1
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Aubuchon LN, Verma P. Endogenous base damage as a driver of genomic instability in homologous recombination-deficient cancers. DNA Repair (Amst) 2024; 141:103736. [PMID: 39096699 DOI: 10.1016/j.dnarep.2024.103736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 07/18/2024] [Accepted: 07/22/2024] [Indexed: 08/05/2024]
Abstract
Homologous recombination (HR) is a high-fidelity DNA double-strand break (DSB) repair pathway. Both familial and somatic loss of function mutation(s) in various HR genes predispose to a variety of cancer types, underscoring the importance of error-free repair of DSBs in human physiology. While environmental sources of DSBs have been known, more recent studies have begun to uncover the role of endogenous base damage in leading to these breaks. Base damage repair intermediates often consist of single-strand breaks, which if left unrepaired, can lead to DSBs as the replication fork encounters these lesions. This review summarizes various sources of endogenous base damage and how these lesions are repaired. We highlight how conversion of base repair intermediates, particularly those with 5'or 3' blocked ends, to DSBs can be a predominant source of genomic instability in HR-deficient cancers. We also discuss how endogenous base damage and ensuing DSBs can be exploited to enhance the efficacy of Poly (ADP-ribose) polymerase inhibitors (PARPi), that are widely used in the clinics for the regimen of HR-deficient cancers.
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Affiliation(s)
- Lindsey N Aubuchon
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Cancer Biology Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Priyanka Verma
- Division of Oncology, Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA; Cancer Biology Graduate Program, Washington University School of Medicine, St. Louis, MO 63110, USA.
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2
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Olave B. DNA nanotechnology in ionic liquids and deep eutectic solvents. Crit Rev Biotechnol 2024; 44:941-961. [PMID: 37518062 DOI: 10.1080/07388551.2023.2229950] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 04/28/2023] [Accepted: 06/01/2023] [Indexed: 08/01/2023]
Abstract
Nucleic acids have the ability to generate advanced nanostructures in a controlled manner and can interact with target sequences or molecules with high affinity and selectivity. For this reason, they have applications in a variety of nanotechnology applications, from highly specific sensors to smart nanomachines and even in other applications such as enantioselective catalysis or drug delivery systems. However, a common disadvantage is the use of water as the ubiquitous solvent. The use of nucleic acids in non-aqueous solvents offers the opportunity to create a completely new toolbox with unprecedented degrees of freedom. Ionic liquids (ILs) and deep eutectic solvents (DESs) are the most promising alternative solvents due to their unique electrolyte and solvent roles, as well as their ability to maintain the stability and functionality of nucleic acids. This review aims to be a comprehensive, critical, and accessible evaluation of how much this goal has been achieved and what are the most critical parameters for accomplishing a breakthrough.
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Affiliation(s)
- Beñat Olave
- University of the Basque Country (UPV/EHU), Donostia-San Sebastian, Spain
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3
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Kunkle DE, Cai Y, Eichman BF, Skaar EP. An interstrand DNA crosslink glycosylase aids Acinetobacter baumannii pathogenesis. Proc Natl Acad Sci U S A 2024; 121:e2402422121. [PMID: 38923984 PMCID: PMC11228520 DOI: 10.1073/pnas.2402422121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024] Open
Abstract
Maintenance of DNA integrity is essential to all forms of life. DNA damage generated by reaction with genotoxic chemicals results in deleterious mutations, genome instability, and cell death. Pathogenic bacteria encounter several genotoxic agents during infection. In keeping with this, the loss of DNA repair networks results in virulence attenuation in several bacterial species. Interstrand DNA crosslinks (ICLs) are a type of DNA lesion formed by covalent linkage of opposing DNA strands and are particularly toxic as they interfere with replication and transcription. Bacteria have evolved specialized DNA glycosylases that unhook ICLs, thereby initiating their repair. In this study, we describe AlkX, a DNA glycosylase encoded by the multidrug resistant pathogen Acinetobacter baumannii. AlkX exhibits ICL unhooking activity similar to that of its Escherichia coli homolog YcaQ. Interrogation of the in vivo role of AlkX revealed that its loss sensitizes cells to DNA crosslinking and impairs A. baumannii colonization of the lungs and dissemination to distal tissues during pneumonia. These results suggest that AlkX participates in A. baumannii pathogenesis and protects the bacterium from stress conditions encountered in vivo. Consistent with this, we found that acidic pH, an environment encountered during host colonization, results in A. baumannii DNA damage and that alkX is induced by, and contributes to, defense against acidic conditions. Collectively, these studies reveal functions for a recently described class of proteins encoded in a broad range of pathogenic bacterial species.
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Affiliation(s)
- Dillon E. Kunkle
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN37232
| | - Yujuan Cai
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37232
| | - Brandt F. Eichman
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37232
- Department of Biochemistry, Vanderbilt University, Nashville, TN37232
| | - Eric P. Skaar
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN37232
- Vanderbilt Institute for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN37232
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37232
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4
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Schulte J, Hotz G, Szinnai G, Christ E, Foderà G, Krüsi K, Nussberger P, Kron S, Schulz I. Exploring the potential of genetic analysis in historical blood spots for patients with iodine-deficient goiter and thyroid carcinomas in Switzerland and Germany (1929-1989). BMC Med Genomics 2024; 17:171. [PMID: 38943113 PMCID: PMC11212273 DOI: 10.1186/s12920-024-01947-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
Iodine deficiency-induced goiter continues to be a global public health concern, with varying manifestations based on geography, patient's age, and sex. To gain insights into clinical occurrences, a retrospective study analyzed medical records from patients with iodine deficiency-induced goiter or thyroid cancer who underwent surgery at the Community Hospital in Riehen, Switzerland, between 1929 and 1989. Despite today's adequate iodine supplementation, a significant risk for iodine-independent goiter remains in Switzerland, suggesting that genetic factors, among others, might be involved. Thus, a pilot study exploring the feasibility of genetic analysis of blood spots from these medical records was conducted to investigate and enhance the understanding of goiter development, potentially identify genetic variations, and explore the influence of dietary habits and other environmental stimuli on the disease.Blood prints from goiter patients' enlarged organs were collected per decade from medical records. These prints had been made by pressing, drawing, or tracing (i.e., pressed and drawn) the removed organs onto paper sheets. DNA analysis revealed that its yields varied more between the prints than between years. A considerable proportion of the samples exhibited substantial DNA degradation unrelated to sample collection time and DNA mixtures of different contributors. Thus, each goiter imprint must be individually evaluated and cannot be used to predict the success rate of genetic analysis in general. Collecting a large sample or the entire blood ablation for genetic analysis is recommended to mitigate potential insufficient DNA quantities. Researchers should also consider degradation and external biological compounds' impact on the genetic analysis of interest, with the dominant contributor anticipated to originate from the patient's blood.
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Affiliation(s)
- Janine Schulte
- Health Department Basel-Stadt, Institute of Forensic Medicine, University Basel, Pestalozzistrasse 22, Basel, 4056, Switzerland
| | - Gerhard Hotz
- Natural History Museum Basel, Augustinergasse 2, Basel, 4001, Switzerland
| | - Gabor Szinnai
- Pediatric Endocrinology/Diabetology, University Children's Hospital Basel UKBB, University of Basel, Basel, 4056, Switzerland
| | - Emanuel Christ
- Division of Endocrinology, Diabetology, Metabolism and Center of Endocrine and Neuroendocrine Tumors, University Hospital Basel, Basel, 4056, Switzerland
| | - Gaspare Foderà
- Documentation Center, Municipal Administration, Riehen, 4125, Switzerland
| | - Karl Krüsi
- Documentation Center, Municipal Administration, Riehen, 4125, Switzerland
| | | | - Sarah Kron
- Health Department Basel-Stadt, Institute of Forensic Medicine, University Basel, Pestalozzistrasse 22, Basel, 4056, Switzerland
| | - Iris Schulz
- Health Department Basel-Stadt, Institute of Forensic Medicine, University Basel, Pestalozzistrasse 22, Basel, 4056, Switzerland.
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5
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Islam T, Shim G, Melton D, Lewis CD, Lei Z, Gates KS. Ultrafast Reaction of the Drug Hydralazine with Apurinic/Apyrimidinic Sites in DNA Gives Rise to a Stable Triazolo[3,4- a]phthalazine Adduct. Chem Res Toxicol 2024; 37:1023-1034. [PMID: 38743824 DOI: 10.1021/acs.chemrestox.4c00098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The clinically used antihypertensive agent hydralazine rapidly generates hydrazone-derived adducts by reaction with apurinic/apyrimidinic (also known as abasic or AP) sites in many different sequences of duplex DNA. The reaction rates are comparable to those of some AP-trapping reagents previously described as "ultrafast." Initially, reversible formation of a hydrazone adduct is followed by an oxidative cyclization reaction that generates a chemically stable triazolo[3,4-a]phthalazine adduct. The net result is that the reaction of hydralazine with AP sites in duplex DNA yields a rapid and irreversible adduct formation. Although the hydrazone and triazolo[3,4-a]phthalazine adducts differ by only two mass units, it was possible to use MALDI-TOF-MS and ESI-QTOF-nanospray-MS to quantitatively characterize mixtures of these adducts by deconvolution of overlapping isotope envelopes. Reactions of hydralazine with the endogenous ketone pyruvate do not prevent the formation of the hydralazine-AP adducts, providing further evidence that these adducts have the potential to form in cellular DNA. AP sites are ubiquitous in cellular DNA, and rapid, irreversible adduct formation by hydralazine could be relevant to the pathogenesis of systemic drug-induced lupus erythematosus experienced by some patients. Finally, hydralazine might be developed as a probe for the detection of AP sites, the study of cellular BER, and marking the location of AP sites in DNA-sequencing analyses.
