The mechanisms that operate in eukaryotic cells to promote replication fork integrity and coordinate replication with other aspects of chromosome maintenance are becoming clear. For example, over 40 days at 25, 37, and 45C, 80% of the DNA embedded in silk was recoverable compared to 20% when unprotected22. Kearsey, S. E. & Cotterill, S. Enigmatic variations: divergent modes of regulating eukaryotic DNA replication. https://doi.org/10.1155/2016/8072463 (2016). Sci. In the meantime, to ensure continued support, we are displaying the site without styles Open Access 20, 713 (1999). Dalgaard, J. (3) Depurination or chemical alterations of bases may occur and not be directly assessed by sequencing or QPCR based approaches. (D) Exchange rate as a function of Pol concentration. Effect of Shear on Plasmid DNA in Solution. For example, a broader variety of storage conditions should be tested to develop a more comprehensive mechanistic model of DNA stability, including models that not only artificially accelerate aging through elevated temperature but through elevated exposure to electromagnetic radiation and/or subatomic particles, high or low pH, hydrolysis and humidity, and mechanical rearrangements (e.g., freeze thaws, liquid handling) at the molecular level. Z., Stasiak, A. References 117 and 118 propose that template switching at nearby inverted repeats generates dicentric chromosomes without a DSB intermediate. J. Forensic Sci. Open Access Mirkin, E. V. & Mirkin, S. M. Replication fork stalling at natural impediments. Both acidic and basic conditions can enhance the hydrolysis rate of DNA by either increasing the electrophilicity of the DNA or the nucleophilicity of water. 2A); (3) an error probability can be calculated to estimate the probability the code will not be able to account for and correct errors given certain error and strand loss rates; (4) the amount of redundancy in the code is tunable in order to achieve a certain error probability or system reliability; (5) the code accounts for multiple copies of each distinct DNA strand, with strand loss or erasure only occurring when all copies of a distinct DNA strand are lost; and (6) the length of the DNA strands can be tuned with effects on density due to the overhead of addresses and indices. Biol. Curr. 61, 212238 (1997). Epple, C. & Leumann, C. Bicyclo(3.2.1]-DNA, a new DNA analog with a rigid backbone and flexibly linked bases: pairing properties with complementary DNA. Cell 94, 819827 (1998). Proc. (Bottom) Molecular mechanisms of damage most relevant to each storage mode. Postow, L., Crisona, N. J., Peter, B. J., Hardy, C. D. & Cozzarelli, N. R. Topological challenges to DNA replication: conformations at the fork. Cosmochim. The active development of DNA-based computation preceded the development of DNA storage systems by over a decade5,6,43,44. Nature Rev. Curr. PubMed Replication fork is formed 3. We thank all members of our laboratories for helpful discussions. DNA stability: a central design consideration for DNA data storage systems, https://doi.org/10.1038/s41467-021-21587-5. ADS FIGURE 1.Single-molecule methods used to study replicative helicases. 26, 425437 (2006). Koster, D. A., Palle, K., Bot., E. S., Bjornsti, M. A. Positive torsional strain causes the formation of a four-way junction at replication forks. D & Pearson, C. E. Repeat instability as the basis for human diseases and as a potential target for therapy. & Lehmann, A. R. 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Experiments exploring a more comprehensive set of parameters and that assess sources of variability in results could provide more confidence in the design and utility of DNA storage technologies. ADS Haracska, L., Torres-Ramos, C. A., Johnson, R. E., Prakash, S. & Prakash, L. Opposing effects of ubiquitin conjugation and SUMO modification of PCNA on replicational bypass of DNA lesions in Saccharomyces cerevisiae. Cell 31, 287293 (2008). Science 355, 950954 (2017). 