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DNA Damage and Repair: Current Research
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DNA Damage and Repair: Current Research

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 30 September 2026 | Viewed by 2864

Special Issue Editors

Dr. Mahara A. Valverde Ramírez

E-Mail Website
Guest Editor
Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, México
Interests: carcinogenesis; molecular oncology; transformation biomarkers; cancer stem cells
Special Issues, Collections and Topics in MDPI journals
Dr. Emilio Rojas

E-Mail Website
Guest Editor
Laboratorio de Genotoxicología, Instituto de Investigaciones Biomédicas, U.N.A.M., Mexico City 04510, Mexico
Interests: DNA damage and repair; gene expression; epigenetic effects; cell transformation; environmental exposure; human exposed populations

Special Issue Information

Dear Colleagues,

We are constantly exposed to a wide range of endogenous and exogenous compounds—originating from metabolism, diet, the environment, clothing, cosmetics, pharmaceuticals, and more—about which relatively little is known regarding their potential to disrupt the homeostasis between DNA damage and its repair via various cellular mechanisms. Furthermore, the body of evidence highlighting the crucial role of DNA repair pathways in numerous diseases, as well as their potential therapeutic applications, continues to grow rapidly.

With this in mind, this Special Volume, "DNA Damage and Repair: Current Research," welcomes the submission of original studies in this field. Our aim is to present a diverse collection of papers that reflect the breadth and depth of ongoing research on DNA damage and repair.

Dr. Mahara A. Valverde Ramírez
Dr. Emilio Rojas
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 250 words) can be sent to the Editorial Office for assessment.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • DNA damage
  • DNA repair
  • endogenous compounds
  • exogenous compounds
  • therapy

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Published Papers (4 papers)