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Affiliation(s)
- Tanhaul Islam
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Garam Shim
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Douglas Melton
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Calvin D Lewis
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Zhentian Lei
- University of Missouri, MU Metabolomics Center, 240f Christopher S. Bond Life Science Center, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
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6
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Möller C, Virzi J, Chang YJ, Keidel A, Chao MR, Hu CW, Cooke MS. DNA modifications: Biomarkers for the exposome? ENVIRONMENTAL TOXICOLOGY AND PHARMACOLOGY 2024; 108:104449. [PMID: 38636743 DOI: 10.1016/j.etap.2024.104449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/25/2024] [Accepted: 04/12/2024] [Indexed: 04/20/2024]
Abstract
The concept of the exposome is the encompassing of all the environmental exposures, both exogenous and endogenous, across the life course. Many, if not all, of these exposures can result in the generation of reactive species, and/or the modulation of cellular processes, that can lead to a breadth of modifications of DNA, the nature of which may be used to infer their origin. Because of their role in cell function, such modifications have been associated with various major human diseases, including cancer, and so their assessment is crucial. Historically, most methods have been able to only measure one or a few DNA modifications at a time, limiting the information available. With the development of DNA adductomics, which aims to determine the totality of DNA modifications, a far more comprehensive picture of the DNA adduct burden can be gained. Importantly, DNA adductomics can facilitate a "top-down" investigative approach whereby patterns of adducts may be used to trace and identify the originating exposure source. This, together with other 'omic approaches, represents a major tool for unraveling the complexities of the exposome and hence allow a better a understanding of the environmental origins of disease.
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Affiliation(s)
- Carolina Möller
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA.
| | - Jazmine Virzi
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Yuan-Jhe Chang
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Alexandra Keidel
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA
| | - Mu-Rong Chao
- Department of Occupational Safety and Health, Chung Shan Medical University, Taichung 402, Taiwan; Department of Occupational Medicine, Chung Shan Medical University Hospital, Taichung 402, Taiwan
| | - Chiung-Wen Hu
- Department of Public Health, Chung Shan Medical University, Taichung 402, Taiwan
| | - Marcus S Cooke
- Oxidative Stress Group, Department of Molecular Biosciences, University of South Florida, Tampa, FL 33620, USA; College of Public Health, University of South Florida, Tampa, FL 33620, USA; Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL 33612, USA.
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7
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Tower J. Selectively advantageous instability in biotic and pre-biotic systems and implications for evolution and aging. FRONTIERS IN AGING 2024; 5:1376060. [PMID: 38818026 PMCID: PMC11137231 DOI: 10.3389/fragi.2024.1376060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/15/2024] [Indexed: 06/01/2024]
Abstract
Rules of biology typically involve conservation of resources. For example, common patterns such as hexagons and logarithmic spirals require minimal materials, and scaling laws involve conservation of energy. Here a relationship with the opposite theme is discussed, which is the selectively advantageous instability (SAI) of one or more components of a replicating system, such as the cell. By increasing the complexity of the system, SAI can have benefits in addition to the generation of energy or the mobilization of building blocks. SAI involves a potential cost to the replicating system for the materials and/or energy required to create the unstable component, and in some cases, the energy required for its active degradation. SAI is well-studied in cells. Short-lived transcription and signaling factors enable a rapid response to a changing environment, and turnover is critical for replacement of damaged macromolecules. The minimal gene set for a viable cell includes proteases and a nuclease, suggesting SAI is essential for life. SAI promotes genetic diversity in several ways. Toxin/antitoxin systems promote maintenance of genes, and SAI of mitochondria facilitates uniparental transmission. By creating two distinct states, subject to different selective pressures, SAI can maintain genetic diversity. SAI of components of synthetic replicators favors replicator cycling, promoting emergence of replicators with increased complexity. Both classical and recent computer modeling of replicators reveals SAI. SAI may be involved at additional levels of biological organization. In summary, SAI promotes replicator genetic diversity and reproductive fitness, and may promote aging through loss of resources and maintenance of deleterious alleles.
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Affiliation(s)
- John Tower
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, United States
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8
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Bagale SS, Deshmukh PU, Lad SB, Sudarsan A, Sudhakar S, Mandal S, Kondabagil K, Pradeepkumar PI. Synthesis of N2- trans-isosafrole-dG-adduct Bearing DNAs and the Bypass Studies with Human TLS Polymerases κ and η. J Org Chem 2024. [PMID: 38739842 DOI: 10.1021/acs.joc.4c00368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Safrole is a natural product present in many plants and plant products, including spices and essential oils. During cellular metabolism, it converts to a highly reactive trans-isosafrole (SF) intermediate that reacts with genomic DNA and forms N2-SF-dG and N6-SF-dA DNA adducts, which are detected in the oral tissue of cancer patients with betel quid chewing history. To study the SF-induced carcinogenesis and to probe the role of low fidelity translesion synthesis (TLS) polymerases in bypassing SF adducts, herein, we report the synthesis of N2-SF-dG modified DNAs using phosphoramidite chemistry. The N2-SF-dG modification in the duplex DNA does not affect the thermal stability and retains the B-form of helical conformation, indicating that this adduct may escape the radar of common DNA repair mechanisms. Primer extension studies showed that the N2-SF-dG adduct is bypassed by human TLS polymerases hpolκ and hpolη, which perform error-free replication across this adduct. Furthermore, molecular modeling and dynamics studies revealed that the adduct reorients to pair with the incoming nucleotide, thus allowing the effective bypass. Overall, the results indicate that hpolκ and hpolη do not distinguish the N2-SF-dG adduct, suggesting that they may not be involved in the safrole-induced carcinogenicity.
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Affiliation(s)
| | - Priyanka U Deshmukh
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Shailesh B Lad
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Akhil Sudarsan
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Sruthi Sudhakar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Soumyadeep Mandal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Kiran Kondabagil
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - P I Pradeepkumar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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9
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Fleming AM, Guerra Castañaza Jenkins BL, Buck BA, Burrows CJ. DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context. J Am Chem Soc 2024; 146. [PMID: 38602473 PMCID: PMC11046481 DOI: 10.1021/jacs.4c00960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/27/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
Molecular details for the impact of DNA damage on folding of potential G-quadruplex sequences (PQSs) to noncanonical DNA structures involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, termed a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest the formation of G4 motifs and demonstrated a folding dependency on the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.
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Affiliation(s)
- Aaron M. Fleming
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
| | | | - Bethany A. Buck
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
| | - Cynthia J. Burrows
- Department of Chemistry, University
of Utah, 315 South 1400 East, Salt
Lake City, Utah 84112-0850, United States
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10
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Worrapitirungsi W, Sathirapatya T, Sukawutthiya P, Vongpaisarnsin K, Varrathyarom P. Assessing the feasibility of free DNA for disaster victim identification and forensic applications. Sci Rep 2024; 14:5411. [PMID: 38443390 PMCID: PMC10914783 DOI: 10.1038/s41598-024-53040-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 01/27/2024] [Indexed: 03/07/2024] Open
Abstract
In tropical disaster victim identification (DVI) scenarios, challenging environmental conditions lead to accelerated DNA degradation in remains. To further enhance the utilization of leached DNA from tissue in the preservative solution (termed "free DNA") as an alternative source, we incorporated new results by assessing its integrity in postmortem and decomposing cadavers preserved in DNA/RNA Shield™ and modified TENT, with silica-based purification (QIAquick®) for faster processing. The psoas muscle tissues of one decomposed and ten cadavers were preserved in each solution at 25 °C and 35 °C for 3 months. Free DNA efficiency was compared with individual reference samples for reliable results in quantity, quality, and STR profiles. The findings revealed that DNA/RNA Shield™ effectively preserves free DNA integrity for extended storage, while modified TENT is more suitable for short-term storage due to higher degradation levels. Moreover, the use of free DNA samples with massive parallel sequencing displays potential for forensic DNA analysis. Successful amplification of the mtDNA control region enables variant calling and heteroplasmy analysis while also serving as quality control using ACTB and enabling differentiation within the 16S rRNA region for microbiome analysis. The simplicity of handling free DNA for PCR-based forensic analysis adds to its potential for various applications, including DVI and field-based analysis of biological evidence.
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Affiliation(s)
- Wikanda Worrapitirungsi
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tikumphorn Sathirapatya
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
| | - Pagparpat Varrathyarom
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
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11
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Bivehed E, Hellman B, Wenson L, Stenerlöw B, Söderberg O, Heldin J. Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling. Nucleic Acids Res 2024; 52:e22. [PMID: 38261985 PMCID: PMC10899772 DOI: 10.1093/nar/gkae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
In the comet assay, tails are formed after single-cell gel electrophoresis if the cells have been exposed to genotoxic agents. These tails include a mixture of both DNA single-strand breaks (SSBs) and double-strand breaks (DSBs). However, these two types of strand breaks cannot be distinguished using comet assay protocols with conventional DNA stains. Since DSBs are more problematic for the cells, it would be useful if the SSBs and DSBs could be differentially identified in the same comet. In order to be able to distinguish between SSBs and DSBs, we designed a protocol for polymerase-assisted DNA damage analysis (PADDA) to be used in combination with the Flash comet protocol, or on fixed cells. By using DNA polymerase I to label SSBs and terminal deoxynucleotidyl transferase to label DSBs with fluorophore-labelled nucleotides. Herein, TK6-cells or HaCat cells were exposed to either hydrogen peroxide (H2O2), ionising radiation (X-rays) or DNA cutting enzymes, and then subjected to a comet protocol followed by PADDA. PADDA offers a wider detection range, unveiling previously undetected DNA strand breaks.
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Affiliation(s)
- Erik Bivehed
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Uppsala SE-751 24, Sweden
| | - Björn Hellman
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Uppsala SE-751 24, Sweden
| | - Leonie Wenson
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Uppsala SE-751 24, Sweden
| | - Bo Stenerlöw
- Department of Immunology, Genetics and Pathology, Uppsala University, Rudbeck Laboratory, Uppsala SE-751 85, Sweden
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Uppsala SE-751 24, Sweden
| | - Johan Heldin
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical Centre, Uppsala SE-751 24, Sweden
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12
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Price NE, Gates KS. Novel Processes Associated with the Repair of Interstrand Cross-Links Derived from Abasic Sites in Duplex DNA: Roles for the Base Excision Repair Glycosylase NEIL3 and the SRAP Protein HMCES. Chem Res Toxicol 2024; 37:199-207. [PMID: 38198604 DOI: 10.1021/acs.chemrestox.3c00345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
Recent studies have defined a novel pathway for the repair of interstrand cross-links derived from the reaction of an adenine residue with an apurinic/apyrimidinic (AP) site on the opposing strand of DNA (dA-AP ICL). Stalling of a replication fork at the dA-AP ICL triggers TRAIP-dependent ubiquitylation of the CMG helicase that recruits the base excision repair glycosylase NEIL3 to the lesion. NEIL3 unhooks the dA-AP ICL to regenerate the native adenine residue on one strand and an AP site on the other strand. Covalent capture of the abasic site by the SRAP protein HMCES protects against genomic instability that would result from cleavage of the abasic site in the context of single-stranded DNA at the replication fork. After repair synthesis moves the HMCES-AP adduct into the context of double-stranded DNA, the DNA-protein cross-link is resolved by a nonproteolytic mechanism involving dissociation of thiazolidine attachment. The AP site in duplex DNA is then repaired by the base excision repair pathway.
