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

Nicholas H. Mandel; Sergei M. Mirkin

doi:10.3791/67229

JoVE Journal > Genetics

Genetik

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

Published: September 13, 2024

doi:

10.3791/67229

Nicholas H. Mandel¹, Sergei M. Mirkin¹

¹Department of Biology,Tufts University

Summary

Here, we outline the procedure for analyzing replication progression through pathogenic, structure-prone repeats using 2-dimensional gel electrophoresis.

Abstract

Two-dimensional neutral/neutral gel-electrophoresis (2DGE) emerged as a benchmark technique to analyze DNA replication through natural impediments. This protocol describes how to analyze replication fork progression through structure-prone, expandable DNA repeats within the simian virus 40 (SV40)-based episome in human cells. In brief, upon plasmid transfection into human cells, replication intermediates are isolated by the modified Hirt protocol and treated with the DpnI restriction enzyme to remove non-replicated DNA. Intermediates are then digested by appropriate restriction enzymes to place the repeat of interest within the origin-distal half of a 3-5 kb-long DNA fragment. The replication intermediates are separated into two perpendicular dimensions, first by size and then by shape. Following Southern blot hybridization, this approach allows researchers to observe fork stalling at various structure-forming repeats on the descending half of the replication Y-arc. Furthermore, this positioning of the stall site allows the visualization of various outcomes of repeat-mediated fork stalling, such as fork reversal, the advent of a converging fork, and recombinational fork restart.

Introduction

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's disease, Friedreich'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 "simple Y" structures or replication forks bridging unreplicated DNA to their replicated counterparts. They further describe other observed intermediates as "bubbles" and "double Ys," 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.

Figure 1: 2D Gel electrophoresis analysis of DNA replication. (A) 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) Sample Y-arc with ascending and descending arms respectively labeled. Abbreviation: 2DGE = Two-dimensional neutral/neutral gel-electrophoresis. Please click here to view a larger version of this figure.

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 × 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.

Protocol

NOTE: The plasmid designed for our outlined 2DGE analysis in mammalian cells should contain an SV40 origin of replication several kb upstream of structure-prone repeats (Figure 2). Leading and lagging synthesis should be kept in mind when choosing what orientation relative to the origin the repeats should be cloned into the plasmid.

Figure 2: Digestion of repeat-containing plasmid for 2DGE analysis. Structure-prone repeats are depicted several kb downstream from the right-moving replication fork. Digestion with unique cutters 1 and 2 will place the repeat sequence on the descending arm of the Y-arc, given the sequence beyond the halfway point of the digested fragment. Abbreviation: 2DGE = Two-dimensional neutral/neutral gel-electrophoresis. Please click here to view a larger version of this figure.

1. Plasmid transfection into mammalian cells

Seed 600,000 HEK293T cells in a 10 cm tissue culture plate prior to transfection. Allow the cells to recover at 37 °C overnight.
NOTE: Many cell lines may be used for this experiment, although cells containing the SV40 Tag are recommended for optimal results. CAUTION: HEK293T cells are considered BSL-2 and all culturing work should be carried out in a biosafety cabinet using appropriate aseptic technique and proper PPE.
When the cells reach 60% confluency, transfect 8 μg of repeat-containing plasmid DNA into the seeded cells using appropriate transfection reagents in accordance with the manufacturer's protocol.
If not isolating intermediates at this time point, aspirate old media and replace with 10 mL of fresh media after 24 h.
Begin collecting cells 24-48 h following transfection.
1. Aspirate media and carefully wash with 10 mL of phosphate-buffered saline (PBS). Detach and collect cells using 0.5 mL of trypsin and spin down at 340 × g for 4 min.
2. Aspirate the supernatant and wash the cell pellets with PBS. Spin again at 340 × g for 4 min and aspirate the supernatant.
  NOTE: The experiment may be paused here by freezing cell pellets at -80 °C. We have found the best resolution isolating replication intermediates 48 h following transfection; however, 24 h has yielded viable results.