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Research

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13 pages, 3288 KB  
Communication
Respiratory Models Reveal DNA Damage Response Modulation by Merkel Cell Polyomavirus
by Sara Passerini, Marta De Angelis, Sara Messina, Daniela Scribano, Cecilia Ambrosi, Ugo Moens, Lucia Nencioni and Valeria Pietropaolo
Int. J. Mol. Sci. 2026, 27(8), 3449; https://doi.org/10.3390/ijms27083449 - 12 Apr 2026
Cited by 1 | Viewed by 631
Abstract
Merkel Cell Polyomavirus is an oncogenic virus associated with Merkel Cell Carcinoma (MCC). However, considering viral detection in respiratory specimens and similarities between MCC and neuroendocrine lung cancer, its plausible role in the respiratory tract is disputed. MCPyV-mediated oncogenesis involves viral antigens interfering [...] Read more.
Merkel Cell Polyomavirus is an oncogenic virus associated with Merkel Cell Carcinoma (MCC). However, considering viral detection in respiratory specimens and similarities between MCC and neuroendocrine lung cancer, its plausible role in the respiratory tract is disputed. MCPyV-mediated oncogenesis involves viral antigens interfering with host signaling as a DNA Damage Response (DDR). In the current study, respiratory models, including lung cancer cell lines (A549 and H1299), and non-malignant bronchial systems (HBEC-KT and a 2D ALI model) were used to investigate DDR genes’ expression following MCPyV infection. Once the capability to support viral replication and transcription was assessed using qPCR and RT-qPCR, respectively, the mRNA levels of DDR genes, including ATM, ATR, Chk1, Chk2, H2AX, Rad51, p53 and p21, were examined. Our findings showed MCPyV replication in all cellular systems, as proven by the detection of viral DNA and transcripts. Viral infection induced an overexpression of DDR genes, suggesting a role of the virus in manipulating DDR to favor its replication or contribute to tumor progression. These preliminary results provide in vitro models for studying the interplay between MCPyV and DDR within malignant and non-malignant contexts across the respiratory tract, laying the basis for future research exploring the clinical relevance of DDR activation in virus-driven malignancies. Full article
(This article belongs to the Special Issue DNA Damage and Repair: Current Research)
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18 pages, 3361 KB  
Article
DNA ‘Breathing’ Recombination Cloning: A Mismatch-Tolerant, Temperature-Dependent Homologous Recombination Cloning Method
by Yun He, Yi Ding, Yan Zhang, Like Liu, Shanhua Lyu and Yinglun Fan
Int. J. Mol. Sci. 2026, 27(6), 2604; https://doi.org/10.3390/ijms27062604 - 12 Mar 2026
Viewed by 450
Abstract
DNA cloning traditionally relies on two approaches: restriction endonuclease digestion-ligation, and homologous recombination involving exonucleases, polymerases, and other enzymes. Here, we present a novel cloning method that requires only restriction endonucleases, eliminating the need for exonucleases or polymerases. The linearized cloning vector and [...] Read more.
DNA cloning traditionally relies on two approaches: restriction endonuclease digestion-ligation, and homologous recombination involving exonucleases, polymerases, and other enzymes. Here, we present a novel cloning method that requires only restriction endonucleases, eliminating the need for exonucleases or polymerases. The linearized cloning vector and the foreign DNA fragment (FDF) containing overlapping sequences were mixed and incubated at the melting temperature of the overlapping DNA sequences for 5 min, then cooled slowly to 0 °C. The mixture was transformed into E. coli and positive transformants were obtained. This cloning method was named DNA ‘breathing’ recombination (DBR) cloning. The overlapping sequence between the linearized vector and the FDF is preferably from 12 to 16 base pairs. Even when the ends of the linearized vector contain mismatches of up to 20 base pairs with the ends of the FDF, the DBR cloning method can still proceed efficiently, enabling truly seamless assembly. Meanwhile, the DBR method supports one-step assembly of multiple fragments. Therefore, the DBR cloning method simplifies experimental operations and reduces experimental costs while maintaining high cloning efficiency. Full article
(This article belongs to the Special Issue DNA Damage and Repair: Current Research)
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14 pages, 3279 KB  
Article
Identification and Characterization of eccDNA in HepG2 Cells Under DOX-Induced DNA Damage
by Jinyuan Zhang, Yuguo Li, Weijie Chen, Xingyi Du, Junnuo Zheng, Junji Chen, Xudong Huang, Chaoyang Pang and Zhiyun Guo
Int. J. Mol. Sci. 2025, 26(22), 10978; https://doi.org/10.3390/ijms262210978 - 13 Nov 2025
Viewed by 929
Abstract
Extrachromosomal circular DNA (eccDNA) has been recognized as a key player in tumorigenesis and progression. However, eccDNA transcriptional regulatory mechanisms under DNA damage in cancer remain poorly characterized. Here, we used doxorubicin to induce DNA damage in the hepatocellular carcinoma cell line HepG2 [...] Read more.
Extrachromosomal circular DNA (eccDNA) has been recognized as a key player in tumorigenesis and progression. However, eccDNA transcriptional regulatory mechanisms under DNA damage in cancer remain poorly characterized. Here, we used doxorubicin to induce DNA damage in the hepatocellular carcinoma cell line HepG2 and performed Circle-seq to profile eccDNAs before and after the damage. We observed a significant increase in the number, length, and chromosomal distribution density of eccDNAs following DNA damage. RNA-seq revealed that the expression of genes carried on eccDNA was positively correlated with eccDNA copy number under DNA damage. Further ATAC-seq profiling identified distinct chromatin characteristics at eccDNA breakpoint regions compared to other regions of eccDNA and linear genomic regions. Additionally, eccDNAs generated under DNA damage preferentially originated from linear genomic regions characterized by low GC content and hypomethylation. Finally, by integrating Hi-C and H3K27ac ChIP-seq, we uncovered that eccDNAs with mobile enhancer activity (ME-eccDNAs) display significantly enhanced chromatin interactions and H3K27ac enrichment after DNA damage. Overall, our findings systematically elucidate the DNA damage-driven mechanisms underlying eccDNA biogenesis, chromatin characteristics and transcriptional regulation in HCC HepG2 cells. Full article
(This article belongs to the Special Issue DNA Damage and Repair: Current Research)
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Other

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11 pages, 513 KB  
Brief Report
In Vitro Genotoxicity Screening and Lipid Oxidation in Pork and Chicken Burgers: Effect of Cooking and Gastrointestinal Digestion
by Amaya Azqueta, Iciar Astiasaran and Diana Ansorena
Int. J. Mol. Sci. 2026, 27(9), 3985; https://doi.org/10.3390/ijms27093985 - 29 Apr 2026
Viewed by 237
Abstract
The intensity of lipid oxidation after cooking and after in vitro gastrointestinal digestion of pork and chicken burgers was assessed. Pan frying with olive or sunflower oils and oven treatment were used as cooking technologies in both types of burgers. Thiobarbituric acid reactive [...] Read more.
The intensity of lipid oxidation after cooking and after in vitro gastrointestinal digestion of pork and chicken burgers was assessed. Pan frying with olive or sunflower oils and oven treatment were used as cooking technologies in both types of burgers. Thiobarbituric acid reactive substances (TBARs) were measured after cooking and in the micellar (bioaccessible) and residual (pellet) fractions after gastrointestinal in vitro digestion. Genotoxicity was assessed in the micellar fraction using the SOS/umu genotoxicity test. Lipid fraction suffered significant oxidation increases in all samples during the digestion process, especially in oven-treated samples. In general, the bioaccessible fraction showed a higher amount of oxidation products than the residual phase. None of the samples showed genotoxicity activity in the SOS/umu test. Full article
(This article belongs to the Special Issue DNA Damage and Repair: Current Research)
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