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DNA
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From Mutation and Repair to Therapeutics
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From Mutation and Repair to Therapeutics

A special issue of DNA (ISSN 2673-8856).

Deadline for manuscript submissions: closed (30 September 2022) | Viewed by 26378

Special Issue Editors

Prof. Dr. Ashis Basu

E-Mail Website
Guest Editor
Department of Chemistry, University of Connecticut, Storrs, CT 06269, USA
Interests: carcinogen-nucleic acid interactions; DNA damage; DNA repair; cross-links in DNA; mechanism of mutation and cancer; chemistry and biology of natural products with antitumor properties
Special Issues, Collections and Topics in MDPI journals
Dr. Deyu Li

E-Mail Website
Guest Editor
Biomedical & Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, USA
Interests: chemical biology of nucleic acid modification: the intersection of DNA repair, metabolism, and antiviral drug design

Special Issue Information

Dear Colleagues,

DNA research has grown from the structural aspects of non-canonical base pairing to pseudoknots and other unorthodox arrangements, from the infrequent misreplication of unaltered bases to DNA lesion-derived mutagenesis, and from biomarkers to therapeutics. This Special Issue of DNA will explore recent advances in some of these areas, with an emphasis on the DNA damage-induced alteration of cellular functions and DNA therapeutics.

In this issue, the primary focus will be on recent advances made in the following topics.

  • DNA adducts and lesions: formation, repair, translesion synthesis, and mutational signatures;
  • DNA modifications in genetics and epigenetics;
  • Nucleic acid modifications as biomarkers in chemistry, biology, and diseases;
  • DNA/RNA therapeutics.

The type of papers that will be considered for publication in this issue are research articles, communications, reviews, and perspectives.

Prof. Dr. Ashis Basu
Dr. Deyu Li
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 100 words) can be sent to the Editorial Office for announcement on this website.

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. DNA is an international peer-reviewed open access quarterly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1000 CHF (Swiss Francs). 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.

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Further information on MDPI's Special Issue polices can be found here.

Published Papers (9 papers)

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Editorial

Jump to: Research, Review

3 pages, 173 KiB  
Editorial
From Mutation and Repair to Therapeutics
by Ashis Basu and Deyu Li
DNA 2023, 3(2), 101-103; https://doi.org/10.3390/dna3020007 - 27 Apr 2023
Viewed by 1264
Abstract
As DNA research has developed, in this Special Issue of DNA, we aimed to explore recent advancements, with an emphasis on the DNA damage-induced alteration of cellular functions [...] Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)

