<meta charset="utf8"></head><body>DNA Replikasyonu ve Çatal Durma Olaylarını Analiz Etmek için 2D Jel Elektroforezi

<ol>
	<li>Liao, X., 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=Repetitive+DNA+sequence+detection+and+its+role+in+the+human+genome.">Repetitive DNA sequence detection and its role in the human genome.</a> Commun Biol. 6 (1), 1-21 (2023).</li><li>Fotsing, S. F., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+impact+of+short+tandem+repeat+variation+on+gene+expression.">The impact of short tandem repeat variation on gene expression.</a> Nat Genet. 51 (11), 1652-1659 (2019).</li><li>Fan, H., Chu, J. -. Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+brief+review+of+short+tandem+repeat+mutation.">A brief review of short tandem repeat mutation.</a> GPB. 5 (1), 7-14 (2007).</li><li>Khristich, A. N., Mirkin, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=On+the+wrong+DNA+track:+Molecular+mechanisms+of+repeat-mediated+genome+instability.">On the wrong DNA track: Molecular mechanisms of repeat-mediated genome instability.</a> J Biol Chem. 295 (13), 4134-4170 (2020).</li><li>Samadashwily, G. M., Raca, G., Mirkin, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Trinucleotide+repeats+affect+DNA+replication+in+vivo.">Trinucleotide repeats affect DNA replication in vivo.</a> Nat Genet. 17 (3), 298-304 (1997).</li><li>Khristich, A. N., Armenia, J. F., Matera, R. M., Kolchinski, A. A., Mirkin, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Large-scale+contractions+of+Friedreich's+ataxia+GAA+repeats+in+yeast+occur+during+DNA+replication+due+to+their+triplex-forming+ability.">Large-scale contractions of Friedreich's ataxia GAA repeats in yeast occur during DNA replication due to their triplex-forming ability.</a> Proc Natl Acad Sci USA. 117 (3), 1628-1637 (2020).</li><li>Shishkin, A. 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=Large-scale+expansions+of+Friedreich's+ataxia+GAA+repeats+in+yeast.">Large-scale expansions of Friedreich's ataxia GAA repeats in yeast.</a> Mol Cell. 35 (1), 82-92 (2009).</li><li>Sundararajan, R., Gellon, L., Zunder, R. M., Freudenreich, C. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Double-strand+break+repair+pathways+protect+against+CAG/CTG+repeat+expansions,+contractions+and+repeat-mediated+chromosomal+fragility+in+Saccharomyces+cerevisiae.">Double-strand break repair pathways protect against CAG/CTG repeat expansions, contractions and repeat-mediated chromosomal fragility in Saccharomyces cerevisiae.</a> Genetics. 184 (1), 65-77 (2010).</li><li>Kim, H. -. 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=Chromosome+fragility+at+GAA+tracts+in+yeast+depends+on+repeat+orientation+and+requires+mismatch+repair.">Chromosome fragility at GAA tracts in yeast depends on repeat orientation and requires mismatch repair.</a> EMBO J. 27 (21), 2896-2906 (2008).</li><li>Polleys, E. J., House, N. C. M., Freudenreich, C. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Role+of+recombination+and+replication+fork+restart+in+repeat+instability.">Role of recombination and replication fork restart in repeat instability.</a> DNA Repair. 56, 156-165 (2017).</li><li>Gold, M. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Restarted+replication+forks+are+error-prone+and+cause+CAG+repeat+expansions+and+contractions.">Restarted replication forks are error-prone and cause CAG repeat expansions and contractions.</a> PLoS Genet. 17 (10), e1009863 (2021).</li><li>Lambert, 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=Homologous+recombination+restarts+blocked+replication+forks+at+the+expense+of+genome+rearrangements+by+template+exchange.">Homologous recombination restarts blocked replication forks at the expense of genome rearrangements by template exchange.