19, 339350 (2005). Proc. Fondazione IFOM, Istituto FIRC di Oncologia Molecolare, IFOM-IEO campus, Via Adamello 16, Milan, 20139, Italy, Dipartimento di Scienze Biomolecolari e Biotecnologie, Universit degli Studi di Milano, Via Celoria 26, Milan, 20133, Italy, You can also search for this author in Google Scholar. Fusion of nearby inverted repeats by a replication-based mechanism leads to formation of dicentric and acentric chromosomes that cause genome instability in budding yeast. in IEEE International Symposium on Information Theory (ISIT) (2019). In E. coli , this means that the entire genome is replicated in just 40 minutes, at a pace of approximately 1,000 nucleotides per second. DNA Polymerase III: -Adds nucleotides in a 5'-->3' (nucleotide) direction (3' --> 5' of DNA) 4. what stabilizes the dna molecule during replication - Brainly.com 8, 148155 (2006). 55, 127138 (2009). This is accomplished by the process of DNA replication. The replication intermediates in Escherichia coli are not the product of DNA processing or uracil excision. Microbiol Mol. 12, 176183 (2014). As freeze thaws cause mechanical stresses on DNA, there is some intuition for why longer DNA strands would be more susceptible to breakage. 12, 7479 (2010). Comprehensive review on the DNA metabolism processes operating during DNA replication. 2, 39, https://doi.org/10.1038/35072071 (2001). Struct. (C). Fanconi anemia is associated with a defect in the BRCA2 partner PALB2. the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in 2. 24, 42674274 (2004). Certain DNA elements, such as centromeres and telomeres, are heterochromatic. Errors represent SEM. K99 GM126143/GM/NIGMS NIH HHS/United States, R00 GM126143/GM/NIGMS NIH HHS/United States, R01 GM115809/GM/NIGMS NIH HHS/United States, T32 CA009673/CA/NCI NIH HHS/United States. Ivessa, A. S., Zhou, J. Q., Schulz, V. P., Monson, E. K. & Zakian, V. A. Saccharomyces Rrm3p, a 5 to 3 DNA helicase that promotes replication fork progression through telomeric and subtelomeric DNA. The line represents a hyperbolic fit, giving a maximum exchange rate of (1.4 0.5) 10. Average number of CMG molecules at elongating replication forks over time, giving 1.0 0.7 (mean SEM; n = 89). Paulovich, A. G., Margulies, R. U., Garvik, B. M. & Hartwell, L. H. RAD9, RAD17, and RAD24 are required for S phase regulation in Saccharomyces cerevisiae in response to DNA damage. Biobank. Sun, W. et al. Proceeding of the Conference on Mass Storage Systems and Technologies (MSST '20) (2020). New approaches could include a combination of deep next-generation sequencing of short-term samples to detect very rare degradation events. Rev. Mueller SH, Fitschen LJ, Shirbini A, Hamdan SM, Spenkelink LM, van Oijen AM. Cell 91, 5969 (1997). DNA Replication Steps and Process - ThoughtCo Cell 15, 607620 (2004). Mol. Nature Struct. Peer review information Nature Communications thanks the anonymous reviewer(s) for their contribution to the peer review of this work. Hence, to maintain the same reliability of information transfer or recovery, error correction forces a trade-off between density of information and tolerance to errors. Nat Commun. Litman, R. et al. These addresses can be read and retrieved using PCR or transcription. Answer: Topoisomerases (red) reduce torsional strain caused by the unwinding of the DNA double helix; DNA helicase (yellow) breaks hydrogen bonds between complementary base-pairs; single-strand binding proteins (SSBs) stabilize the separated strands and prevent them from rejoining . Xia, B. et al. Saccharomyces cerevisiae RAD5-encoded DNA repair protein contains DNA helicase and zinc-binding sequence motifs and affects the stability of simple repetitive sequences in the genome. The idea of now merging these two fields to perform in-storage computation has intriguing implications including potentially providing the ability to directly search45 and edit46 DNA databases. The basic idea DNA replication is semiconservative, meaning that each strand in the DNA double helix acts as a template for the synthesis of a new, complementary strand. 71, 1335 (2007). In this reaction, RF-C recognizes the 3' hydroxyl (OH) ends generated by the action of DNA polymerase (see Bloom's chapter in the same special issue). Given that the accuracy of data retrieval is paramount for cold storage systems, additional studies assessing accelerated degradation due to other parameters other than temperature would provide increased confidence in extrapolated stabilities. Anal. Cobb, J. Natl Acad. The leading-strand tail appears as a bright spot that moves in a unidirectional manner while simultaneously increasing in intensity. Nucleic Acids Res. Gangavarapu, V., Prakash, S. & Prakash, L. Requirement of RAD52 group genes for postreplication repair of UV-damaged DNA in Saccharomyces cerevisiae. ACS Synth. & Keung, A.J. Madisen, L. The effects of storage of blood and isolated DNA on the integrity of DNA. There are likely experimental details affecting the accurate interpretation of measurements including the manipulation of DNA itself in setting up experiments, or confounding parameters like DNA solubility. 