Research

Jump to: Editorial, Review

15 pages, 1935 KiB  
Article
An Enzyme-Linked Immunosorbent Assay for the Detection of Mitochondrial DNA–Protein Cross-Links from Mammalian Cells
by Wenyan Xu and Linlin Zhao
DNA 2022, 2(4), 264-278; https://doi.org/10.3390/dna2040019 - 11 Nov 2022
Cited by 5 | Viewed by 2918
Abstract
DNA–Protein cross-links (DPCs) are cytotoxic DNA lesions with a protein covalently bound to the DNA. Although much has been learned about the formation, repair, and biological consequences of DPCs in the nucleus, little is known regarding mitochondrial DPCs. This is due in part [...] Read more.
DNA–Protein cross-links (DPCs) are cytotoxic DNA lesions with a protein covalently bound to the DNA. Although much has been learned about the formation, repair, and biological consequences of DPCs in the nucleus, little is known regarding mitochondrial DPCs. This is due in part to the lack of robust and specific methods to measure mitochondrial DPCs. Herein, we reported an enzyme-linked immunosorbent assay (ELISA)-based method for detecting mitochondrial DPCs formed between DNA and mitochondrial transcription factor A (TFAM) in cultured human cells. To optimize the purification and detection workflow, we prepared model TFAM-DPCs via Schiff base chemistry using recombinant human TFAM and a DNA substrate containing an abasic (AP) lesion. We optimized the isolation of TFAM-DPCs using commercial silica gel-based columns to achieve a high recovery yield for DPCs. We evaluated the microplate, DNA-coating solution, and HRP substrate for specific and sensitive detection of TFAM-DPCs. Additionally, we optimized the mtDNA isolation procedure to eliminate almost all nuclear DNA contaminants. For proof of concept, we detected the different levels of TFAM-DPCs in mtDNA from HEK293 cells under different biological conditions. The method is based on commercially available materials and can be amended to detect other types of DPCs in mitochondria. Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)
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10 pages, 2283 KiB  
Article
Size- and Stereochemistry-Dependent Transcriptional Bypass of DNA Alkyl Phosphotriester Adducts in Mammalian Cells
by Ying Tan, Jiabin Wu, Garrit Clabaugh, Lin Li, Hua Du and Yinsheng Wang
DNA 2022, 2(4), 221-230; https://doi.org/10.3390/dna2040016 - 5 Oct 2022
Cited by 4 | Viewed by 2235
Abstract
Environmental, endogenous and therapeutic alkylating agents can react with internucleotide phosphate groups in DNA to yield alkyl phosphotriester (PTE) adducts. Alkyl-PTEs are induced at relatively high frequencies and are persistent in mammalian tissues; however, their biological consequences in mammalian cells have not been [...] Read more.
Environmental, endogenous and therapeutic alkylating agents can react with internucleotide phosphate groups in DNA to yield alkyl phosphotriester (PTE) adducts. Alkyl-PTEs are induced at relatively high frequencies and are persistent in mammalian tissues; however, their biological consequences in mammalian cells have not been examined. Herein, we assessed how alkyl-PTEs with different alkyl group sizes and stereochemical configurations (SP and RP diastereomers of Me and nPr) affect the efficiency and fidelity of transcription in mammalian cells. We found that, while the RP diastereomer of Me- and nPr-PTEs constituted moderate and strong blockages to transcription, respectively, the SP diastereomer of the two lesions did not appreciably perturb transcription efficiency. In addition, none of the four alkyl-PTEs induced mutant transcripts. Furthermore, polymerase η assumed an important role in promoting transcription across the SP-Me-PTE, but not any of other three lesions. Loss of other translesion synthesis (TLS) polymerases tested, including Pol κ, Pol ι, Pol ξ and REV1, did not alter the transcription bypass efficiency or mutation frequency for any of the alkyl-PTE lesions. Together, our study provided important new knowledge about the impact of alkyl-PTE lesions on transcription and expanded the substrate pool of Pol η in transcriptional bypass. Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)
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Review