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Affiliation(s)
- Nathan E Price
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
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13
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Gomina A, Islam T, Shim G, Lei Z, Gates KS. Formation and Properties of DNA Adducts Generated by Reactions of Abasic Sites with 1,2-Aminothiols Including Cysteamine, Cysteine Methyl Ester, and Peptides Containing N-Terminal Cysteine Residues. Chem Res Toxicol 2024; 37:395-406. [PMID: 38181204 DOI: 10.1021/acs.chemrestox.3c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2024]
Abstract
The reaction of 1,2-aminothiol groups with aldehyde residues in aqueous solution generates thiazolidine products, and this process has been developed as a catalyst-free click reaction for bioconjugation. The work reported here characterized reactions of the biologically relevant 1,2-aminothiols including cysteamine, cysteine methyl ester, and peptides containing N-terminal cysteine residues with the aldehyde residue of apurinic/apyrimidinic (AP) sites in DNA oligomers. These 1,2-aminothiol-containing compounds rapidly generated adducts with AP sites in single-stranded and double-stranded DNA. NMR and MALDI-TOF-MS analyses provided evidence that the reaction generated a thiazolidine product. Conversion of an AP site to a thiazolidine-AP adduct protected against the rapid cleavage normally induced at AP sites by the endonuclease action of the enzyme APE1 and the AP-lyase activity of the biogenic amine spermine. In the presence of excess 1,2-aminothiols, the thiazolidine-AP adducts underwent slow strand cleavage via a β-lyase reaction that generated products with 1,2-aminothiol-modified sugar residues on the 3'-end of the strand break. In the absence of excess 1,2-aminothiols, the thiazolidine-AP adducts dissociated to release the parent AP-containing oligonucleotide. The properties of the thiazolidine-AP adducts described here mirror critical properties of SRAP proteins HMCES and YedK that capture AP sites in single-stranded regions of cellular DNA and protect them from cleavage.
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Affiliation(s)
- Anuoluwapo Gomina
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Tanhaul Islam
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Garam Shim
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
| | - Zhentian Lei
- MU Metabolomics Center, University of Missouri, 240F Christopher S. Bond Life Science Center, Columbia, Missouri 65211, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, 125 Chemistry Building, Columbia, Missouri 65211, United States
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14
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Kaur R, Wetmore SD. Is Metal Stabilization of the Leaving Group Required or Can Lysine Facilitate Phosphodiester Bond Cleavage in Nucleic Acids? A Computational Study of EndoV. J Chem Inf Model 2024; 64:944-959. [PMID: 38253321 DOI: 10.1021/acs.jcim.3c01775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Endonuclease V (EndoV) is a single-metal-dependent enzyme that repairs deaminated DNA nucleobases in cells by cleaving the phosphodiester bond, and this enzyme has proven to be a powerful tool in biotechnology and medicine. The catalytic mechanism used by EndoV must be understood to design new disease detection and therapeutic solutions and further exploit the enzyme in interdisciplinary applications. This study has used a mixed molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) approach to compare eight distinct catalytic pathways and provides the first proposed mechanism for bacterial EndoV. The calculations demonstrate that mechanisms involving either direct or indirect metal coordination to the leaving group of the substrate previously proposed for other nucleases are unlikely for EndoV, regardless of the general base (histidine, aspartate, and substrate phosphate moiety). Instead, distinct catalytic pathways are characterized for EndoV that involve K139 stabilizing the leaving group, a metal-coordinated water stabilizing the transition structure, and either H214 or a substrate phosphate group activating the water nucleophile. In silico K139A and H214A mutational results support the newly proposed roles of these residues. Although this is a previously unseen combination of general base, general acid, and metal-binding architecture for a one-metal-dependent endonuclease, our proposed catalytic mechanisms are fully consistent with experimental kinetic, structural, and mutational data. In addition to substantiating a growing body of literature, suggesting that one metal is enough to catalyze P-O bond cleavage in nucleic acids, this new fundamental understanding of the catalytic function will promote the exploration of new and improved applications of EndoV.
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Affiliation(s)
- Rajwinder Kaur
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
| | - Stacey D Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive West, Lethbridge, Alberta T1K 3M4, Canada
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15
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Fleming AM, Jenkins BLGC, Buck BA, Burrows CJ. DNA Damage Accelerates G-Quadruplex Folding in a Duplex-G-Quadruplex-Duplex Context. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576387. [PMID: 38293204 PMCID: PMC10827223 DOI: 10.1101/2024.01.20.576387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Molecular details for DNA damage impact on the folding of potential G-quadruplex sequences (PQS) to non-canonical DNA structures that are involved in gene regulation are poorly understood. Here, the effects of DNA base damage and strand breaks on PQS folding kinetics were studied in the context of the VEGF promoter sequence embedded between two DNA duplex anchors, referred to as a duplex-G-quadruplex-duplex (DGD) motif. This DGD scaffold imposes constraints on the PQS folding process that more closely mimic those found in genomic DNA. Folding kinetics were monitored by circular dichroism (CD) to find folding half-lives ranging from 2 s to 12 min depending on the DNA damage type and sequence position. The presence of Mg2+ ions and the G-quadruplex (G4)-binding protein APE1 facilitated the folding reactions. A strand break placing all four G runs required for G4 formation on one side of the break accelerated the folding rate by >150-fold compared to the undamaged sequence. Combined 1D 1H-NMR and CD analyses confirmed that isothermal folding of the VEGF-DGD constructs yielded spectral signatures that suggest formation of G4 motifs, and demonstrated a folding dependency with the nature and location of DNA damage. Importantly, the PQS folding half-lives measured are relevant to replication, transcription, and DNA repair time frames.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
| | | | - Bethany A Buck
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, UT 84112-0850 United States
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16
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Osawa T, Obika S. Synthesis of Coumarin-Conjugated Oligonucleotides via Knoevenagel Condensation to Prepare an Oligonucleotide Library. Chem Pharm Bull (Tokyo) 2024; 72:143-148. [PMID: 38296555 DOI: 10.1248/cpb.c23-00295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
Abstract
DNA-encoded libraries (DELs) are attracting attention as a screening tool in the early stages of drug discovery. In the development of DELs, drug candidate compounds are chemically synthesized on barcode DNA. Therefore, it is important to perform the synthesis under mild conditions so as to not damage the DNA. On the other hand, coumarins are gaining increasing research focus not only because they possess excellent fluorescence properties, but also because many medicines contain a coumarin skeleton. Among the various reactions developed for the synthesis of coumarins thus far, Knoevenagel condensation followed by intramolecular cyclization under mild conditions can yield coumarins. In this study, we developed a new synthetic method for preparing a coumarin-conjugated oligonucleotide library via Knoevenagel condensation. The results showed that coumarins substituted at the 5-, 6-, 7-, or 8-positions could be constructed on DNA to afford a total of 26 coumarin-conjugated DNAs. Moreover, this method was compatible with enzymatic ligation, demonstrating its utility in DEL synthesis. The developed strategy for the construction of coumarin scaffolds based on Knoevenagel condensation may contribute to the use of DELs in drug discovery and medicinal chemistry.
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Affiliation(s)
- Takashi Osawa
- Graduate School of Pharmaceutical Sciences, Osaka University
| | - Satoshi Obika
- Graduate School of Pharmaceutical Sciences, Osaka University
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University
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17
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Minko IG, Moellmer SA, Luzadder MM, Tomar R, Stone MP, McCullough AK, Lloyd RS. Interaction of mitoxantrone with abasic sites - DNA strand cleavage and inhibition of apurinic/apyrimidinic endonuclease 1, APE1. DNA Repair (Amst) 2024; 133:103606. [PMID: 38039951 PMCID: PMC11257150 DOI: 10.1016/j.dnarep.2023.103606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/04/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023]
Abstract
Mitoxantrone (1,4-dihydroxy-5,8-bis[2-(2-hydroxyethylamino)ethylamino]-anthracene-9,10-dione) is a clinically-relevant synthetic anthracenedione that functions as a topoisomerase II poison by trapping DNA double-strand break intermediates. Mitoxantrone binds to DNA via both stacking interactions with DNA bases and hydrogen bonding with the sugar-phosphate backbone. It has been shown that mitoxantrone inhibits apurinic/apyrimidinic (AP) endonuclease 1 (APE1)-catalyzed incision of DNA containing a tetrahydrofuran (THF) moiety and more recently, that mitoxantrone forms Schiff base conjugates at AP sites in DNA. In this study, mitoxantrone-mediated inhibition of APE1 at THF sites was shown to be consistent with preferential binding to, and thermal stabilization of DNA containing a THF site as compared to non-damaged DNA. Investigations into the properties of mitoxantrone at AP and 3' α,β-unsaturated aldehyde sites demonstrated that in addition to being a potent inhibitor of APE1 at these biologically-relevant substrates (∼ 0.5 μM IC50 on AP site-containing DNA), mitoxantrone also incised AP site-containing DNA by catalyzing β- and β/δ-elimination reactions. The efficiency of these reactions to generate the 3' α,β-unsaturated aldehyde and 3' phosphate products was modulated by DNA structure. Although these cell-free reactions revealed that mitoxantrone can generate 3' phosphates, cells lacking polynucleotide kinase phosphatase did not show increased sensitivity to mitoxantrone treatment. Consistent with its ability to inhibit APE1 activity on DNAs containing either an AP site or a 3' α,β-unsaturated aldehyde, combined exposures to clinically-relevant concentrations of mitoxantrone and a small molecule APE1 inhibitor revealed additive cytotoxicity. These data suggest that in a cellular context, mitoxantrone may interfere with APE1 DNA repair functions.