</a> Mol Cell. 39 (3), 346-359 (2010).</li><li>Burssed, B., Zamariolli, M., Bellucco, F. T., Melaragno, M. I. <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+structural+chromosomal+rearrangement+formation.">Mechanisms of structural chromosomal rearrangement formation.</a> Mol Cytogenet. 15 (1), 23 (2022).</li><li>Paulson, H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Repeat+expansion+diseases.">Repeat expansion diseases.</a> Handb Clin Neurol. 147, 105-123 (2018).</li><li>Malik, I., Kelley, C. P., Wang, E., Todd, P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Molecular+mechanisms+underlying+nucleotide+repeat+expansion+disorders.">Molecular mechanisms underlying nucleotide repeat expansion disorders.</a> Nat Rev Mol Cell Biol. 22 (9), 589-607 (2021).</li><li>Emanuel, B. S., Zackai, E. H., Medne, L., Adam, M. P. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Emanuel+Syndrome.">Emanuel Syndrome.</a> GeneReviews&#174;. , (1993).</li><li>Brewer, B. J., Fangman, W. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+localization+of+replication+origins+on+ARS+plasmids+in+S.+cerevisiae.">The localization of replication origins on ARS plasmids in S. cerevisiae.</a> Cell. 51 (3), 463-471 (1987).</li><li>Bell, L., Byers, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Separation+of+branched+from+linear+DNA+by+two-dimensional+gel+electrophoresis.">Separation of branched from linear DNA by two-dimensional gel electrophoresis.</a> Anal Biochem. 130 (2), 527-535 (1983).</li><li>Voineagu, I., Narayanan, V., Lobachev, K. S., Mirkin, S. 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+stalling+at+unstable+inverted+repeats:+Interplay+between+DNA+hairpins+and+fork+stabilizing+proteins.">Replication stalling at unstable inverted repeats: Interplay between DNA hairpins and fork stabilizing proteins.</a> Proc Natl Acad Sci USA. 105 (29), 9936-9941 (2008).</li><li>Nguyen, J. H. G., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Differential+requirement+of+Srs2+helicase+and+Rad51+displacement+activities+in+replication+of+hairpin-forming+CAG/CTG+repeats.">Differential requirement of Srs2 helicase and Rad51 displacement activities in replication of hairpin-forming CAG/CTG repeats.</a> Nucleic Acids Res. 45 (8), 4519-4531 (2017).</li><li>Krasilnikova, M. M., Mirkin, S. M., Kohwi, Y. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Analysis+of+triplet+repeat+replication+by+two-dimensional+gel+electrophoresis.">Analysis of triplet repeat replication by two-dimensional gel electrophoresis.</a> Trinucleotide Repeat Protocols. , (2004).</li><li>Follonier, C., Oehler, J., Herrador, R., Lopes, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Friedreich's+ataxia-associated+GAA+repeats+induce+replication-fork+reversal+and+unusual+molecular+junctions.">Friedreich's ataxia-associated GAA repeats induce replication-fork reversal and unusual molecular junctions.</a> Nat Struct Mol Biol. 20 (4), 486-494 (2013).</li><li>Chandok, G. S., Patel, M. P., Mirkin, S. M., Krasilnikova, M. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Effects+of+Friedreich's+ataxia+GAA+repeats+on+DNA+replication+in+mammalian+cells.">Effects of Friedreich's ataxia GAA repeats on DNA replication in mammalian cells.</a> Nucleic Acids Res. 40 (9), 3964-3974 (2012).</li><li>Rastokina, 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=Large-scale+expansions+of+Friedreich's+ataxia+GAA&#8226;TTC+repeats+in+an+experimental+human+system:+role+of+DNA+replication+and+prevention+by+LNA-DNA+oligonucleotides+and+PNA+oligomers.">Large-scale expansions of Friedreich's ataxia GAA&#8226;TTC repeats in an experimental human system: role of DNA replication and prevention by LNA-DNA oligonucleotides and PNA oligomers.