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20 pages, 719 KiB  
Review
Kinetic Studies on the 2-Oxoglutarate/Fe(II)-Dependent Nucleic Acid Modifying Enzymes from the AlkB and TET Families
by Zhiyuan Peng, Jian Ma, Christo Z. Christov, Tatyana Karabencheva-Christova, Nicolai Lehnert and Deyu Li
DNA 2023, 3(2), 65-84; https://doi.org/10.3390/dna3020005 - 30 Mar 2023
Cited by 4 | Viewed by 2808
Abstract
Nucleic acid methylations are important genetic and epigenetic biomarkers. The formation and removal of these markers is related to either methylation or demethylation. In this review, we focus on the demethylation or oxidative modification that is mediated by the 2-oxoglutarate (2-OG)/Fe(II)-dependent AlkB/TET family [...] Read more.
Nucleic acid methylations are important genetic and epigenetic biomarkers. The formation and removal of these markers is related to either methylation or demethylation. In this review, we focus on the demethylation or oxidative modification that is mediated by the 2-oxoglutarate (2-OG)/Fe(II)-dependent AlkB/TET family enzymes. In the catalytic process, most enzymes oxidize 2-OG to succinate, in the meantime oxidizing methyl to hydroxymethyl, leaving formaldehyde and generating demethylated base. The AlkB enzyme from Escherichia coli has nine human homologs (ALKBH1-8 and FTO) and the TET family includes three members, TET1 to 3. Among them, some enzymes have been carefully studied, but for certain enzymes, few studies have been carried out. This review focuses on the kinetic properties of those 2-OG/Fe(II)-dependent enzymes and their alkyl substrates. We also provide some discussions on the future directions of this field. Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)
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20 pages, 1279 KiB  
Review
DNA Damage and the Gut Microbiome: From Mechanisms to Disease Outcomes
by Yun-Chung Hsiao, Chih-Wei Liu, Yifei Yang, Jiahao Feng, Haoduo Zhao and Kun Lu
DNA 2023, 3(1), 13-32; https://doi.org/10.3390/dna3010002 - 1 Feb 2023
Cited by 8 | Viewed by 4585
Abstract
Both the number of cells and the collective genome of the gut microbiota outnumber their mammalian hosts, and the metabolic and physiological interactions of the gut microbiota with the host have not yet been fully characterized. Cancer remains one of the leading causes [...] Read more.
Both the number of cells and the collective genome of the gut microbiota outnumber their mammalian hosts, and the metabolic and physiological interactions of the gut microbiota with the host have not yet been fully characterized. Cancer remains one of the leading causes of death, and more research into the critical events that can lead to cancer and the importance of the gut microbiota remains to be determined. The gut microbiota can release microbial molecules that simulate host endogenous processes, such as inflammatory responses, or can alter host metabolism of ingested substances. Both of these reactions can be beneficial or deleterious to the host, and some can be genotoxic, thus contributing to cancer progression. This review focused on the molecular evidence currently available on the mechanistic understanding of how the gut microbiota are involved in human carcinogenesis. We first reviewed the key events of carcinogenesis, especially how DNA damage proceeds to tumor formulation. Then, the current knowledge on host DNA damage attributed to the gut microbiota was summarized, followed by the genotoxic endogenous processes the gut microbiota can induce. Finally, we touched base on the association between specific gut microbiota dysbiosis and different types of cancer and concluded with the up-to-date knowledge as well as future research direction for advancing our understanding of the relationship between the gut microbiota and cancer development. Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)
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23 pages, 2179 KiB  
Review
Complex Roles of NEIL1 and OGG1: Insights Gained from Murine Knockouts and Human Polymorphic Variants
by R. Stephen Lloyd
DNA 2022, 2(4), 279-301; https://doi.org/10.3390/dna2040020 - 1 Dec 2022
Cited by 8 | Viewed by 2850
Abstract
DNA glycosylases promote genomic stability by initiating base excision repair (BER) in both the nuclear and mitochondrial genomes. Several of these enzymes have overlapping substrate recognition, through which a degree of redundancy in lesion recognition is achieved. For example, OGG1 and NEIL1 both [...] Read more.
DNA glycosylases promote genomic stability by initiating base excision repair (BER) in both the nuclear and mitochondrial genomes. Several of these enzymes have overlapping substrate recognition, through which a degree of redundancy in lesion recognition is achieved. For example, OGG1 and NEIL1 both recognize and release the imidazole-ring-fragmented guanine, FapyGua as part of a common overall pathway to cleanse the genome of damaged bases. However, these glycosylases have many differences, including their differential breadth of substrate specificity, the contrasting chemistries through which base release occurs, the subsequent steps required to complete the BER pathway, and the identity of specific protein-binding partners. Beyond these differences, the complexities and differences of their in vivo biological roles have been primarily elucidated in studies of murine models harboring a knockout of Neil1 or Ogg1, with the diversity of phenotypic manifestations exceeding what might have been anticipated for a DNA glycosylase deficiency. Pathologies associated with deficiencies in nuclear DNA repair include differential cancer susceptibilities, where Ogg1-deficient mice are generally refractory to carcinogenesis, while deficiencies in Neil1-deficient mice confer cancer susceptibility. In contrast to NEIL1, OGG1 functions as a key transcription factor in regulating inflammation and other complex gene cascades. With regard to phenotypes attributed to mitochondrial repair, knockout of either of these genes results in age- and diet-induced metabolic syndrome. The adverse health consequences associated with metabolic syndrome can be largely overcome by expression of a mitochondrial-targeted human OGG1 in both wild-type and Ogg1-deficient mice. The goal of this review is to compare the roles that NEIL1 and OGG1 play in maintaining genomic integrity, with emphasis on insights gained from not only the diverse phenotypes that are manifested in knockout and transgenic mice, but also human disease susceptibility associated with polymorphic variants. Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)
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16 pages, 1357 KiB  
Review
The Domino Effect: Nucleosome Dynamics and the Regulation of Base Excision Repair Enzymes
by Julia C. Cook and Sarah Delaney
DNA 2022, 2(4), 248-263; https://doi.org/10.3390/dna2040018 - 10 Nov 2022
Cited by 2 | Viewed by 2690
Abstract
DNA damage is induced by exogenous and endogenous sources, creating a variety of lesions. However, the cellular repair machinery that addresses and corrects this damage must contend with the fact that genomic DNA is sequestered in the nucleoprotein complex of chromatin. As the [...] Read more.
DNA damage is induced by exogenous and endogenous sources, creating a variety of lesions. However, the cellular repair machinery that addresses and corrects this damage must contend with the fact that genomic DNA is sequestered in the nucleoprotein complex of chromatin. As the minimal unit of DNA compaction, the nucleosome core particle (NCP) is a major determinant of repair and poses unique barriers to DNA accessibility. This review outlines how the base excision repair (BER) pathway is modulated by the NCP and describes the structural and dynamic factors that influence the ability of BER enzymes to find and repair damage. Structural characteristics of the NCP such as nucleobase positioning and occupancy will be explored along with factors that impact the dynamic nature of NCPs to increase mobilization of nucleosomal DNA. We will discuss how altering the dynamics of NCPs initiates a domino effect that results in the regulation of BER enzymes. Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)
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Graphical abstract