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Affiliation(s)
- Irina G Minko
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Samantha A Moellmer
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Michael M Luzadder
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA
| | - Rachana Tomar
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Station B Box 351822, Nashville, TN 37235, USA
| | - Michael P Stone
- Department of Chemistry and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Station B Box 351822, Nashville, TN 37235, USA
| | - Amanda K McCullough
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA
| | - R Stephen Lloyd
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, OR 97239, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR 97239, USA.
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18
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Ma H, Sun Z, Xue L, Zhao X, Zhang J, Zhang H, Yang K, Hu YJ. Simple and Practical DNA Quantification Method for DNA-Encoded Library Synthesis. ACS OMEGA 2023; 8:48050-48055. [PMID: 38144051 PMCID: PMC10733999 DOI: 10.1021/acsomega.3c06768] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 12/26/2023]
Abstract
Over the past three decades, DNA-encoded library (DEL) technologies have become one of the most relevant strategies for hit-finding. Recent advances in synthetic methodologies for DNA-encoded libraries rendered the increased chemical space available, but it is unknown how every variety of chemistry affects DNA's integrity. Available assays to quantify DNA damage are restricted to electrophoresis, ligation efficiency, and mostly qPCR quantification and sequencing, which may contain predisposition and inconsistency. We developed an external standard method through LC-MS analysis to accurately quantify DNA damage throughout the chemical transformations. An assessment was conducted on on-DNA chemical reactions that are frequently employed in DEL synthesis, and these results were compared to traditional qPCR measurements. Our study provides a simple, practicable, and accurate measurement for DNA degradation during DEL synthesis. Our finding reveals substantial disagreement among the usual DNA-damaging assessment methods, which have been largely neglected so far.
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Affiliation(s)
- Hangke Ma
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, China
| | - Zhaomei Sun
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, China
| | - Lijun Xue
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, China
| | - Xue Zhao
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, China
| | - Jie Zhang
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, China
| | - Huanqing Zhang
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, China
| | - Kexin Yang
- Pharmaron
Beijing Co., Ltd., 6 Taihe Road, BDA, Beijing 100176, P. R. China
| | - Yun Jin Hu
- Pharmaron
(Ningbo) Technology Development Co., Ltd., No. 800 Bin-Hai Fourth Road, Hangzhou Bay New Zone, Ningbo 315336, China
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19
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Simon SA, Schmidt K, Griesdorn L, Soares AR, Bornemann TLV, Probst AJ. Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction. BMC Genomics 2023; 24:727. [PMID: 38041056 PMCID: PMC10693096 DOI: 10.1186/s12864-023-09853-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 11/28/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs. RESULTS We generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies. CONCLUSION Our results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.
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Affiliation(s)
- Sophie A Simon
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany.
| | - Katharina Schmidt
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
| | - Lea Griesdorn
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
| | - André R Soares
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Till L V Bornemann
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany
| | - Alexander J Probst
- Environmental Metagenomics, Faculty of Chemistry, Research Center One Health Ruhr of the University Alliance Ruhr, University of Duisburg-Essen, Essen, Germany.
- Centre of Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
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20
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Gusti Ngurah Putu EP, Cattiaux L, Lavergne T, Pommier Y, Bombard S, Granzhan A. Unprecedented reactivity of polyamines with aldehydic DNA modifications: structural determinants of reactivity, characterization and enzymatic stability of adducts. Nucleic Acids Res 2023; 51:10846-10866. [PMID: 37850658 PMCID: PMC10639052 DOI: 10.1093/nar/gkad837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/19/2023] Open
Abstract
Apurinic/apyrimidinic (AP) sites, 5-formyluracil (fU) and 5-formylcytosine (fC) are abundant DNA modifications that share aldehyde-type reactivity. Here, we demonstrate that polyamines featuring at least one secondary 1,2-diamine fragment in combination with aromatic units form covalent DNA adducts upon reaction with AP sites (with concomitant cleavage of the AP strand), fU and, to a lesser extent, fC residues. Using small-molecule mimics of AP site and fU, we show that reaction of secondary 1,2-diamines with AP sites leads to the formation of unprecedented 3'-tetrahydrofuro[2,3,4-ef]-1,4-diazepane ('ribodiazepane') scaffold, whereas the reaction with fU produces cationic 2,3-dihydro-1,4-diazepinium adducts via uracil ring opening. The reactivity of polyamines towards AP sites versus fU and fC can be tuned by modulating their chemical structure and pH of the reaction medium, enabling up to 20-fold chemoselectivity for AP sites with respect to fU and fC. This reaction is efficient in near-physiological conditions at low-micromolar concentration of polyamines and tolerant to the presence of a large excess of unmodified DNA. Remarkably, 3'-ribodiazepane adducts are chemically stable and resistant to the action of apurinic/apyrimidinic endonuclease 1 (APE1) and tyrosyl-DNA phosphoesterase 1 (TDP1), two DNA repair enzymes known to cleanse a variety of 3' end-blocking DNA lesions.
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Affiliation(s)
- Eka Putra Gusti Ngurah Putu
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| | - Laurent Cattiaux
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| | - Thomas Lavergne
- DCM, CNRS UMR5250, Université Grenoble Alpes, 38000 Grenoble, France
| | - Yves Pommier
- Laboratory of Molecular Pharmacology & Developmental Therapeutics Branch, CCR-NCI, NIH, Bethesda, MD 20892, USA
| | - Sophie Bombard
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
| | - Anton Granzhan
- CMBC, CNRS UMR9187, INSERM U1196, Institut Curie, PSL Research University, 91405 Orsay, France
- CMBC, CNRS UMR9187, INSERM U1196, Université Paris Saclay, 91405 Orsay, France
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21
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Wang H, Zhao G, Zhang T, Li Y, Zhang G, Li Y. Comparative Study of DNA Barcode Integrity Evaluation Approaches in the Early-Stage Development of DNA-Compatible Chemical Transformation. ACS Pharmacol Transl Sci 2023; 6:1724-1733. [PMID: 37974618 PMCID: PMC10644510 DOI: 10.1021/acsptsci.3c00181] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Indexed: 11/19/2023]
Abstract
DNA-encoded libraries (DEL) have emerged as an important drug discovery technical platform for target-based compound library selection. The success rate of DEL depends on both the chemical diversity of combinatorial libraries and the accuracy of DNA barcoding. Therefore, it is critical that the chemistry applied to library construction should efficiently transform on a wide range of substrates while preserving the integrity of DNA tags. Although several analytical methods have been developed to measure DNA damage caused by DEL chemical reactions, efficient and cost-effective evaluation criteria for DNA damage detection are still demanding. Herein, we set standards for evaluating the DNA compatibility of chemistry development at the laboratory level. Based on four typical DNA damage models of three different DEL formats, we evaluated the detection capabilities of four analytical methods, including ultraperformance liquid chromatography (UPLC-MS), electrophoresis, quantitative polymerase chain reaction (qPCR), and Sanger sequencing. This work systematically revealed the scope and capability of different analytical methods in assessing DNA damages caused by chemical transformation. Based on the results, we recommended UPLC-MS and qPCR as efficient methods for DNA barcode integrity analysis in the early-stage development of DNA-compatible chemistry. Meanwhile, we identified that Sanger sequencing was unreliable to assess DNA damage in this application.
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Affiliation(s)
- Huicong Wang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Guixian Zhao
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Tianyang Zhang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yangfeng Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Gong Zhang
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
| | - Yizhou Li
- Chongqing
Key Laboratory of Natural Product Synthesis and Drug Research, School
of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Chemical
Biology Research Center, School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, P. R. China
- Beijing
National Laboratory for Molecular Sciences, Beijing 100190, P. R. China
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22
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Nian L, Xiaohua L, Rongcheng L, Song-Bai L. Types of DNA damage and research progress. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023:1-21. [PMID: 37948546 DOI: 10.1080/15257770.2023.2277194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023]
Abstract
DNA damage is a modification in the structure of DNA under the influence of endogenous or exogenous factors. DNA damage can cause different types of diseases and is closely related to genetic mutations, cancer, and aging. The cause of the corresponding reaction process is essential for the study of related cancers and other genetically related diseases. Therefore, it is essential to gain a deeper understanding of the various types of DNA damage. This paper provides a comprehensive review of recent advances in the types of DNA damage and associated reaction processes, including damage to DNA bases, nucleotides, and strands, as well as the biological implications of the damage.
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Affiliation(s)
- Liu Nian
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Li Xiaohua
- Thyroid and breast surgery, Wuzhong People's Hospital of Suzhou City, Suzhou, China
| | - Li Rongcheng
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
| | - Liu Song-Bai
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, Suzhou, China
- Suzhou Key Laboratory of Medical Biotechnology, Suzhou Vocational Health College, Suzhou, China
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23
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Zhang Q, Ali T, Lin Z, Peng X. Development of 4,4'-dibromobinaphthalene analogues with potent photo-inducible DNA cross-linking capability and cytotoxicity towards breast MDA-MB 468 cancer cells. Bioorg Chem 2023; 140:106769. [PMID: 37633128 DOI: 10.1016/j.bioorg.2023.106769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 07/25/2023] [Accepted: 08/06/2023] [Indexed: 08/28/2023]
Abstract
Photoinduced DNA cross-linking process showed advantages of high spatio-temporal resolution and control. We have designed, synthesized, and characterized several 4,4'-dibromo binaphthalene analogues (1a-f) that can be activated by 350 nm irradiation to induce various DNA damage, including DNA interstrand cross-links (ICL) formation, strand cleavages, and alkaline labile DNA lesions. The degree and types of DNA damage induced by these compounds depend on the leaving groups of the substrates, pH value of the buffer solution, and DNA sequences. The DNA ICL products were produced from the carbocations formed via the oxidation of free radicals photo-generated from 1a-f. Most of these compounds alone exhibited minimum cytotoxicity towards cancer cells while 350 nm irradiation greatly improved their anticancer effects (up to 40-fold enhancement) because of photo-induced cellular DNA damage. This work provides guidance for further design of photo-inducible DNA cross-linking agents as potent photo-activated anticancer prodrugs with good control over toxicity and selectivity.
