ArticleAnalytical biochemistry2013
Trapping and breaking of in vivo nicked DNA during pulsed field gel electrophoresis.
Article in Analytical biochemistry, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 19 citations in OpenAlex.
- Catastrophic chromosome fragmentation probes the nucleoid structure and dynamics in Escherichia coli.Nucleic acids research · 2022Article
- Thymine-starvation-induced chromosomal fragmentation is not required for thymineless death in Escherichia coli.Molecular microbiology · 2022Article
- Nitric oxide precipitates catastrophic chromosome fragmentation by bolstering both hydrogen peroxide and Fe(II) Fenton reactants in E. coli.The Journal of biological chemistry · 2022Article
- DisA Restrains the Processing and Cleavage of Reversed Replication Forks by the RuvAB-RecU Resolvasome.International journal of molecular sciences · 2021Article
- Catalase inhibition by nitric oxide potentiates hydrogen peroxide to trigger catastrophic chromosome fragmentation in Escherichia coli.Genetics · 2021Article
- Detection and quantification of γ-H2AX using a dissociation enhanced lanthanide fluorescence immunoassay.Scientific reports · 2021Article
- Extrachromosomal DNA amplicons in antimalarial-resistant Plasmodium falciparum.Molecular microbiology · 2021Article
- Reactive Oxygen Species Production Is a Major Factor Directing the Postantibiotic Effect of Fluoroquinolones in Streptococcus pneumoniae.Antimicrobial agents and chemotherapy · 2019Article
- Guidelines for DNA recombination and repair studies: Cellular assays of DNA repair pathways.Microbial cell (Graz, Austria) · 2019Review
- Enrichment of megabase-sized DNA molecules for single-molecule optical mapping and next-generation sequencing.Scientific reports · 2017Article
- Pulsed-field gel electrophoresis does not break E. coli chromosome undergoing excision repair after UV irradiation.Analytical biochemistry · 2017Article
- Degradation of RNA during lysis of Escherichia coli cells in agarose plugs breaks the chromosome.PloS one · 2017Article
- Prompt repair of hydrogen peroxide-induced DNA lesions prevents catastrophic chromosomal fragmentation.DNA repair · 2016Article
- Static and Dynamic Factors Limit Chromosomal Replication Complexity in Escherichia coli, Avoiding Dangers of Runaway Overreplication.Genetics · 2016Article
- Reactive Oxygen Species Contribute to the Bactericidal Effects of the Fluoroquinolone Moxifloxacin in Streptococcus pneumoniae.Antimicrobial agents and chemotherapy · 2016Article
- Cyanide enhances hydrogen peroxide toxicity by recruiting endogenous iron to trigger catastrophic chromosomal fragmentation.Molecular microbiology · 2015Article
- Replication fork inhibition in seqA mutants of Escherichia coli triggers replication fork breakage.Molecular microbiology · 2014Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Pulsed field gel electrophoresis (PFGE) offers a high-resolution approach to quantify chromosomal fragmentation in bacteria, measured as percentage of chromosomal DNA entering the gel. The degree of separation in pulsed field gel (PFG) depends on the size of DNA as well as various conditions of electrophoresis such as electric field strength, time of electrophoresis, switch time, and buffer composition. Here we describe a new parameter, the structural integrity of the sample DNA itself, that influences its migration through PFGs. We show that subchromosomal fragments containing both spontaneous and DNA damage-induced nicks are prone to breakage during PFGE. Such breakage at single-strand interruptions results in artifactual decrease in molecular weight of linear DNA making accurate determination of the number of double-strand breaks difficult. Although breakage of nicked subchromosomal fragments is field strength independent, some high-molecular-weight subchromosomal fragments are also trapped within wells under the standard PFGE conditions. This trapping can be minimized by lowering the field strength and increasing the time of electrophoresis. We discuss how breakage of nicked DNA may be mechanistically linked to trapping. Our results suggest how to optimize conditions for PFGE when quantifying chromosomal fragmentation induced by DNA damage.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.