17 pages, 2313 KiB  
Review
Multi-Faceted Roles of ERCC1-XPF Nuclease in Processing Non-B DNA Structures
by Tonia T. Li and Karen M. Vasquez
DNA 2022, 2(4), 231-247; https://doi.org/10.3390/dna2040017 - 11 Oct 2022
Cited by 4 | Viewed by 2846
Abstract
Genetic instability can result from increases in DNA damage and/or alterations in DNA repair proteins and can contribute to disease development. Both exogenous and endogenous sources of DNA damage and/or alterations in DNA structure (e.g., non-B DNA) can impact genome stability. Multiple repair [...] Read more.
Genetic instability can result from increases in DNA damage and/or alterations in DNA repair proteins and can contribute to disease development. Both exogenous and endogenous sources of DNA damage and/or alterations in DNA structure (e.g., non-B DNA) can impact genome stability. Multiple repair mechanisms exist to counteract DNA damage. One key DNA repair protein complex is ERCC1-XPF, a structure-specific endonuclease that participates in a variety of DNA repair processes. ERCC1-XPF is involved in nucleotide excision repair (NER), repair of DNA interstrand crosslinks (ICLs), and DNA double-strand break (DSB) repair via homologous recombination. In addition, ERCC1-XPF contributes to the processing of various alternative (i.e., non-B) DNA structures. This review will focus on the processing of alternative DNA structures by ERCC1-XPF. Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)
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16 pages, 5162 KiB  
Review
Contributing Factors for Mutagenic DNA Lesion Bypass by DNA Polymerase Eta (polη)
by Hunmin Jung
DNA 2022, 2(4), 205-220; https://doi.org/10.3390/dna2040015 - 28 Sep 2022
Cited by 5 | Viewed by 2536
Abstract
The integrity of DNA replication is under constant threat from various exogenous and endogenous factors along with some epigenetic factors. When there is damage to the genome, cells respond to the damage in two major ways, DNA damage repair and DNA damage tolerance. [...] Read more.
The integrity of DNA replication is under constant threat from various exogenous and endogenous factors along with some epigenetic factors. When there is damage to the genome, cells respond to the damage in two major ways, DNA damage repair and DNA damage tolerance. One of the major mechanisms for DNA damage tolerance is DNA lesion bypass, which is performed by specific DNA polymerases called Y-family DNA polymerases including DNA polymerase eta (polη). Ever since the discovery of polη’s unique role in bypassing cyclobutane pyrimidine dimer (CPD), a wide range of DNA lesions have been experimentally shown to be bypassed by polη. The structural study of polη was greatly boosted by the first elucidation of the N-terminal catalytic domain of polη by X-ray crystallography in 2010. Ever since, a lot of polη catalytic domain crystal structures have been published, which were complexed with an incoming nucleotide and a lesion containing DNA including pyrimidine dimers, cisplatin GpG adduct, 8-oxoguanine (oxoG), 8-oxoadenine (oxoA), N7-methylguanine (N7mG), O6-methylguanine (O6mG), hypoxanthine (HX), and many others. Though polη’s active site is known to be rigid with few conformational changes, there are several contributing factors that could facilitate the lesion bypass such as catalytic metals, syn–anti conformational equilibrium, tautomerization, and specific residues of polη. Each of these components are discussed in detail in this review. Full article
(This article belongs to the Special Issue From Mutation and Repair to Therapeutics)
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