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Affiliation(s)
- Qi Zhang
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States
| | - Taufeeque Ali
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States
| | - Zechao Lin
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States
| | - Xiaohua Peng
- Department of Chemistry and Biochemistry and the Milwaukee Institute for Drug Discovery, University of Wisconsin-Milwaukee, 3210 N. Cramer Street, Milwaukee, WI 53211, United States.
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24
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Bivehed E, Hellman B, Fan Y, Haglöf J, Buratovic S. DNA integrity under alkaline conditions: An investigation of factors affecting the comet assay. MUTATION RESEARCH. GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2023; 891:503680. [PMID: 37770137 DOI: 10.1016/j.mrgentox.2023.503680] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 10/03/2023]
Abstract
The effect of pH on DNA integrity was assessed using a three-step approach. The comet assay was used on a whole genome level, with three different protocols: neutral (no alkaline unwinding), flash (pH 12.5 with 2.5 min unwinding), and the conventional alkaline protocol (pH>13 with 40 min unwinding). Real-time quantitative PCR (RT-qPCR) was then used to study the isolated DNA, revealing that gene amplification decreased with increasing pH, indicating DNA degradation. Specially designed molecular beacons were used to examine DNA at the molecular level, with or without alkali-labile site (ALS) insertions. At pH 12.5, fluorescence in the hairpins with ALS started to increase after 30 min, while at pH> 13, this increase was already observed after 5 min, indicating a significant increase in DNA strand breaks. Liquid chromatography analysis was also used, demonstrating that the hairpins remained intact up to pH 10, even after 1 h exposure, whereas, at pH 12.5, partial conversion into strand breaks occurred after 30 min. At pH> 13, the hairpins were almost completely degraded after 30 min. The flash protocol effectively detects DNA single- and double-strand breaks and identified these damages after 2.5 min of alkaline treatment at pH 12.5. When the hairpins were exposed to pH 12.5 for 60 min, ALS were converted to strand breaks, demonstrating the sensitivity of this approach to detect changes in DNA structure. These findings indicate that pH poses a substantial risk to DNA integrity, leading to significantly higher background levels of DNA damage compared to conditions closer to neutrality. Our study demonstrates the importance of understanding the influence of pH on DNA stability and provides insights into risks associated with alkaline environments, especially at pH> 13.
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Affiliation(s)
- Erik Bivehed
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, Uppsala SE-751 24, Sweden.
| | - Björn Hellman
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, Uppsala SE-751 24, Sweden
| | - Yuting Fan
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, Uppsala SE-751 24, Sweden
| | - Jakob Haglöf
- Department of Medicinal Chemistry, Uppsala University, Box 574, Uppsala SE-751 23, Sweden
| | - Sonja Buratovic
- Department of Pharmaceutical Biosciences, Uppsala University, Box 591, Uppsala SE-751 24, Sweden
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25
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Wu H, Zhang Y, Xu H, Xu B, Chen J, Guo L, Liu Q, Xie J. Urinary Profile of Alkylated DNA Adducts and DNA Oxidative Damage in Sulfur Mustard-Exposed Rats Revealed by Mass Spectrometry Quantification. Chem Res Toxicol 2023; 36:1495-1502. [PMID: 37625021 DOI: 10.1021/acs.chemrestox.3c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Alkylation reagents, represented by sulfur mustard (SM), can damage DNA molecules directly as well as lead to oxidative stress, causing DNA lesions indirectly. Correspondingly, two types of biomarkers including alkylated DNA adducts and oxidative DNA adducts are commonly involved in the research of DNA damage evaluation caused by these agents. However, the correlations and differences of the occurrence, duration, severity, and traceability between alkylation and oxidation lesions on the DNA molecular level reflected by these two types of biomarkers have not been systematically studied. A simultaneous determination method for four alkylated DNA adducts, i.e., N7-(2-hydroxyethylthioethyl)2'-guanine (N7-HETEG), O6-(2-hydroxyethylthioethyl)-2'-guanine (O6-HETEG), N3-(2-hydroxyethylthioethyl)-2'-adenine (N3-HETEA), and bis(2-ethyl-N7-guanine)thioether (Bis-G), and the oxidative adduct 8-hydroxy-2'-deoxyguanosine (8-OH-dG) in urine samples by isotope-dilution high-performance liquid chromatography-tandem mass spectrometry (ID-HPLC-MS/MS) was built with a lower limit of detection of 0.02 ng/mL (except Bis-G, 0.05 ng/mL) and a recovery of 79-111%. The profile of these adducts was simultaneously monitored in urine samples after SD rats' dermal exposure to SM in three dose levels (1, 3, and 10 mg/kg). The time-effect and dose-effect experiments revealed that when exposed to SM, DNA alkylation lesions would happen earlier than those of oxidation. For the two types of biomarkers, alkylated DNA adducts showed an obvious dose-effect relationship and could be used as internal exposure dose and effect biomarkers, while 8-OH-dG did not show a correlation with exposure dose, demonstrating that it was more suitable as a biomarker for DNA oxidative lesions but not an indicator for the extent of cytotoxicity and internal exposure.
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Affiliation(s)
- Haijiang Wu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Yajiao Zhang
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Hua Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Bin Xu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jia Chen
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Lei Guo
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Qin Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
| | - Jianwei Xie
- State Key Laboratory of Toxicology and Medical Countermeasures, and Laboratory of Toxicant Analysis, Institute of Pharmacology and Toxicology, Academy of Military Medical Sciences, Beijing 100850, China
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26
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Kozal JS, Lynch HN, Klapacz J, Schoeny RS, Jean PA, Maier A. Mode of action assessment for propylene dichloride as a human carcinogen. Chem Biol Interact 2023; 382:110382. [PMID: 36754223 DOI: 10.1016/j.cbi.2023.110382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/16/2023] [Accepted: 02/04/2023] [Indexed: 02/09/2023]
Abstract
As part of a systematic review of the non-cancer and cancer hazards of propylene dichloride (PDC), with a focus on potential carcinogenicity in workers following inhalation exposures, we determined that a mode of action (MOA)-centric framing of cancer effects was warranted. In our MOA analysis, we systematically reviewed the available mechanistic evidence for PDC-induced carcinogenesis, and we mapped biologically plausible MOA pathways and key events (KEs), as guided by the International Programme on Chemical Safety (IPCS)-MOA framework. For the identified pathways and KEs, biological concordance, essentiality of KEs, concordance of empirical observations among KEs, consistency, and analogy were evaluated. The results of this analysis indicate that multiple biologically plausible pathways may contribute to the cancer MOA for PDC, but that the relevant pathways vary by exposure route and level, tissue type, and species; further, more than one pathway may occur concurrently at high exposure levels. While several important data gaps exist, evidence from in vitro mechanistic studies, in vivo experimental animal studies, and ex vivo human tumor tissue analyses indicates that the predominant MOA pathway likely involves saturation of cytochrome p450 2E1 (CYP2E1)-glutathione (GSH) detoxification (molecular initiating event; MIE), accumulation of CYP2E1-oxidative metabolites, cytotoxicity, chronic tissue damage and inflammation, and ultimately tumor formation. Tumors may occur through several subsets of inflammatory KEs, including inflammation-induced aberrant expression of activation-induced cytidine deaminase (AID), which causes DNA strand breaks and mutations and can lead to tumors with a characteristic mutational signature found in occupational cholangiocarcinoma. Dose concordance analysis showed that low-dose mutagenicity (from any pathway) is not a driving MOA, and that prevention of target tissue damage and inflammation (associated with saturation of CYP2E1-GSH detoxification) is expected to also prevent the cascade of processes responsible for tumor formation.
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Affiliation(s)
| | | | - Joanna Klapacz
- Toxicology and Environmental Research and Consulting, The Dow Chemical Company, Midland, MI, 48674, USA
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27
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Smerdon MJ, Wyrick JJ, Delaney S. A half century of exploring DNA excision repair in chromatin. J Biol Chem 2023; 299:105118. [PMID: 37527775 PMCID: PMC10498010 DOI: 10.1016/j.jbc.2023.105118] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/23/2023] [Accepted: 07/25/2023] [Indexed: 08/03/2023] Open
Abstract
DNA in eukaryotic cells is packaged into the compact and dynamic structure of chromatin. This packaging is a double-edged sword for DNA repair and genomic stability. Chromatin restricts the access of repair proteins to DNA lesions embedded in nucleosomes and higher order chromatin structures. However, chromatin also serves as a signaling platform in which post-translational modifications of histones and other chromatin-bound proteins promote lesion recognition and repair. Similarly, chromatin modulates the formation of DNA damage, promoting or suppressing lesion formation depending on the chromatin context. Therefore, the modulation of DNA damage and its repair in chromatin is crucial to our understanding of the fate of potentially mutagenic and carcinogenic lesions in DNA. Here, we survey many of the landmark findings on DNA damage and repair in chromatin over the last 50 years (i.e., since the beginning of this field), focusing on excision repair, the first repair mechanism studied in the chromatin landscape. For example, we highlight how the impact of chromatin on these processes explains the distinct patterns of somatic mutations observed in cancer genomes.