2. Isolation of replication intermediates

Resuspend the cells in 1.5 mL of modified Hirt lysis buffer [10 mM tris-HCl (pH 7.5), 10 mM ethylenediaminetetraacetic acid (EDTA)] in 50 mL conical tubes and begin cell lysis.
1. Add sodium dodecyl sulfate (SDS) to a final concentration of 0.6% (approximately 650 μL of stock 2% SDS) and proteinase K to a final concentration of 100 μg/mL (approximately 10 μL of stock 20 mg/mL proteinase K) to remove nucleases.
2. Mix gently by pipetting until homogeneous and incubate the mixture at 37 °C for at least 90 min.
Increase NaCl concentration to 1 M (approximately 540 μL of stock 5 M NaCl) and mix gently until homogeneous. Incubate overnight (18-24 h) at 4 °C to allow for precipitation of cell debris, RNA, and protein by salting out.
NOTE: The mixture will be highly viscous, so take care and be patient while mixing well.
The following day, separate the DNA from cell debris, RNA, and protein.
1. Centrifuge the mixture at 29,500 × g for 45 min at 4 °C.
2. Transfer the supernatant containing DNA, add one volume of phenol:chloroform:isoamyl alcohol 25:24:1 (v/v), and mix briefly until homogeneous.
  CAUTION: Phenol:chloroform:isoamyl alcohol is a hazardous material and should be handled with appropriate PPE in a chemical fume hood.
3. Centrifuge again at 15,000 × g for 5 min at room temperature. Transfer the aqueous layer to a new conical tube.
Precipitate and wash the isolated DNA.
1. Add one volume of pure isopropanol and incubate at room temperature for at least 5 min. Spin down the DNA at 15,000 × g for 30 min at 4 °C.
2. Decant the supernatant and wash the pellet with cold 70% ethanol to remove excess salt.
3. Spin once more at 15,000 × g for 30 min at 4 °C, air dry, and gently resuspend the pellet in Tris-EDTA (TE) buffer (10 mM Tris-HCl, 1 mM EDTA).
  NOTE: The experiment can be paused here, and samples can be frozen at -20 °C; however, freeze/thaw cycling should be avoided as this can decrease the quality of the DNA replication intermediates.

3. Sample preparation and 2-dimensional gel electrophoresis

Digest the isolated intermediates of plasmid replication.
1. Add 100 units of the appropriate restriction enzymes to the sample to digest the plasmid DNA, specifically placing the repeat-containing sequence on the origin-distal half of the linear fragment (Figure 2). In addition, add DpnI to cut the methylated DNA, thus removing any plasmid DNA that was not fully replicated in cultured human cells.
  NOTE: For best results, restriction enzymes should be unique cutters that yield a 3-5 kb fragment that places the structure-prone sequence on the descending arm of the Y-arc.
2. Incubate the samples at 37 °C for 6-10 h to allow full plasmid digestion.
3. Precipitate the DNA with either 2.5 volumes of cold pure ethanol and incubate at -20 °C overnight, or add one volume of isopropanol and incubate at room temperature for 5 min.
4. Centrifuge the digested and precipitated samples at 15,000 × g for 30 min at 4 °C.
5. Decant the supernatant and wash the sample with cold 70% ethanol. Spin again at 15,000 × g for 30 min at 4 °C.
6. Decant the supernatant, air dry for 10 min, and resuspend the samples in 15 μL of TE buffer.
Prepare the first-dimension agarose gel at 0.4-0.5% in 1x Tris-borate-EDTA (TBE) (89 mM tris base, 89 mM boric acid, 2 mM EDTA). Allow the solution to solidify for at least 1 h.
Begin loading the samples into the first dimension.
1. Load the ladder within the first 3 cm relative to the gel's leftmost edge. Then, load the entirety of the prepared samples, ensuring 3 cm between each pair.
2. Run the gel in 1x TBE for 19-24 h at 0.85 V/cm to separate the intermediates with respect to their size. Ensure the chamber is covered to protect the samples from light, which may cause damage to the DNA.
The following day, remove the gel from the buffer and estimate the location of the digested linear fragment using a ruler.
1. Excise the first 3 cm of the gel containing the ladder and stain the gel segment in 1x TBE containing 0.3 μg/mL ethidium bromide for 10-15 min. Visualize the ladder using a gel documentation system.
2. Add 1.3 cm to the estimated location, yielding value a. Then, subtract 7.5 cm from value a, yielding value b. Align the ruler against the first-dimension gel and cut horizontally across at values a and b. Then, cut vertically down the 3 cm space reserved for each sample. Refer to Figure 3 for a visual schematic.
3. In a new casting tray, rotate the segments clockwise and place them in the position of the sample wells (Figure 3).
Prepare the second-dimension agarose gel at a concentration of 1-1.3% in 1x TBE at 0.3 μg/mL ethidium bromide.
1. Upon cooling to approximately 55 °C, pour the second-dimension gel over the rotated first-dimension segments and allow it to solidify for at least 1 h.
2. Transfer the second dimension to a chamber with 1x TBE at 0.3 μg/mL ethidium bromide, and allow the gel to equilibrate for at least 30 min.
3. Run the gel, again covered, for 9-10 h at 4.23 V/cm at 4 °C to separate the intermediates with respect to their shape.