</a> Nucleic Acids Res. 51 (16), 8532-8549 (2023).</li><li>Giannattasio, 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=Visualization+of+recombination-mediated+damage-bypass+by+template+switching.">Visualization of recombination-mediated damage-bypass by template switching.</a> Nat Struct Mol Biol. 21 (10), 884-892 (2014).</li><li>Hisey, J. 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=Pathogenic+CANVAS+(AAGGG)n+repeats+stall+DNA+replication+due+to+the+formation+of+alternative+DNA+structures.">Pathogenic CANVAS (AAGGG)n repeats stall DNA replication due to the formation of alternative DNA structures.</a> Nucleic Acids Res. 52 (8), 4361-4374 (2024).</li><li>Kalejta, R. F., Lin, H. B., Dijkwel, P. A., Hamlin, J. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterizing+replication+intermediates+in+the+amplified+CHO+dihydrofolate+reductase+domain+by+two+novel+gel+electrophoretic+techniques.">Characterizing replication intermediates in the amplified CHO dihydrofolate reductase domain by two novel gel electrophoretic techniques.</a> Mol Cell Biol. 16 (9), 4923-4931 (1996).</li><li>Little, R. D., Platt, T. H., Schildkraut, C. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Initiation+and+termination+of+DNA+replication+in+human+rRNA+genes.">Initiation and termination of DNA replication in human rRNA genes.</a> Mol Cell Biol. 13 (10), 6600-6613 (1993).</li><li>Fanning, E., Zhao, K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=SV40+DNA+replication:+From+the+A+gene+to+a+nanomachine.">SV40 DNA replication: From the A gene to a nanomachine.</a> Virology. 384 (2), 352-359 (2009).</li><li>Sogo, J. M., Stahl, H., Koller, T., Knippers, R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Structure+of+replicating+simian+virus+40+minichromosomes:+The+replication+fork,+core+histone+segregation+and+terminal+structures.">Structure of replicating simian virus 40 minichromosomes: The replication fork, core histone segregation and terminal structures.</a> J Mol Biol. 189 (1), 189-204 (1986).</li><li>Weisshart, K., Taneja, P., Fanning, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+replication+protein+A+binding+site+in+simian+virus+40+(SV40)+T+antigen+and+its+role+in+the+initial+steps+of+SV40+DNA+replication.">The replication protein A binding site in simian virus 40 (SV40) T antigen and its role in the initial steps of SV40 DNA replication.</a> J Virol. 72 (12), 9771-9781 (1998).</li><li>Sowd, G. A., Fanning, E. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+Wolf+in+sheep's+clothing:+SV40+co-opts+host+genome+maintenance+proteins+to+replicate+viral+DNA.">A Wolf in sheep's clothing: SV40 co-opts host genome maintenance proteins to replicate viral DNA.</a> PLoS Pathog. 8 (11), e1002994 (2012).</li><li>. BLAST: Basic Local Alignment Search Tool Available from: <a target="_blank" href="https://blast.ncbi.nlm.nih.gov/Blast.cgi">https://blast.ncbi.nlm.nih.gov/Blast.cgi</a> (2024)</li><li>Hirt, B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Selective+extraction+of+polyoma+DNA+from+infected+mouse+cell+cultures.">Selective extraction of polyoma DNA from infected mouse cell cultures.</a> J Mol Biol. 26 (2), 365-369 (1967).</li><li>Lopes, M., Foiani, M., Sogo, J. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiple+mechanisms+control+chromosome+integrity+after+replication+fork+uncoupling+and+restart+at+irreparable+UV+lesions.">Multiple mechanisms control chromosome integrity after replication fork uncoupling and restart at irreparable UV lesions.</a> Mol Cell. 21 (1), 15-27 (2006).</li></ol>