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Affiliation(s)
- Michael J Smerdon
- Biochemistry and Biophysics, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA.
| | - John J Wyrick
- Genetics and Cell Biology, School of Molecular Biosciences, Washington State University, Pullman, Washington, USA
| | - Sarah Delaney
- Department of Chemistry, Brown University, Providence, Rhode Island, USA
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28
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Bellamri M, Brandt K, Cammerrer K, Syeda T, Turesky RJ, Cannon JR. Nuclear DNA and Mitochondrial Damage of the Cooked Meat Carcinogen 2-Amino-1-methyl-6-phenylimidazo[4,5- b]pyridine in Human Neuroblastoma Cells. Chem Res Toxicol 2023; 36:1361-1373. [PMID: 37421305 PMCID: PMC10626466 DOI: 10.1021/acs.chemrestox.3c00109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Abstract
Animal fat and iron-rich diets are risk factors for Parkinson's disease (PD). The heterocyclic aromatic amines (HAAs) harman and norharman are neurotoxicants formed in many foods and beverages, including cooked meats, suggesting a role for red meat in PD. The structurally related carcinogenic HAAs 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), 2-amino-3,8-dimethylmidazo[4,5-f]quinoxaline (MeIQx), and 2-amino-9H-pyrido[2,3-b]indole (AαC) also form in cooked meats. We investigated the cytotoxicity, DNA-damaging potential, and mitochondrial damage of HAAs and their genotoxic HONH-HAA metabolites in galactose-dependent SH-SY5Y cells, a human neuroblastoma cell line relevant for PD-related neurotoxicity. All HAAs and HONH-HAAs induced weak toxicity except HONH-PhIP, which was 1000-fold more potent than the other chemicals. HONH-PhIP DNA adduct formation occurred at 300-fold higher levels than adducts formed with HONH-MeIQx and HONH-AαC, assuming similar cellular uptake rates. PhIP-DNA adduct levels occurred at concentrations as low as 1 nM and were threefold or higher and more persistent in mitochondrial DNA than nuclear DNA. N-Acetyltransferases (NATs), sulfotransferases, and kinases catalyzed PhIP-DNA binding and converted HONH-PhIP to highly reactive ester intermediates. DNA binding assays with cytosolic, mitochondrial, and nuclear fractions of SH-SY5Y fortified with cofactors revealed that cytosolic AcCoA-dependent enzymes, including NAT1, mainly carried out HONH-PhIP bioactivation to form N-acetoxy-PhIP, which binds to DNA. Furthermore, HONH-PHIP and N-acetoxy-PhIP inhibited mitochondrial complex-I, -II, and -III activities in isolated SH-SY5Y mitochondria. Mitochondrial respiratory chain complex dysfunction and DNA damage are major mechanisms in PD pathogenesis. Our data support the possible role of PhIP in PD etiology.
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Affiliation(s)
- Medjda Bellamri
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, Minnesota 55455, United States
| | - Kyle Brandt
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, Minnesota 55455, United States
| | - Kari Cammerrer
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, Minnesota 55455, United States
| | - Tauqeerunnisa Syeda
- School of Health Sciences, Purdue Institute for Integrative Neurosciences, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana 47907, United States
| | - Robert J Turesky
- Masonic Cancer Center and Department of Medicinal Chemistry, Cancer and Cardiovascular Research Building, University of Minnesota, 2231 6th Street, Minneapolis, Minnesota 55455, United States
| | - Jason R Cannon
- School of Health Sciences, Purdue Institute for Integrative Neurosciences, Purdue University, West Lafayette, Indiana 47907, United States
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana 47907, United States
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29
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Merrifield JL, Pimentel EB, Peters-Clarke TM, Nesbitt DJ, Coon JJ, Martell JD. DNA-Compatible Copper/TEMPO Oxidation for DNA-Encoded Libraries. Bioconjug Chem 2023; 34:1380-1386. [PMID: 37540561 PMCID: PMC10831869 DOI: 10.1021/acs.bioconjchem.3c00254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/06/2023]
Abstract
Aldehydes are important synthons for DNA-encoded library (DEL) construction, but the development of a DNA-compatible method for the oxidation of alcohols to aldehydes remains a significant challenge in the field of DEL chemistry. We report that a copper/TEMPO catalyst system enables the solution-phase DNA-compatible oxidation of DNA-linked primary activated alcohols to aldehydes. The semiaqueous, room-temperature reaction conditions afford oxidation of benzylic, heterobenzylic, and allylic alcohols in high yield, with DNA compatibility verified by mass spectrometry, qPCR, Sanger sequencing, and ligation assays. Subsequent transformations of the resulting aldehydes demonstrate the potential of this method for robust library diversification.
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Affiliation(s)
- Justice L. Merrifield
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Edward B. Pimentel
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Trenton M. Peters-Clarke
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Daniel J. Nesbitt
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- National Center for Quantitative Biology of Complex Systems, Madison, Wisconsin 53706, United States
- Morgridge Institute for Research, Madison, Wisconsin 53515, United States
| | - Jeffrey D. Martell
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin 53705, United States
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30
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Xiao S, Fleming AM, Burrows CJ. Sequencing for oxidative DNA damage at single-nucleotide resolution with click-code-seq v2.0. Chem Commun (Camb) 2023; 59:8997-9000. [PMID: 37401666 PMCID: PMC10909242 DOI: 10.1039/d3cc02699j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Oxidative damage to DNA nucleotides has many cellular outcomes that could be aided by the development of sequencing methods. Herein, the previously reported click-code-seq method for sequencing a single damage type is redeveloped to enable the sequencing of many damage types by making simple changes to the protocol (i.e., click-code-seq v2.0).
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Affiliation(s)
- Songjun Xiao
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Aaron M Fleming
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, UT 84112-0850, USA.
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31
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Wang Y, Su M, Chen Y, Huang X, Ruan L, Lv Q, Li L. Research progress on the role and mechanism of DNA damage repair in germ cell development. Front Endocrinol (Lausanne) 2023; 14:1234280. [PMID: 37529603 PMCID: PMC10390305 DOI: 10.3389/fendo.2023.1234280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 06/28/2023] [Indexed: 08/03/2023] Open
Abstract
In the complex and dynamic processes of replication, transcription, and translation of DNA molecules, a large number of replication errors or damage can occur which lead to obstacles in the development process of germ cells and result in a decreased reproductive rate. DNA damage repair has attracted widespread attention due to its important role in the maintenance and regulation of germ cells. This study reports on a systematic review of the role and mechanism of DNA damage repair in germline development. First, the causes, detection methods, and repair methods of DNA damage, and the mechanism of DNA damage repair are summarized. Second, a summary of the causes of abnormal DNA damage repair in germ cells is introduced along with common examples, and the relevant effects of germ cell damage. Third, we introduce the application of drugs related to DNA damage repair in the treatment of reproductive diseases and related surgical treatment of abnormal DNA damage, and summarize various applications of DNA damage repair in germ cells. Finally, a summary and discussion is given of the current deficiencies in DNA damage repair during germ cell development and future research development. The purpose of this paper is to provide researchers engaged in relevant fields with a further systematic understanding of the relevant applications of DNA damage repair in germ cells and to gain inspiration from it to provide new research ideas for related fields.
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Affiliation(s)
- Yan Wang
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Mengrong Su
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Yujie Chen
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Xinyu Huang
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Lian Ruan
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Qizhuang Lv
- College of Basic Medical Sciences, China Three Gorges University, Yichang, Hubei, China
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
| | - Li Li
- College of Biology & Pharmacy, Yulin Normal University, Yulin, China
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32
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Lyubitelev A, Studitsky V. Inhibition of Cancer Development by Natural Plant Polyphenols: Molecular Mechanisms. Int J Mol Sci 2023; 24:10663. [PMID: 37445850 PMCID: PMC10341686 DOI: 10.3390/ijms241310663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/08/2023] [Accepted: 06/09/2023] [Indexed: 07/15/2023] Open
Abstract
Malignant tumors remain one of the main sources of morbidity and mortality around the world. A chemotherapeutic approach to cancer treatment poses a multitude of challenges, primarily due to the low selectivity and genotoxicity of the majority of chemotherapeutic drugs currently used in the clinical practice, often leading to treatment-induced tumors formation. Highly selective antitumor drugs can largely resolve this issue, but their high selectivity leads to significant drawbacks due to the intrinsic tumor heterogeneity. In contrast, plant polyphenols can simultaneously affect many processes that are involved in the acquiring and maintaining of hallmark properties of malignant cells, and their toxic dose is typically much higher than the therapeutic one. In the present work we describe the mechanisms of the action of polyphenols on cancer cells, including their effects on genetic and epigenetic instability, tumor-promoting inflammation, and altered microbiota.
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Affiliation(s)
| | - Vasily Studitsky
- Biology Faculty, Lomonosov Moscow State University, 119234 Moscow, Russia;
- Fox Chase Cancer Center, Philadelphia, PA 19111, USA
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33
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Li J, Hu Z, Liu D, Wang P. Mass spectrometry-based assays for assessing replicative bypass and repair of DNA alkylation in cells. RSC Adv 2023; 13:15490-15497. [PMID: 37223415 PMCID: PMC10201546 DOI: 10.1039/d2ra08340j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 05/15/2023] [Indexed: 05/25/2023] Open
Abstract
Endogenous metabolism and environmental exposure can give rise to DNA alkylation, which can elicit deleterious biological consequences. In the search for reliable and quantitative analytical methods to elucidate the impact of DNA alkylation on the flow of genetic information, mass spectrometry (MS) has attracted increasing attention, owing to its unambiguous determination of molecular mass. The MS-based assays obviate conventional colony-picking methods and Sanger sequencing procedures, and retained the high sensitivity of postlabeling methods. With the help of the CRISPR/Cas9 gene editing method, MS-based assays showed high potential in studying individual functions of repair proteins and translesion synthesis (TLS) polymerases in DNA replication. In this mini-review, we have summarized the development of MS-based competitive and replicative adduct bypass (CRAB) assays and their recent applications in assessing the impact of alkylation on DNA replication. With further development of MS instruments for high resolving power and high throughput, these assays should be generally applicable and efficient in quantitative measurement of the biological consequences and repair of other DNA lesions.
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Affiliation(s)
- Jiaxian Li
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Zhihai Hu
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Dandan Liu
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
| | - Pengcheng Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan Jinan Shandong 250022 P. R. China
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34
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Chillar K, Eriyagama AMDN, Yin Y, Shahsavari S, Halami B, Apostle A, Fang S. Oligonucleotide synthesis under mild deprotection conditions. NEW J CHEM 2023; 47:8714-8722. [PMID: 37915883 PMCID: PMC10617641 DOI: 10.1039/d2nj03845e] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023]
Abstract
Over a hundred non-canonical nucleotides have been found in DNA and RNA. Many of them are sensitive toward nucleophiles. Because known oligonucleotide synthesis technologies require nucleophilic conditions for deprotection, currently there is no suitable technology for their synthesis. The recently disclosed method regarding the use of 1,3-dithian-2-yl-methyl (Dim) for phosphate protection and 1,3-dithian-2-yl-methoxycarbonyl (Dmoc) for amino protection can solve the problem. With Dim-Dmoc protection, oligodeoxynucleotide (ODN) deprotection can be achieved with NaIO4 followed by aniline. Some sensitive groups have been determined to be stable under these conditions. Besides serving as a base, aniline also serves as a nucleophilic scavenger, which prevents deprotection side products from reacting with ODN. For this reason, excess aniline is needed. Here, we report the use of alkyl Dim (aDim) and alkyl Dmoc (aDmoc) for ODN synthesis. With aDim-aDmoc protection, deprotection is achieved with NaIO4 followed by K2CO3. No nucleophilic scavenger such as aniline is needed. Over 10 ODNs including one containing the highly sensitive N4-acetylcytidine were synthesized. Work on extending the method for sensitive RNA synthesis is in progress.