Figure 3: Excision of first-dimension intermediates prior to second-dimension separation. Following visualization of the ladder, the mobility of unreplicated fragments can be estimated. (I) This value can then be used to determine appropriate cut sites (a and b) to excise it and its replicated counterparts (II). The section of the gel should then be rotated and placed in the position of wells for the second-dimension separation. Abbreviation: CW = clockwise. Please click here to view a larger version of this figure.

4. Southern blotting and hybridization with radiolabeled probe

Remove the second-dimension gel from the chamber and depurinate the DNA fragments for 10 min in a 0.24 M HCl solution with gentle rocking. Rinse the gel with deionized water and soak it in 0.4 M NaOH for 10-15 min.
CAUTION: HCl and NaOH are corrosive and should be handled with appropriate PPE in a chemical fume hood.
Begin assembling the Southern blot to facilitate the transfer of the separated intermediates from the gel to the membrane. Refer to Figure 4 for a comprehensive schematic.
1. Fill a sufficiently sized container with 1 L of 0.4 M NaOH.
2. Align a long glass sheet across the container and fold (along the length) two long sheets of chromatography paper perpendicular across the glass sheet, extending into the container of NaOH.
3. Wet the top of the paper with NaOH and carefully remove any air bubbles under its surface.
4. Soak three sheets of chromatography paper with NaOH and place them over the folded paper, again removing any bubbles.
5. Flip the second-dimension gel upside-down and transfer it over the papers.
6. Wet a positively charged nylon membrane (0.45 μm pore size) with DI water and place it over the gel.
7. Finally, add three more sheets of paper, wet with DI water, over the membrane.
8. Cover any exposed NaOH in the bottom container with plastic wrap to prevent evaporation. Place a stack of either napkins or paper towels over the blot, ensuring it is 0.3-0.5 m tall. Place a weight on the top, compressing the entire blot to facilitate tight capillary action. Allow at least 2 days for DNA to transfer to the membrane.
  NOTE: The length and width of the chromatography paper and membrane depend on the size of the agarose gel used for the second dimension. For the most efficient transfer, use paper and membrane with the same dimensions as those of the gel.
Following transfer, crosslink the DNA to the membrane using a UV crosslinker at 120 μJ/cm² for 1 min.
NOTE: The experiment may be paused here by placing the membrane in an airtight, dry, and clean sheet protector at room temperature.
Wash the membrane 2x for 5 min with 2x saline sodium citrate (SSC buffer) (0.3 M NaCl, 0.03 M sodium citrate).
Prehybridize the membrane with 0.18 mL/cm² of Church & Gilbert's hybridization buffer [1 mM EDTA, 1% bovine serum albumin (BSA), 0.5 M sodium phosphate, 7% SDS] at 65 °C, rotating in a hybridization incubator for at least 2 h.
NOTE: The membrane may prehybridize for several days.
Prepare the radiolabeled probe using α-³²P dATP or dCTP and a DNA labeling kit in accordance with the manufacturer's protocol.
CAUTION: Radiolabeled dNTPs are hazardous, and appropriate PPE should be worn when handling them. All radioactive work should be performed behind shielding, and trained individuals should be monitored for radiation uptake using dosimeters.
1. Design a 400-900 bp linear DNA fragment complementary to the restriction digested sequence (Figure 2) and amplify the fragment using polymerase chain reaction (PCR).
  NOTE: We recommend having a stock PCR fragment of 50-100 ng/μL
2. Combine 100 ng of the complementary PCR fragment with DNA Pol I, Klenow fragment (3' 5' exo-) buffer, and random decanucleotide oligos.
3. Denature the fragment at 100 °C for 10 min.
4. Add 5 units of DNA Pol I, Klenow fragment (3' 5' exo-), 50 μCi of α-³²P dNTP, and 30-50 μmol of dNTP mix deficient in radiolabeled dNTP type to the sample.
5. Incubate at 37 °C for 10 min to allow for polymerization and radiolabeled dNTP incorporation.
6. Add 30-50 μmol of previously absent dNTP type to the sample and incubate at 37 °C for 10 min.
7. Purify the radiolabeled fragment using a spin column at 3,000 × g for 2 min.
Add radiolabeled probe to 50 mL of hybridization buffer and incubate with the membrane overnight at 65 °C rotating in a hybridization incubator.
The following day, remove the probe and wash the membrane 2x with wash buffer 1 (0.1x SSC, 0.1% SDS) at 42 °C and 2x with wash buffer 2 (2x SSC, 0.1% SDS) at 65 °C.
NOTE: All washes should be performed with fast rotations for 15 min in the incubator.
Dry the membrane for 10 min and place it in a thin, transparent sheet protector. Store the sealed membrane in a controlled, radiation-resistant cassette with a phosphor-sensitive screen. Allow the membrane to be exposed to the screen for 1-10 days.
Visualize the results using a biomolecular imager set to phosphor imaging. Wash and re-expose if necessary.