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>10x TBE Buffer</td>
			<td>Bio Rad</td>
			<td>1610733</td>
			<td></td>
		</tr>
		<tr>
			<td>20x SSC Buffer</td>
			<td>Fisher Scientific</td>
			<td>BP1325-1</td>
			<td></td>
		</tr>
		<tr>
			<td>293T cells</td>
			<td>ATCC</td>
			<td>CRL-3216</td>
			<td></td>
		</tr>
		<tr>
			<td>a-32P dATP, 3000 Ci/mmol&#160;</td>
			<td>Revvity</td>
			<td>BLU512H250UC</td>
			<td></td>
		</tr>
		<tr>
			<td>Agarose</td>
			<td>Fisher Scientific</td>
			<td>BP160-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Amersham Hybond-N+</td>
			<td>Fisher Scientific</td>
			<td>RPN303B</td>
			<td></td>
		</tr>
		<tr>
			<td>BAS Storage Phosphor Screens</td>
			<td>Fisher Scientific</td>
			<td>28956482</td>
			<td></td>
		</tr>
		<tr>
			<td>Church and Gibert&#39;s hybriddization buffer</td>
			<td>Fisher Scientific</td>
			<td>50-103-5408</td>
			<td></td>
		</tr>
		<tr>
			<td>DecaLabel DNA labeling kit</td>
			<td>ThermoFisher Scientific</td>
			<td>K0622</td>
			<td></td>
		</tr>
		<tr>
			<td>DMEM, high gluctose, GltaMAX Supplement, pyruvate</td>
			<td>ThermoFisher Scientific</td>
			<td>10569010</td>
			<td></td>
		</tr>
		<tr>
			<td>DpnI</td>
			<td>New England Biolabs</td>
			<td>R0176S</td>
			<td>Additional restriction enzymes will need to be purchased as well</td>
		</tr>
		<tr>
			<td>EDTA 0.5 M, pH 8</td>
			<td>Fisher Scientific</td>
			<td>BP2482500</td>
			<td></td>
		</tr>
		<tr>
			<td>Ethanol, 70%</td>
			<td>Fisher Scientific</td>
			<td>BP82031GAL</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum&#160;</td>
			<td>VWR</td>
			<td>97068-085</td>
			<td></td>
		</tr>
		<tr>
			<td>Hydrochloric acid solution, 12 M</td>
			<td>Millipore Sigma</td>
			<td>13-1683</td>
			<td></td>
		</tr>
		<tr>
			<td>Isopropanol</td>
			<td>Fisher Scientific</td>
			<td>BP26184</td>
			<td></td>
		</tr>
		<tr>
			<td>jetPRIME DNA and siRNA Transfection Reagent with Buffer</td>
			<td>VWR</td>
			<td>101000027</td>
			<td></td>
		</tr>
		<tr>
			<td>MycoZap Plus-CL</td>
			<td>VWR</td>
			<td>75870-448</td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Millipore Sigma</td>
			<td>746398-500G</td>
			<td></td>
		</tr>
		<tr>
			<td>Nalgene Oak Ridge High-Speed Centrifuge Tubes</td>
			<td>ThermoFisher Scientific</td>
			<td>3139-0050</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffer Saline, pH 7.4</td>
			<td>ThermoFisher Scientific</td>
			<td>10010023</td>
			<td></td>
		</tr>
		<tr>
			<td>Phosphate Buffer Saline, pH 7.5</td>
			<td>ThermoFisher Scientific</td>
			<td>10010024</td>
			<td></td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>ThermoFisher Scientific</td>
			<td>EO0491</td>
			<td></td>
		</tr>
		<tr>
			<td>Proteinase K</td>
			<td>ThermoFisher Scientific</td>
			<td>EO0492</td>
			<td></td>
		</tr>
		<tr>
			<td>Pure Cellulose Chromatography Paper</td>
			<td>Fisher Scientific</td>
			<td>05-714-4</td>
			<td></td>
		</tr>
		<tr>
			<td>Pure Cellulose Chromatography Paper</td>
			<td>Fisher Scientific</td>
			<td>05-714-5</td>
			<td></td>
		</tr>
		<tr>
			<td>Ruler</td>
			<td>Fisher Scientific</td>
			<td>09-016</td>
			<td></td>
		</tr>
		<tr>
			<td>Scalpel</td>
			<td>Fisher Scientific</td>
			<td>12-460-451</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium dodecyl sulfate</td>
			<td>Millipore Sigma</td>
			<td>436143-25G</td>
			<td></td>
		</tr>
		<tr>
			<td>Sodium hydroxide</td>
			<td>Fisher Scientific</td>
			<td>S25548</td>
			<td></td>
		</tr>
		<tr>
			<td>Sorval LYNX 4000 Superspeed Centrifuge</td>
			<td>ThermoFisher Scientific</td>
			<td>75006580</td>
			<td></td>
		</tr>
		<tr>
			<td>Sub-cell Horizontal Electrophoresis System</td>
			<td>Bio Rad</td>
			<td>1704401</td>
			<td></td>
		</tr>
		<tr>
			<td>TH13-6 x 50 Swinging Bucket Rotor</td>
			<td>ThermoFisher Scientific</td>
			<td>75003010</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-HCl 1 M, pH 7.5</td>
			<td>Fisher Scientific</td>
			<td>BP1757-500</td>
			<td></td>
		</tr>
		<tr>
			<td>Trypsin-EDTA (0.25%), phenol red</td>
			<td>ThermoFisher Scientific</td>
			<td>25200056</td>
			<td></td>
		</tr>
	</tbody>
</table>

