			<td>Bio-Rad</td>
			<td>7311550</td>
			<td></td>
		</tr>
		<tr>
			<td>Potassium Glutamate (L-glutamic acid potassium salt monohydrate)</td>
			<td>Sigma</td>
			<td>G1501-1KG</td>
			<td></td>
		</tr>
		<tr>
			<td>Protease inhibitor cocktail (cOmplete, EDTA free)</td>
			<td>Roche</td>
			<td>5056489001</td>
			<td></td>
		</tr>
		<tr>
			<td>Pump 11 Elite Infusion/Withdrawal Programmable Single Syringe</td>
			<td>Harvard Apparatus</td>
			<td>70-4504</td>
			<td></td>
		</tr>
		<tr>
			<td>QIAquick PCR Purification Kit</td>
			<td>QIAGEN</td>
			<td>28104</td>
			<td></td>
		</tr>
		<tr>
			<td>Razor blade</td>
			<td>VWR International Ltd</td>
			<td>233-0156</td>
			<td></td>
		</tr>
		<tr>
			<td>rCutSmart Buffer; 10x</td>
			<td>NEB</td>
			<td>B6004S</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium acetate</td>
			<td>Thermo Fisher Scientific</td>
			<td>S/2120/53</td>
			<td></td>
		</tr>
		<tr>
			<td>Sortase (pentamutant)</td>
			<td>N/A</td>
			<td>N/A</td>
			<td>Purified based on: https://doi.org/10.1073/pnas.1101046108</td>
		</tr>
		<tr>
			<td>Spin-X Centrifuge Tube Filters; 0.22 &#181;m cellulose acetate&#160;</td>
			<td>Fisher Scientific</td>
			<td>10310361</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterile scalpel</td>
			<td>N/A</td>
			<td>N/A</td>
			<td></td>
		</tr>
		<tr>
			<td>Steritop Vacuum Driven Disposable Filtration System; 0.22 um; PES;&#160;</td>
			<td>Millipore</td>
			<td>S2GPT05RE</td>
			<td></td>
		</tr>
		<tr>
			<td>Streptavidin (1 mg/mL) in 1x PBS buffer</td>
			<td>Sigma</td>
			<td>S4762-10MG</td>
			<td>20 &#181;L aliquotes</td>
		</tr>
		<tr>
			<td>SYBR Gold</td>
			<td>Thermo Fisher Scientific</td>
			<td>S11494</td>
			<td>Highly sensitive nucleic acid stain we used to visualise DNA fork substrate.</td>
		</tr>
		<tr>
			<td>SYTOX orange; 5 &#181;M in DMSO</td>
			<td>Thermo Fisher Scientific</td>
			<td>S11368</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA ligase</td>
			<td>NEB</td>
			<td>M0202M</td>
			<td></td>
		</tr>
		<tr>
			<td>T4 DNA Ligase Reaction Buffer&#160;</td>
			<td>NEB</td>
			<td>B0202S</td>
			<td></td>
		</tr>
		<tr>
			<td>TEMED</td>
			<td>Sigma-Aldrich</td>
			<td>T9281-25ML&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>TEV protease (1 mg/mL); EZCut&#160;</td>
			<td>Biovision</td>
			<td>7847-10000</td>
			<td></td>
		</tr>
		<tr>
			<td>Tissue grinders, Dounce type (40 mL, Wheaton)</td>
			<td>DWK Life Sciences</td>
			<td>432-1273</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris base</td>
			<td>Sigma-Aldrich</td>
			<td>T1503</td>
			<td>Used to prepare Tris Buffer (pH 8)</td>
		</tr>
		<tr>
			<td>Tris HCl</td>
			<td>Sigma-Aldrich</td>
			<td>T3253</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Promega UK Ltd</td>
			<td>H5152</td>
			<td></td>
		</tr>
	</tbody>
</table>