Figure 4: Assembly of Southern blot. Comprehensive schematic of a typical apparatus used for Southern blot transfer of intermediates from the second dimension onto a nylon membrane. Please click here to view a larger version of this figure.

Representative Results

If successful, upon visualization, a sharp arc of replication forks can be observed extending up and out from the massive 1n spot (Figure 5A). The size of a fragment, or percentage that is replicated, determines the fragment's mobility in the first dimension. As the intermediates develop a more jointed structure, they will begin to travel more slowly in the second dimension. Therefore, if an intermediate has traveled slowly in both dimensions, it can be asserted that it is a highly replicated molecule with significant junctional variation from conventional replication forks. In the case of lagging-strand synthesis of the (GAA)₁₀₀ repeat, fork stalling is indicated by a darkened defined spot on the arc (I), representing an accretion of replication forks upon encounter of the repeat (Figure 5B), likely due to triplex formation. This is accompanied by heavier, more branched intermediates (II and III) above the stall site. We have described the nature of these intermediates in more depth in Rastokina et al. 2023²⁴. In short, these likely represent a combination of forks reversing in response to the stall (II), in addition to the advent of the converging fork (Figure 5B) (III).

One observation that may be made upon visualization is a less-than ideal, broad arc. At worst, this may present as a complete doubling of the arc. Typically, this represents poor separation of intermediates in the first dimension. This may be attributed to several factors, the most likely of which is either salt or protein contamination in the replication intermediate sample. A phenol:chloroform purification after digesting intermediates, followed by extensive washing with 70% ethanol, can minimize this risk. However, it should be noted that additional phenol exposure can increase the chance of denaturing intermediates, which may present as a darkened intensity of linear DNA under the arc, representing collapsed replication intermediates (Figure 5C).