5. Cell 131, 12351247 (2007). Andreassen, P. R., D'Andrea, A. D. & Taniguchi, T. ATR couples FANCD2 monoubiquitination to the DNA-damage response. Right: length of the lagging strand (yellow), leading strand (blue), and parental DNA (gray) as a function of time. United States Data Center Energy Usage Report (Lawrence Berkeley National Laboratory, 2016). Cell 131, 12281230 (2007). 2023 Apr 29;14(5):1012. doi: 10.3390/genes14051012. 1 with generic unit processes. While constant exposure to UV is unlikely for a DNA storage system, it may reflect a general principle of length-dependent degradation sensitivities. Cotta-Ramusino, C. et al. (A) Example kymographs showing activity of pre-assembled replisomes on single DNA substrates in the absence of excess polymerases in solution. This review has focused on empirical measurements of DNA stability under a range of different conditions. https://www.networkworld.com/article/3295937/migrate-data-to-the-cloud-how-appliances-from-amazon-google-microsoft-and-ibm-stack-up.html (2018). Lower perror significantly reduces the residual likelihood of error. Tsao, Y. P., Russo, A., Nyamuswa, G., Silber, R. & Liu, L. F. Interaction between replication forks and topoisomerase I-DNA cleavable complexes: studies in a cell-free SV40 DNA replication system. Publishers note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Blood 100, 24142420 (2002). Slower and gentler pipetting stillled to more than 50% of lambda DNA being fragmented39. References 5 and 6 map replication origins and identify their replication time. Opin. The use of many standard buffers such as PBS and TE could help maintain pH levels at appropriate targets. Chung, W. J. et al. 16, https://doi.org/10.1097/PDM.0b013e31803c558a (2007). Genes Dev. Mutations within strands, or loss of strands due to breakage or degradation would lead to potential decoding errors or even complete loss of information. USA 105, 99369941 (2008). However, as the overall probability of breakage per nt decreases (to the left), all strands are less likely to break, and this gives longer strands an advantage since they can hold a larger fraction of information per strand and the outer code can work effectively even with a relatively small number of error correction symbols. In the meantime, to ensure continued support, we are displaying the site without styles In many cases, the adsorption of the DNA onto a matrix stabilized the DNA. The robustness and failure rates of information storage systems are of utmost importance as the reliability of data retrieval must be concretely reported, verifiable, and trustworthy62,63,64,65. In addition to computation, there is also the hope that DNA storage systems may be capable of dramatically lower latencies of operation than the current multi-hour to multi-day process of reading and writing information. Nature Cell Biol. Hansen, R. S., Canfield, T. K., Lamb, M. M., Gartler, S. M. & Laird, C. D. Association of fragile X syndrome with delayed replication of the FMR1 gene. and JavaScript. Smith, S. & Morin, P. A. Optimal storage conditions for highly dilute DNA samples: a role for trehalose as a preserving agent. Given the asymmetry of the DNA molecule, DNA synthesis must occur continuously on one strand (leading) and discontinuously on the opposite strand (lagging strand). Keywords: The Ctf4 and MTC components of the replisome are not shown for clarity. 8, 358366 (2006). (B) Example kymograph showing the DNA (left), labeled CMG (middle), and the CMG intensity as a function of time (right). Ramrez Montero D, Snchez H, van Veen E, van Laar T, Solano B, Diffley JFX, Dekker NH. & Ellington, A. D. Synthetic DNA synthesis and assembly: putting the synthetic in synthetic biology. DNA polymerase will add the free DNA nucleotides using complementary base pairing (A-T and C-G) to the 3' end of the primer this will allow the new DNA strand to form. A homoduplex DNA formed between two strands that have either the same number or a different number of repeats (usually triple repeats). 