electrophoretic analysis of replication through structure-prone dna repeats within the sv40-based human episome

Short tandem repeats (STR) are small, typically 2-9 base pairs (bp), repetitive sequences of DNA that constitute around 3% of the human genome1. STR play an important role in gene regulation2; however, their repetitive composition leaves them prone to non-canonical DNA secondary structure formation and subsequent genetic instability3,4. From left-handed helices to hairpins/cruciforms, to three and four-stranded helices, these alternative DNA structures cause intrinsic challenges for the replisome. A natural prerequisite for secondary structure formation is DNA unwinding, which is a prerequisite for DNA replication. This presents a unique conundrum for genome functioning as many of these structures can form during replication, hindering replisome progression and ultimately causing replication fork stalling5,6,7, or in severe cases, fork collapse and DNA breakage8,9. Both the restart of stalled forks and DNA repair pathways have been shown to lead to repeat instability, such as repeat expansions10,11 and complex genome rearrangements (CGR)12,13. These events can result in the development of roughly 60 human diseases known as repeat expansion disorders, including Fragile X syndrome, Huntington&#39;s disease, Friedreich&#39;s ataxia, and others14,15 as well as CGR diseases, such as Emmanuel syndrome16. Therefore, to better understand the mechanisms of human disease driven by repeat instability, it is imperative to study the details of replication fork progression through those repeats.
A technique for studying replication progression emerged in the mid-1980s when Brewer and Fangman sought to provide direct evidence that replication initiation in Saccharomyces cerevisiae occurs at autonomous replication sequence (commonly known as ARS) elements17. In doing so, they separated structures of yeast replication intermediates in agarose, adapting an earlier method from Bell and Byers known as 2-dimensional Neutral/Neutral gel-electrophoresis (2DGE)18. This technique utilized the fact that nonlinear DNA travels differently in agarose gel than its linear equivalent of the same mass. More specifically, in 2DGE, isolated DNA is separated in two perpendicular dimensions, first primarily by size and then primarily by shape, to create a comprehensive map of replication at a particular region of interest. In their original paper, Brewer and Fangman demonstrated this as an arc composed of &#34;simple Y&#34; structures or replication forks bridging unreplicated DNA to their replicated counterparts. They further describe other observed intermediates as &#34;bubbles&#34; and &#34;double Ys,&#34; representing replication origins and converging forks, respectively.
2DGE can be used to study the relative populations of DNA replication intermediates at a given time. Therefore, if one population of intermediates is more prevalent than another, this would be evident upon visualization. This makes 2DGE an especially useful tool for studying replication progression through challenging sequences, like structure-forming repeats. For example, if the region analyzed contains a sequence capable of inducing replication fork stalling, this would present as a bulge on the arc (Figure 1A), indicating an accumulation of replication forks at that locus. This can be seen with the replication of both hairpin-forming repeat sequences in yeast19,20,21 and triplex-forming repeats in human cells22,23,24. In addition to stalling, 2DGE can be used to observe DNA structures that do not conform to the standard simple Ys formed during replication, as in the case of recombinant intermediates25. These intermediates have a heavier and more branched X-shaped structure and, therefore, travel slower in both the first- and second dimensions than standard replication forks. Similar results can also be observed with regards to replication fork reversal20,24,26. In response to strong replication stress, eukaryotic cells have been shown to utilize replication fork reversal to rescue stalled forks. These reversed forks have similar molecular weight to stalled forks; yet their chicken-foot structure results in slower electrophoretic mobility in the second dimension relative to their Y-shaped complements, resulting in an extension up and out from the arc.
<img alt="Figure 1" class="xfigimg" src="/files/ftp_upload/67229/67229fig01.jpg" /> 
Figure 1: 2D Gel electrophoresis analysis of DNA replication. (A)&#160;Schematic of a typical 2DGE depicting replication through a structure-forming repeat capable of inducing fork stalling. Intermediate size and structure will influence electrophoretic mobility. (B)&#160;Sample Y-arc with ascending and descending arms respectively labeled. Abbreviation: 2DGE = Two-dimensional neutral/neutral gel-electrophoresis. <a href="https://www.jove.com/files/ftp_upload/67229/67229fig01large.jpg" target="_blank">Please click here to view a larger version of this figure.</a>
Naturally, one of the most important aspects of 2DGE concerns the quality and quantity of replication intermediates. However, the resolution of 2DGE analysis of replication through endogenous loci in mammalian cells is insufficient for a single copy target sequence within the 6 &#215; 109 bp diploid human genome, though it has been done for multi-copy genes, such as heavily amplified DHFR locus27 or ribosomal RNA28. SV40-based replication is an efficient and well-characterized means of studying replication in eukaryotic cells29. It provides a reliable model of eukaryotic replication that utilizes most of the host replisome machinery to replicate the viral genome, which is parceled into nucleosomes upon infection30,31. Two notable exceptions from the mammalian replisome are that the T-antigen (Tag), instead of the host CMG complex, serves as replicative DNA helicase, and DNA polymerase delta synthesizes both leading and lagging DNA strands32. We have taken advantage of this system by placing pathogenic stretches of structure-forming repeats downstream from an SV40 origin of replication within a plasmid that was originally created in the Massimo Lopes lab22. Importantly, this plasmid also contains the gene encoding for Tag itself, thus resulting in its constitutive and extremely potent replication upon transfection into a variety of cultured human cells. This feature gives rise to a large quantity of products, ideal for 2DGE analysis of the intermediates formed during and in response to the replication of pathogenic repeats in human cells. Here, we describe a detailed method of visualizing the replication of structure-forming repeats within the SV40-based human episome using 2-dimensional gel electrophoresis.