In the worst-case scenario, visualization may result in a complete absence of replication intermediates, evidenced by the lack of arc (Figure 5D). It is unlikely that the absence of an arc is attributed to denatured replication intermediates, as there is no darkened spot under the expected area of the arc. Given the presence of a particularly small 1n spot (IV), the overall quantity of DNA present in this depicted example is minimal, and, therefore, this issue may be caused by under-replication of the plasmid or an overall poor transfection or isolation of DNA.

Figure 5: Potential outcomes of 2DGE analysis. (A) Successful 2DGE analysis of replication through the structure-forming (GAA)₁₀₀ repeat in HEK293T cells. (I) refers to forks stalled at the repeat, whereas (II) and (III) refer to more structured intermediates that arise in response to the stall. An illustration of the 2.7 kb fragment is depicted above. (B) Representative intermediates that arise during replication of the (GAA)₁₀₀ repeat. Using siRNA knockdowns of replication fork reversal and restart genes, genetic controls were established to identify the nature of these intermediates. (C) Depiction of unresolved replication intermediates that may appear if forks are denatured during isolation. (D) An unsuccessful 2DGE experiment as shown by a complete absence of replication intermediates. IV represents linear, unreplicated fragments of the digested plasmid. Abbreviation: 2DGE = Two-dimensional neutral/neutral gel-electrophoresis. Please click here to view a larger version of this figure.

Discussion

2DGE provides a semi-quantitative and comprehensive image of the relative populations of intermediates that arise during the replication of a particular sequence. Given that the fragile molecular structures of replication forks must be maintained throughout this procedure, great care should be implemented to prevent physical shearing and chemical denaturation. Therefore, it is highly recommended that any alkaline treatment be avoided during plasmid isolation. To avoid this, we and others have implemented a modified form of the Hirt isolation of DNA, established by Hirt in 1967³³. Here, DNA is separated from proteins, RNA, and other cellular debris by treating cell lysate with 1 M NaCl at 4 °C overnight. While this method has proven exceptional for preserving the quality of replication intermediates, it does not appear to fully separate plasmid DNA from genomic DNA. This should be kept in mind when designing the sequence for radiolabeled probing, as the designed probe should not have high sequence similarity with any genomic DNA to best avoid off-target binding. Further, the integrity of replication intermediates may be greatly increased through UV-psoralen crosslinking. Here, cells can be incubated with psoralen for several minutes in the dark before being UV irradiated at 366 nm³⁴, thus creating covalent bonds between the DNA molecules. In addition to reinforcing the cohesiveness of intermediate structures, this may also alleviate any concern of structures forming during isolation rather than in vivo.

One aspect that should be considered when designing this experiment is repeat placement on the resolved final arc. The first half of the arc extending out from the 1n spot is denoted as the ascending arm, while the second half is known as the descending arm (Figure 1B). To observe replication fork stalling, repeat placement on either arm of the arc should be sufficient. However, to observe more structured intermediates that arise at repeat sequences, such as postreplicative junctions, we recommend placing the repeat sequence on the descending arm. This is largely due to the slower electrophoretic mobility of these intermediates in both dimensions, which may result in co-migration with simple Ys structures farther along in their progression if the repeat-containing sequence were placed on the ascending arm, thus hindering any detailed analysis. For the best resolution, we recommend placing the repeat sequence somewhere between 60% and 90% within the fragment of interest relative to the origin of replication.

Attention to detail should be utilized during the DNA transfer step and subsequent treatment of the membrane. It is extremely important that the Southern blot is assembled in a manner that facilitates an even and tight transfer of DNA to the membrane. This means that all components on the transfer are free of air bubbles and that the apparatus is uniform across its surface. To assist in this, it is standard to flip the second-dimension gel over prior to adding it to the Southern blot. The bottom of the gel is assumed to be flatter than the top; therefore, flipping the gel over ensures the smoothest possible transfer of DNA to the membrane.