17, 6476 (2003). Podivinsky, E., Love, J. L., van der Colff, L. & Samuel, L. Effect of storage regime on the stability of DNA used as a calibration standard for real-time polymerase chain reaction. Bonnet, J. et al. R. Soc. Johnson, R. E. et al. Mankouri, H. W. & Hickson, I. D. Top3 processes recombination intermediates and modulates checkpoint activity after DNA damage. Biol. Biobank. To obtain Degradation rates have also been reported in a mix of many different environmental, temperature, buffer, and temporal conditions. Genome-organizing factors Top2 and Hmo1 prevent chromosome fragility at sites of S phase transcription. Mol. Liberi, G. et al. Mol. It underscores the need to tailor error correction and system parameters like strand length and copy number to different settings including error rates that vary according to environmental conditions and data storage applications. Secondary structures, highly transcribed DNA sequences and damaged DNA stall replication forks, which then require checkpoint factors and specialized enzymatic activities for their stabilization and subsequent advance. Proc Natl Acad Sci U S A. 2017 Jan 24;114(4):675-680. doi: 10.1073/pnas.1619748114. Documents the role of sumoylation in the resolution of recombination intermediates formed during the replication of damaged templates. https://doi.org/10.1038/s41467-019-09517-y (2019). Describes the consequences of RF collapse in the triggering of recombination and genome instability. References 73 and74 document the role of the replication checkpoint in preventing the regression of stalled RFs. eCollection 2020 May. 39, 159161 (2007). 56, 36133616 (2020). 27, 379390 (1987). Sci. DNA Replication - Labeling - Google Docs To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. One of the three biologically active double helical structures of DNA. Maintaining genome stability at the replication fork - Nature Rev. _____________________________ Strand that is copied discontinuously because it is traveling away from. Biotechnol. Nature 362, 709715 (1993). Cell 127, 509522 (2006). Rev. Single-stranded binding proteins bind to and stabilize single-stranded DNA during DNA replication until the single-stranded DNA can be used as a template for a new strand to bind to. Biol. In fact, broken chromosomes are often the source of DNA rearrangements and can change the genetic program of a cell.These . D Relationship between information density and strand length as a function of the probability of strand breakage. Cell 138, 870884 (2009). 13, 890898 (2013). 43, 511524 (2017). Article J. Biol. Molecular Events of DNA Replication | Learn Science at Scitable - Nature 27, 77587764 (2007). The successful recovery of DNA from fossils or microbes preserved in permafrost, some millions of years old, is commonly used as motivating evidence for the long-term stability of DNA17,18. 9.2 DNA Replication - Concepts of Biology | OpenStax A cruciform junction that is formed by the intertwining of sister duplexes in the replicated portion of a replicon. Fierro-Fernandez, M., Hernandez, P., Krimer, D. B., Stasiak, A. 11, 165170 (2010). Biopreserv. Biol. 15, 20602068 (2001). Biochem. Preprint at bioRxiv https://doi.org/10.1101/2020.05.25.115477 (2020). Zhang, Y. W. et al. The Fanconi anaemia gene FANCC promotes homologous recombination and error-prone DNA repair. Novel control of S phase of the cell cycle by ubiquitin-conjugating enzyme H7. This is because the current high cost of DNA synthesis and sequencing can be justified when they are infrequent and amortized over many years16. All strands comprising one file share a common address sequence located on one or both ends of the strands. CAS These mechanisms ensure that the local DNA damage response, which enables replication fork progression and DNA repair in S phase, is coupled with cell cycle transitions. Second, estimations of DNA stability from natural samples may be overly optimistic for DNA storage applications. & Elledge, S. J. Mrc1 is a replication fork component whose phosphorylation in response to DNA replication stress activates Rad53. Cell 29, 141148 (2008). (B) A magnetic trap uses a magnetic field to apply force (10-100 pN) and torque to a paramagnetic bead and thus measure . Quality control mechanisms exclude incorrect polymerases from the eukaryotic replication fork. Sci. Recall that adenine nucleotides pair