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Affiliation(s)
- Komal Chillar
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Adikari M D N Eriyagama
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Yipeng Yin
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Shahien Shahsavari
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Bhaskar Halami
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Alexander Apostle
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
| | - Shiyue Fang
- Department of Chemistry, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
- Health Research Institute, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA
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35
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Abuja PM, Pabst D, Bourgeois B, Loibner M, Ulz C, Kufferath I, Fackelmann U, Stumptner C, Kraemer R, Madl T, Zatloukal K. Residual Humidity in Paraffin-Embedded Tissue Reduces Nucleic Acid Stability. Int J Mol Sci 2023; 24:8010. [PMID: 37175716 PMCID: PMC10178321 DOI: 10.3390/ijms24098010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 04/11/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023] Open
Abstract
Molecular diagnostics in healthcare relies increasingly on genomic and transcriptomic methodologies and requires appropriate tissue specimens from which nucleic acids (NA) of sufficiently high quality can be obtained. Besides the duration of ischemia and fixation type, NA quality depends on a variety of other pre-analytical parameters, such as storage conditions and duration. It has been discussed that the improper dehydration of tissue during processing influences the quality of NAs and the shelf life of fixed tissue. Here, we report on establishing a method for determining the amount of residual water in fixed, paraffin-embedded tissue (fixed by neutral buffered formalin or a non-crosslinking fixative) and its correlation to the performance of NAs in quantitative real-time polymerase chain reaction (qRT-PCR) analyses. The amount of residual water depended primarily on the fixative type and the dehydration protocol and, to a lesser extent, on storage conditions and time. Moreover, we found that these parameters were associated with the qRT-PCR performance of extracted NAs. Besides the cross-linking of NAs and the modification of nucleobases by formalin, the hydrolysis of NAs by residual water was found to contribute to reduced qRT-PCR performance. The negative effects of residual water on NA stability are not only important for the design and interpretation of research but must also be taken into account in clinical diagnostics where the reanalysis of archived tissue from a primary tumor may be required (e.g., after disease recurrence). We conclude that improving the shelf life of fixed tissue requires meticulous dehydration and dry storage to minimize the degradative influence of residual water on NAs.
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Affiliation(s)
- Peter M. Abuja
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Daniela Pabst
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Benjamin Bourgeois
- Gottfried Schatz Research Centre for Cell Signalling, Metabolism and Ageing, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Martina Loibner
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Christine Ulz
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Iris Kufferath
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Ulrike Fackelmann
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Cornelia Stumptner
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
| | - Rainer Kraemer
- Berghof Products & Instruments GmbH, 72800 Eningen, Germany
| | - Tobias Madl
- Gottfried Schatz Research Centre for Cell Signalling, Metabolism and Ageing, Molecular Biology and Biochemistry, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
| | - Kurt Zatloukal
- Diagnostic & Research Centre for Molecular Biomedicine, Institute of Pathology, Medical University of Graz, Neue Stiftingtalstrasse 6, 8010 Graz, Austria
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36
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Anuradha A, Undavalli SB, Kumar AJ. DNA mutilation: A telltale sign of cancer inception. J Oral Maxillofac Pathol 2023; 27:374-381. [PMID: 37854902 PMCID: PMC10581300 DOI: 10.4103/jomfp.jomfp_513_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/05/2023] [Accepted: 03/10/2023] [Indexed: 10/20/2023] Open
Abstract
DNA damage is a discrepancy in its chemical structure precipitated by a multitude of factors. Most DNA damages can be repaired efficiently through diverse restorative mechanisms subjective to the type of damage. DNA-damaging agents elicit a medley of cellular retorts like cell cycle arrest, followed by DNA repair mechanisms or apoptosis. An unrepaired DNA damage in a nonreplicating cell does not generally engender mutations but a similar scenario in replicating cell routes to permanent modification of genetic material shrugging to carcinogenesis. DNA mutilation can be allied to disarray in bases, debasement of backbone, or crosslinks. Base damages or backbone damages like single-strand and double-strand DNA breaks are usually produced by reactive oxygen species and ionizing radiation. This substantial DNA damage has broadly been considered to be caused by various exogenous and endogenous agents with variable rates of causality and decrees of risk, sourcing toward cancer or other diseases, necessitating furtherance in diagnostics at sequential points. The purpose of this article is to review in detail the various types of DNA damages, their contributory factors, and recent developments in their identification.
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Affiliation(s)
- A Anuradha
- Department of Oral and Maxillofacial Pathology, St Joseph Dental College and Hospital, Duggirala, Eluru, Andhra Pradesh, India
| | | | - A Jagadeesh Kumar
- Department of Oral and Maxillofacial Pathology, St Joseph Dental College and Hospital, Duggirala, Eluru, Andhra Pradesh, India
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37
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Schulze Johann K, Bauer H, Wiegand P, Pfeiffer H, Vennemann M. Detecting DNA damage in stored blood samples. Forensic Sci Med Pathol 2023; 19:50-59. [PMID: 36355320 PMCID: PMC10014702 DOI: 10.1007/s12024-022-00549-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/18/2022] [Indexed: 11/11/2022]
Abstract
Several commercially available quantitative real-time PCR (qPCR) systems enable highly sensitive detection of human DNA and provide a degradation index (DI) to assess DNA quality. From routine casework in forensic genetics, it was observed that DNA degradation in forensic samples such as blood samples stored under sub-optimal conditions leads to visible effects in multiplex analyses of short tandem repeat markers (STRs) due to decreased amplification efficiencies in longer amplicons. It was further noticed that degradation indices often remain below the value that is considered to be critical. Thus, the aim of this work was to systematically analyze this effect and to compare conventional qPCR assays with a modified qPCR approach using uracil DNA glycosylase (UNG) and DNA quality assessment methods based on electrophoresis. Blood samples were stored at three different storage temperatures for up to 316 days. Significantly increased DNA recovery was observed from samples stored at high temperatures (37 °C) compared samples stored at room temperature and 4 °C. We observed typical effects of degradation in STR analyses but no correlation between DI and storage time in any of the storage conditions. Adding UNG slightly increased the sensitivity of detecting DNA degradation in one of the qPCR kits used in this study. This observation was not confirmed when using a second qPCR system. Electrophoretic systems did also not reveal significant correlations between integrity values and time. Methods for detecting DNA degradation are usually limited to the detection of DNA fragmentation, and we conclude that degradation affecting forensic STR typing is more complex.
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Affiliation(s)
- Kristina Schulze Johann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany.
| | - Hannah Bauer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081, Ulm, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149, Münster, Germany
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38
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Wu M, Ma G, Lin Y, Oger P, Cao P, Zhang L. Biochemical Characterization and Mutational Studies of Endonuclease Q from the Hyperthermophilic Euryarchaeon Thermococcus gammatolerans. DNA Repair (Amst) 2023; 126:103490. [PMID: 37028219 DOI: 10.1016/j.dnarep.2023.103490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/25/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023]
Abstract
Endonuclease Q (EndoQ) can effectively cleave DNA containing deaminated base(s), thus providing a potential pathway for repair of deaminated DNA. EndoQ is ubiquitous in some Archaea, especially in Thermococcales, and in a small group of bacteria. Herein, we report biochemical characteristics of EndoQ from the hyperthermophilic euryarchaeon Thermococcus gammatolerans (Tga-EndoQ) and the roles of its six conserved residues in DNA cleavage. The enzyme can cleave uracil-, hypoxanthine-, and AP (apurinic/apyrimidinic) site-containing DNA with varied efficiencies at high temperature, among which uracil-containing DNA is its most preferable substrate. Additionally, the enzyme displays maximum cleavage efficiency at above 70 oC and pH 7.0 ∼ 8.0. Furthermore, Tga-EndoQ still retains 85% activity after heated at 100 oC for 2 hrs, suggesting that the enzyme is extremely thermostable. Moreover, the Tga-EndoQ activity is independent of a divalent ion and NaCl. Mutational data demonstrate that residues E167 and H195 in Tga-EndoQ are essential for catalysis since the E167A and H195A mutants completely abolish the cleavage activity. Besides, residues S18 and R204 in Tga-EndoQ are involved in catalysis due to the reduced activities observed for the S18A and R204A mutants. Overall, our work has augmented biochemical function of archaeal EndoQ and provided insight into its catalytic mechanism.
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Affiliation(s)
- Mai Wu
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China
| | - Guangyu Ma
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China
| | - Yushan Lin
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China
| | - Philippe Oger
- Université de Lyon, INSA de Lyon, CNRS UMR, 5240 Lyon, France
| | - Peng Cao
- Faculty of Environment and Life, Beijing University of Technology, 100 Pingleyuan, Chaoyang District, Beijing 100124, China.
| | - Likui Zhang
- College of Environmental Science and Engineering, Yangzhou University, Yangzhou City, China.