If a strong background is present in the final resolution of the blot, this may be indicative of the non-specific binding of the radiolabeled probe. This can be alleviated in a number of ways. First, it should be checked that the probe does not contain high sequence similarity to any genomic DNA. This can be easily verified using the Nucleotide Basic Local Alignment Search Tool (BLAST), which is readily available through the NIH website³⁵. Otherwise, nonspecifically bound probes can be removed through additional stringent washes. We recommend beginning with two additional washes of buffer 1 (0.1x SSC, 0.1% SDS) at 42 °C in 15 min intervals each; however, more washes may be needed. Finally, the temperature at which hybridization occurs may be altered as well. For most probes containing a G/C content of 40-60%, 65 °C tends to be sufficient, though this is not a static value. Efficient binding of the probe is dependent on its melting temperature and, therefore, may require alterations to the hybridization temperature.

Given that 2DGE provides an overview of the relative populations of replication intermediates at a given time, one of its greatest drawbacks is that it does not provide a strong measure of replication progression timing. For this purpose, we recommend using single-molecule analysis like DNA combing. Further, while 2DGE allows for analysis of the replication intermediates that arise in response to stalling, genetic controls must be established to uncover their exact identity, which can be timely. Although costly, electron microscopy remains superior in identifying the exact structure of DNA molecules.

Offenlegungen

The authors have nothing to disclose.

Acknowledgements

We thank Jorge Cebrian and Anastasia Rastokina who started developing this approach in our lab, Massimo Lopes for providing us with pML113 plasmid and invaluable advice, Ylli Doksani for insightful discussions, and members of the Mirkin lab for their support. The work in the Mirkin lab is supported by the National Institute of General Medical Sciences [R35GM130322] and NSF-BSF [2153071].

Materials

10x TBE Buffer	Bio Rad	1610733
20x SSC Buffer	Fisher Scientific	BP1325-1
293T cells	ATCC	CRL-3216
a-³²P dATP, 3000 Ci/mmol	Revvity	BLU512H250UC
Agarose	Fisher Scientific	BP160-500
Amersham Hybond-N+	Fisher Scientific	RPN303B
BAS Storage Phosphor Screens	Fisher Scientific	28956482
Church and Gibert's hybriddization buffer	Fisher Scientific	50-103-5408
DecaLabel DNA labeling kit	ThermoFisher Scientific	K0622
DMEM, high gluctose, GltaMAX Supplement, pyruvate	ThermoFisher Scientific	10569010
DpnI	New England Biolabs	R0176S	Additional restriction enzymes will need to be purchased as well
EDTA 0.5 M, pH 8	Fisher Scientific	BP2482500
Ethanol, 70%	Fisher Scientific	BP82031GAL
Fetal Bovine Serum	VWR	97068-085
Hydrochloric acid solution, 12 M	Millipore Sigma	13-1683
Isopropanol	Fisher Scientific	BP26184
jetPRIME DNA and siRNA Transfection Reagent with Buffer	VWR	101000027
MycoZap Plus-CL	VWR	75870-448
NaCl	Millipore Sigma	746398-500G
Nalgene Oak Ridge High-Speed Centrifuge Tubes	ThermoFisher Scientific	3139-0050
Phosphate Buffer Saline, pH 7.4	ThermoFisher Scientific	10010023
Phosphate Buffer Saline, pH 7.5	ThermoFisher Scientific	10010024
Proteinase K	ThermoFisher Scientific	EO0491
Proteinase K	ThermoFisher Scientific	EO0492
Pure Cellulose Chromatography Paper	Fisher Scientific	05-714-4
Pure Cellulose Chromatography Paper	Fisher Scientific	05-714-5
Ruler	Fisher Scientific	09-016
Scalpel	Fisher Scientific	12-460-451
Sodium dodecyl sulfate	Millipore Sigma	436143-25G
Sodium hydroxide	Fisher Scientific	S25548
Sorval LYNX 4000 Superspeed Centrifuge	ThermoFisher Scientific	75006580
Sub-cell Horizontal Electrophoresis System	Bio Rad	1704401
TH13-6 x 50 Swinging Bucket Rotor	ThermoFisher Scientific	75003010
Tris-HCl 1 M, pH 7.5	Fisher Scientific	BP1757-500
Trypsin-EDTA (0.25%), phenol red	ThermoFisher Scientific	25200056

Referenzen

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