with thymine nucleotides . Nature Cell Biol. Organick, L. et al. Biol. DNA Replication (E. coli) - McGraw Hill Education High-throughput techniques enable advances in the roles of DNA and RNA secondary structures in transcriptional and post-transcriptional gene regulation, Identification of Nanog as a novel inhibitor of Rad51, Histone dynamics during DNA replication stress, Delayed DNA break repair for genome stability, Sites of chromosomal instability in the context of nuclear architecture and function. J. Bacteriol. Doksani, Y., Bermejo, R., Fiorani, S., Haber, J. E. & Foiani, M. Replicon dynamics, dormant origin firing, and terminal fork integrity after double-strand break formation. A contortion in DNA that is important for DNA packaging and DNA and RNA synthesis. _____________________________ Stabilizes the DNA molecule during replication 7. And each has to be performed precisely to produce two identical strands of DNA. The Mcm27 complex has in vitro helicase activity. B Relationship between log decoder error probability during RS decoding and DNA strand length, including the effects of symbol error rate (mutations, insertions, and deletion, Perror) and copy number. The line represents a hyperbolic fit, giving a maximum exchange rate of (2.3 0.2) 10, (A) Example kymograph showing the DNA (left) and labeled Pol (middle) and corresponding labeled Pol intensity at the fork (right). Rev. Genet. Biotechnol. For example, locked nucleic acid monomers possess a methylene bridge between a 2 oxygen and the 4 carbon of the pentose ring and offer substantial resistance to nuclease enzymes present abundantly in the ambient environment. Annu. The DNA molecule is unwound and prepared for synthesis by the action of DNA gyrase, DNA helicase and the single-stranded DNA binding proteins. EMBO J. 1). In fact, it is not simply that shorter strands are better for high strand loss rates but that there can be optimal lengths that balance the overhead needed for file addresses and indices with the encoding overhead required to account for strand loss. Genet. Allentoft, M. E. et al. Interplay between the Smc5/6 complex and the Mph1 helicase in recombinational repair. PubMed 11, 13151324 (2009). Topoisomerases sense supercoiling and act to either generate or dissipate it by changing DNA topology. 91, 1226812274 (2019). Shao, W., Khin, S. & Kopp, W. C. Characterization of effect of repeated freeze and thaw cycles on stability of genomic DNA using pulsed field gel electrophoresis. The images or other third party material in this article are included in the articles Creative Commons license, unless indicated otherwise in a credit line to the material. Sung, P. & Klein, H. Mechanism of homologous recombination: mediators and helicases take on regulatory functions. PubMed Single-strand binding protein: -Stabilizes DNA strand. 22, 18161827 (2008). Nat. Zegerman, P. & Diffley, J. F. DNA replication as a target of the DNA damage checkpoint. Together with the checkpoint-mediated pathway, small ubiquitin-related modifier (SUMO) and ubiquitin modifications are crucial in regulating the stability and activity of key components of DNA replication and repair machineries. 23, 28762886 (2009). Kohll, A. X. et al. PubMed Nucleic Acids Res. Shore, D. & Bianchi, A. Telomere length regulation: coupling DNA end processing to feedback regulation of telomerase. 9, 297308 (2008). Mol. 2, and in particular demonstrate how relationships between copy number, strand loss, strand length, information density can be modeled and used to inform system design. Mirkin, S. M. DNA structures, repeat expansions and human hereditary disorders. A DNA lesion in which the nucleotides carry bulky groups. (C) Single-molecule rate distribution. New Insights into the Mechanism of DNA Duplication by the Eukaryotic Replisome. Sci. Ma, S., Saaem, I. CAS Ed. Genes Dev. Aguilera, A. 12791292, https://doi.org/10.1039/c6bm00741d (2017). Assessment of DNA encapsulation, a new room-temperature DNA storage method. First, the physical processes of encapsulation and retrieval take some time, suggesting this approach is best suited for cold storage applications. An essential complex for DNA replication that promotes polymerase- loading and the activity of the MCM helicase. Kai, M. & Wang, T. S. Checkpoint activation regulates mutagenic translesion synthesis. 