<meta charset="utf8"></head><body>Yazar Gündemi: Replikasyon Çatalı Durma ve Genişleme Mekanizmalarını Ortaya Çıkarmak için Patojenik Tekrarların DNA Replikasyonunu Karakterize Etme

SV40 Tabanlı İnsan Epizomu İçinde Yapıya Eğilimli DNA Tekrarları Yoluyla Replikasyonun Elektroforetik Analizi

The scope of our research is to characterize DNA replication of unstable pathogenic repeats in human cells. We hope to answer questions such as, what specific repeats cause replication fork stalling? What unique secondary structures are these repeats forming?And how do these repeats expand during DNA replication? While we know that many of these structure forming repeats can impair DNA replication, it's still unclear what exact steps happen next. We're hoping that this protocol will help answer this question and shed light on the mechanisms of how these pathogenic repeats expand.2D gels provide the unique opportunity to actually visualize the structures in relative populations of molecules that can arise during DNA replication. Within one single experiment, you essentially have the complete map of what replication progression looks like through a specific DNA sequence.

Two-dimensional neutral/neutral gel-electrophoresis (2DGE) emerged as a benchmark technique to analyze DNA replication through natural impediments. This ...

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Research

JoVE Journal

Genetics

Electrophoretic Analysis of Replication Through Structure-Prone DNA Repeats Within the SV40-Based Human Episome

382 Görüntüleme.  Tufts University. Araştırmamızın kapsamı, insan hücrelerinde kararsız patojenik tekrarların DNA replikasyonunu karakterize etmektir. Çoğaltma çatalının durmasına neden olan belirli tekrarlar gibi soruları yanıtlamayı umuyoruz. Bu tekrarlar hangi benzersiz ikincil yapıları oluşturuyor?Ve bu tekrarlar DNA replikasyonu sırasında nasıl genişler? Bu yapı oluşturan tekrarların birçoğunun DNA replikasyonunu bozabileceğini bilsek de, bundan sonra h...

Video: Yazar Gündemi: Replikasyon Çatalı Durma ve Genişleme Mekanizmalarını Ortaya Çıkarmak için Patojenik Tekrarların DNA Replikasyonunu Karakterize Etme