single-molecule real-time visualization of dna unwinding by cmg helicase

DNA replication is tightly regulated, as a cell must duplicate its genome accurately to prevent mutations, disease, or death. Eukaryotic DNA replication is carried out by the replisome complex, which unwinds parental DNA and uses single-stranded DNA (ssDNA) as a template to synthesize new DNA onto. In the G1 phase, catalytically inactive double hexamers of MCM2-7 are loaded onto double-stranded DNA (dsDNA) at replication origins1. In the S phase, MCM2-7 complexes are activated by the binding of CDC45 and GINS2 to form 11-subunit CMG complexes (CDC45, MCM2-7, GINS). Each CMG initiates DNA unwinding in opposite directions, forming the core unit that the replisome arranges itself around3.
Two decades ago the CMG helicase was first identified as an 11-subunit complex, essential for DNA replication4. Since then, our understanding of CMG has advanced considerably, from loading and activation5,6, to DNA unwinding and termination7. Traditional biochemical and structural biology techniques have been critical to many of these discoveries; however, these methods were often limited in their ability to study the more dynamic aspects of CMG. Single-molecule methods use physical manipulation of individual biomolecules to measure or visualize their activity one molecule at a time. This can be used to provide insight into the real-time dynamics of proteins that are often missed or undetectable by other techniques8,9.
Here, we describe a total internal reflection fluorescence (TIRF) microscopy assay to visualize DNA unwinding by CMG helicase in real time. Purified, fluorescently labeled CMG is loaded onto the free 3&#39; end of long DNA containing a pre-made DNA fork structure. Linear DNA is stretched on a biotin-PEG coverslip in a microfluidic flow cell by tethering each end of the DNA sequentially to the surface. This approach allows for more uniform DNA tethering, which significantly reduces the variation that must be accounted for during data analysis. In the presence of ATP-&#947;-s, CMG is loaded onto the single-stranded DNA at the 3&#39; end of the fork. ATP-&#947;-s is a slowly hydrolyzable ATP analog, which permits CMG binding onto DNA but not unwinding. Subsequent addition of ATP, along with purified, fluorescently tagged RPA, activates CMG and initiates extensive DNA unwinding. Visually, CMG translocates along the DNA, leaving a growing tract of RPA-bound ssDNA behind it. The untethered DNA end travels with CMG, forming a &#34;tight ball&#34; due to compaction caused by RPA binding. The flow cell design allows the buffer to be exchanged at any point during unwinding, giving great control during and over each experiment.
This protocol is divided into four methods, which can be performed independently of one another. Section 1 describes the preparation of a 20-kb linear forked DNA substrate for single-molecule assays. Section 2 outlines the purification and fluorescent labeling of Drosophila melanogaster CMG (DmCMG). Key information about the expression of DmCMG is included in the notes section. Section 3 covers the preparation of a microfluidic flow cell that can be used on a TIRF microscope. Section 4 describes how to carry out the single-molecule DNA unwinding assay.

<meta charset="utf8"></head><body>Autor im Rampenlicht: Entschlüsselung der Dynamik der eukaryotischen DNA-Replikation durch Einzelmolekül-Visualisierung

Einzelmolekül-Echtzeit-Visualisierung der DNA-Abwicklung durch CMG-Helikase

Faithful genome duplication is essential for preserving the genetic stability of dividing cells. DNA replication is carried out during the S phase by a ...

single-molecule-real-time-visualization-dna-unwinding-cmg

Research

JoVE Journal

Biochemistry

Single-Molecule Real-Time Visualization of DNA Unwinding by CMG Helicase

911 Aufrufe.  The Francis Crick Institute. In unserem Labor untersuchen wir die molekularen Mechanismen der eukaryotischen DNA-Replikation. Wir wollen die Dynamik der Genomduplikation auf der Ebene einzelner Moleküle verstehen. Wir visualisieren die DNA-Replikation mit mehreren Systemen, einschließlich gereinigter Proteine und Extrakte aus Xenopus-Eiern.Vieles von dem, was wir über die DNA-Replikation wissen, stammt aus Massenexperimenten, Zellbildgebung und Strukturbiologie. Diese Methoden ...

Serie: Autor im Rampenlicht: Entschlüsselung der Dynamik der eukaryotischen DNA-Replikation durch Einzelmolekül-Visualisierung

Faithful genome duplication is essential for preserving the genetic stability of dividing cells. DNA replication is carried out during the S phase by a dynamic complex of proteins termed the replisome. At the heart of the replisome is the&#160;CDC45-MCM2-7-GINS (CMG) helicase, which separates the two strands of the DNA double helix such that DNA polymerases can copy each strand. During genome duplication, replisomes must overcome a plethora of obstacles and challenges. Each of these threatens genome stability, as failure to replicate DNA completely and accurately can lead to mutations, diseases, or cell death. Therefore, it is of great interest to understand how CMG functions in the replisome during both normal replication and replication stress. Here, we describe a total internal reflection fluorescence (TIRF) microscopy assay using recombinant purified proteins, which allows for real-time visualization of surface-tethered stretched DNA molecules by individual CMG complexes. This assay provides a powerful platform to investigate CMG behavior at the single-molecule level, allowing helicase dynamics to be directly observed with real-time control over reaction conditions.

This protocol demonstrates performing a single-molecule assay for live visualization of DNA unwinding by CMG helicase. It describes (1) preparing a DNA substrate, (2) purifying fluorescently labeled Drosophila melanogaster CMG helicase, (3) preparing a microfluidic flow cell for total internal reflection fluorescence (TIRF) microscopy, and (4) the single-molecule DNA unwinding assay.