5, 10211029 (2006). Shows that tRNA transcription causes RF pausing. Segurado, M. & Diffley, J. F. Separate roles for the DNA damage checkpoint protein kinases in stabilizing DNA replication forks. In this system, shorter strands achieve superior density at high strand breakage rates. Oncogene 23, 12061213 (2004). These addresses typically are complementary to short DNA oligomers used to amplify the files through PCR3 or to extract them through affinity-based methods55. Rev. 8, 947956 (2007). Structural and biochemical studies have revealed the basic principles of how the replisome duplicates genomic DNA, but little is known about its dynamics during DNA replication. Robust chemical preservation of digital information on DNA in silica with error-correcting codes. Bauer, T., Weller, P., Hammes, W. P. & Hertel, C. The effect of processing parameters on DNA degradation in food. Image modified from OpenStax, CC BY 3.0. Clermont, D. et al. Biol. Aberrant DNA replication is a major source of the mutations and chromosome rearrangements that are associated with pathological disorders. Cancer Res. Mol. Sci. Each of these consists of reactions between enzymes and the DNA macromolecule. Lou, Z., Minter-Dykhouse, K. & Chen, J. BRCA1 participates in DNA decatenation. Nat Commun 12, 1358 (2021). Bochman, M. L. & Schwacha, A. PubMed Central Shishkin, A. SSB from , a monomer of which has a molecular weight of 19 kDa, forms a stable homotetramer and effectively presents four OB folds to ssDNA. Separable, Ctf4-mediated recruitment of DNA Polymerase for initiation of DNA synthesis at replication origins and lagging-strand priming during replication elongation. Biol. Mechanisms of DNA damage, repair and mutagenesis - PMC 281, 2263522646 (2006). Current experimental systems tend to operate in a regime with large numbers of copies; however, even if future systems may wish to be more lean, this analysis suggests copy number requirements may not need to be as high as intuition may suggest particularly if strand length designs remain in the 200500nt range. Trapmann, S. et al. Single-molecule experiments have significantly changed the classical model of highly stable replication machines by showing that components exchange with free . What Stabilizes The Dna Molecule During Replication Curr. Dynamic and scalable DNA-based information storage. in Proceedings of the 1988 ACM SIGMOD International Conference on Management of Data 109116 (1988). We further assume that multiple copies of a strand exponentially reduce the likelihood of loss because all copies of the strand must be lost to cause an erasure. Article Schwob, E. Flexibility and governance in eukaryotic DNA replication. With automation, the pipetting actions could be slowed significantly to be less turbulent; however, this might present a significant trade-off in increasing the time required to perform each physical operation or manipulation. Depurination would result in missing or incorrect nucleotides during sequencing, while 8-oxo-dG can lead to cross-linking between DNA strands which inhibits both rehydration of dried DNA as well as amplification and sequencing of the DNA. Blawat, M. et al. Genes (Basel). The replication of DNA occurs during the synthesis phase, or S phase, of the cell cycle, before the cell enters mitosis or meiosis. https://doi.org/10.1145/2872362.2872397 (2016). Science 297, 602606 (2002). Natl Acad. The Saccharomyces cerevisiae helicase Rrm3p facilitates replication past nonhistone protein-DNA complexes. In addition, while many studies have quantified DNA degradation through some form of quantitative PCR, mass measurements, or even next-generation sequencing, the definition of DNA degradation remains unprecise and too limited despite its considerable impact on the physical design and encoding of reliable storage systems. Das-Bradoo, S. et al. 2012 Jul 6;287(28):23740-7. doi: 10.1074/jbc.M112.368951. Nature Rev. Cancer Res. Chem. A layer by layer design with alternating DNA and cationic polyethylenimine with a silica final encapsulation has achieved the best storage density to date in such systems, ~3.4wt% DNA25. Furthermore, for search-type functions that rely on DNADNA hybridizations, stable hybridizations for ~20nt sequences occur at between ~50 and 60C. A., Krasilnikova, M. M. & Mirkin, S. M. Replisome stalling and stabilization at CGG repeats, which are responsible for chromosomal fragility.