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39
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Sanchez-Contreras M, Sweetwyne MT, Tsantilas KA, Whitson JA, Campbell MD, Kohrn BF, Kim HJ, Hipp MJ, Fredrickson J, Nguyen MM, Hurley JB, Marcinek DJ, Rabinovitch PS, Kennedy SR. The multi-tissue landscape of somatic mtDNA mutations indicates tissue-specific accumulation and removal in aging. eLife 2023; 12:e83395. [PMID: 36799304 PMCID: PMC10072880 DOI: 10.7554/elife.83395] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Accepted: 02/15/2023] [Indexed: 02/18/2023] Open
Abstract
Accumulation of somatic mutations in the mitochondrial genome (mtDNA) has long been proposed as a possible mechanism of mitochondrial and tissue dysfunction that occurs during aging. A thorough characterization of age-associated mtDNA somatic mutations has been hampered by the limited ability to detect low-frequency mutations. Here, we used Duplex Sequencing on eight tissues of an aged mouse cohort to detect >89,000 independent somatic mtDNA mutations and show significant tissue-specific increases during aging across all tissues examined which did not correlate with mitochondrial content and tissue function. G→A/C→T substitutions, indicative of replication errors and/or cytidine deamination, were the predominant mutation type across all tissues and increased with age, whereas G→T/C→A substitutions, indicative of oxidative damage, were the second most common mutation type, but did not increase with age regardless of tissue. We also show that clonal expansions of mtDNA mutations with age is tissue- and mutation type-dependent. Unexpectedly, mutations associated with oxidative damage rarely formed clones in any tissue and were significantly reduced in the hearts and kidneys of aged mice treated at late age with elamipretide or nicotinamide mononucleotide. Thus, the lack of accumulation of oxidative damage-linked mutations with age suggests a life-long dynamic clearance of either the oxidative lesions or mtDNA genomes harboring oxidative damage.
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Affiliation(s)
| | - Mariya T Sweetwyne
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | | | - Jeremy A Whitson
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | | | - Brenden F Kohrn
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Hyeon Jeong Kim
- Department of Biology, University of WashingtonSeattleUnited States
| | - Michael J Hipp
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Jeanne Fredrickson
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Megan M Nguyen
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - James B Hurley
- Department of Biochemistry, University of WashingtonSeattleUnited States
| | - David J Marcinek
- Department of Radiology, University of WashingtonSeattleUnited States
| | - Peter S Rabinovitch
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, University of WashingtonSeattleUnited States
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40
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Singh A, Yadav RK, Shati A, Kamboj NK, Hasssan H, Bharadwaj S, Rana R, Yadava U. Understanding the self-assembly dynamics of A/T absent 'four-way DNA junctions with sticky ends' at altered physiological conditions through molecular dynamics simulations. PLoS One 2023; 18:e0278755. [PMID: 36753480 PMCID: PMC9907842 DOI: 10.1371/journal.pone.0278755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Accepted: 11/22/2022] [Indexed: 02/09/2023] Open
Abstract
Elucidation of structure and dynamics of alternative higher-order structures of DNA such as in branched form could be targeted for therapeutics designing. Herein, we are reporting the intrinsically dynamic and folds transitions of an unusual DNA junction with sequence d(CGGCGGCCGC)4 which self-assembles into a four-way DNA junction form with sticky ends using long interval molecular simulations under various artificial physiological conditions. The original crystal structure coordinates (PDB ID: 3Q5C) for the selected DNA junction was considered for a total of 1.1 μs molecular dynamics simulation interval, including different temperature and pH, under OPLS-2005 force field using DESMOND suite. Following, post-dynamics structure parameters for the DNA junction were calculated and analyzed by comparison to the crystal structure. We show here that the self-assembly dynamics of DNA junction is mitigated by the temperature and pH sensitivities, and discloses peculiar structural properties as function of time. From this study it can be concluded on account of temperature sensitive and pH dependent behaviours, DNA junction periodic arrangements can willingly be synthesized and redeveloped for multiple uses like genetic biomarkers, DNA biosensor, DNA nanotechnology, DNA Zipper, etc. Furthermore, the pH dis-regulation behaviour may be used to trigger the functionality of DNA made drug-releasing nanomachines.
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Affiliation(s)
- Akanksha Singh
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
| | | | - Ali Shati
- Department of Biology, Faculty of Science, King Khaild University, Abha, Saudi Arabia
| | - Nitin Kumar Kamboj
- School of Physical Sciences, DIT University, Dehradun, Uttarakhand, India
| | - Hesham Hasssan
- Department of Pathology, College of Medicine, King Khaild University, Abha, Saudi Arabia
- Department of Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
- * E-mail: (SB); (RR); (UY)
| | - Rashmi Rana
- Department of Research, Sir Ganga Ram Hospital, New Delhi, India
- * E-mail: (SB); (RR); (UY)
| | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyaya Gorakhpur University, Gorakhpur, India
- * E-mail: (SB); (RR); (UY)
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41
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Wu J, Cai Z. Enrichment of nucleobase adducts from genomic DNA in the cytoplasm by solid-phase extraction. J Chromatogr B Analyt Technol Biomed Life Sci 2023; 1215:123574. [PMID: 36586340 DOI: 10.1016/j.jchromb.2022.123574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022]
Abstract
The exact levels of some DNA adducts, like N7-deoxyguanosine (N7-dG), can be under-calculated since these adducts may depurinate due to their chemical instability, leading to corresponding nucleobase adducts being released into the cytoplasm. To accurately quantify the levels of DNA adducts, it is necessary to consider those modified nucleobases. However, high levels and diversity of cytoplasmic small molecule metabolites (SMMs) can strongly interfere with the detection of adducts, and it is almost impossible to remove them with nucleobase adducts being well retained. Therefore, we aimed to establish an optimized enrichment method based on solid-phase extraction (SPE) to reduce the co-elution of SMMs with target analytes. In this vein, we employed three bisphenols (BPA, BPF, and BPAF) as examples, prepared corresponding N7-guanine (N7-Gua) adducts, loaded on an Oasis hydrophilic-lipophilic balance ® (HLB) cartridge, used a series of mobile phases containing different percentage of methanol for elution, and evaluated the levels of these adducts in each eluent. First, we found that neutral samples led to the best retention for all three adducts compared with acidified or basified ones. We next employed normal distribution fitting model to characterize the elution of analytes from H2O/methanol with different pHs and observed that neutral mobile phases resulted in more hydrophobic elution for all three adducts. Besides, N7-BPA-Gua and N7-BPF-Gua obtained narrow fitted peaks at neutral pH, while N7-BPAF-Gua had minimized elution windows at low pH. After optimization, we exposed 293T cells to the aforementioned bisphenols and quantified the N7-Gua adducts in the cytoplasm and the corresponding N7-dG adducts in genomic DNA. The results revealed that with the same levels of BPs exposure, BPAF led to the highest levels of adducts in both cytoplasm and genomic DNA samples, followed by BPA and BPF in order. In summary, our research established an appropriate model to describe the elution of DNA adducts in the SPE, applied it to optimize the loading and elution conditions, and discussed the genotoxicity of bisphenols by accurate quantification of both cleaved and uncleaved N7-dG adducts.
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Affiliation(s)
- Jiabin Wu
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, People's Republic of China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong, People's Republic of China.
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42
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Chakraborty A, Hazra TK. Highly Sensitive Radioactivity-Based DNA 3'-Phosphatase Activity Assay for Polynucleotide Kinase 3'-Phosphatase. Methods Mol Biol 2023; 2701:39-54. [PMID: 37574474 DOI: 10.1007/978-1-0716-3373-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Endogenous and exogenous genotoxic agents can generate various types of non-ligatable DNA ends at the site of strand break in the mammalian genome. If not repaired, such lesions will impede transcription and replication and can lead to various cellular pathologies. Among various "dirty" DNA ends, 3'-phosphate is one of the most abundant lesions generated in the mammalian cells. Polynucleotide kinase 3'-phosphatase (PNKP) is the major DNA end-processing enzyme for resolving 3'-phosphate termini in the mammalian cells, and thus, it is involved in DNA base excision repair (BER), single-strand break repair, and classical nonhomologous end joining (C-NHEJ)-mediated DNA double-strand break (DSB) repair. The 3'-OH ends generated following PNKP-mediated processing of 3'-P are utilized by a DNA polymerase to fill in the gap, and subsequently, the nick is sealed by a DNA ligase to complete the repair process. Here we describe two novel assay systems to detect phosphate release by PNKP's 3'-phosphatase activity and PNKP-mediated in vitro single-strand break repair with minimal repair components (PNKP, DNA polymerase, and DNA ligase) using either purified proteins or cell-free nuclear extracts from mammalian cells/tissues. These assays are highly reproducible and sensitive, and the researchers would be able to detect any significant difference in PNKP's 3'-phosphatase activity as well as PNKP-mediated single-strand break repair activity in diseased mammalian cells/tissues vs normal healthy controls.
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Affiliation(s)
- Anirban Chakraborty
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Texas Medical Branch, Galveston, TX, USA
| | - Tapas K Hazra
- Department of Internal Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Texas Medical Branch, Galveston, TX, USA.
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43
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Schulze Johann K, Bauer H, Wiegand P, Pfeiffer H, Vennemann M. Whole-genome sequencing of artificial single-nucleotide variants induced by DNA degradation in biological crime scene traces. Int J Legal Med 2023; 137:33-45. [PMID: 36352329 PMCID: PMC9816238 DOI: 10.1007/s00414-022-02911-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
The aim of this study was to identify artificial single-nucleotide variants (SNVs) in degraded trace DNA samples. In a preliminary study, blood samples were stored for up to 120 days and whole-genome sequencing was performed using the Snakemake workflow dna-seq-gatk-variant-calling to identify positions that vary between the time point 0 sample and the aged samples. In a follow-up study on blood and saliva samples stored under humid and dry conditions, potential marker candidates for the estimation of the age of a blood stain (= time since deposition) were identified. Both studies show that a general decrease in the mean fragment size of the libraries over time was observed, presumably due to the formation of abasic sites during DNA degradation which are more susceptible to strand breaks by mechanical shearing of DNA. Unsurprisingly, an increase in the number of failed genotype calls (no coverage) was detected over time. Both studies indicated the presence of artificial SNVs with the majority of changes happening at guanine and cytosine positions. This confirms previous studies and can be explained by depurination through hydrolytic attacks which more likely deplete guanine while deamination leads to cytosine to thymine variants. Even complete genotype switches from homozygote 0/0 genotypes to the opposite 1/1 genotypes were observed. While positions with such drastic changes might provide suitable candidate markers for estimating short-term time since deposition (TsD), 11 markers were identified which show a slower gradual change of the relative abundance of the artificial variant in both blood and saliva samples, irrespective of storage conditions.
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Affiliation(s)
| | - Hannah Bauer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
| | - Peter Wiegand
- Institute of Legal Medicine, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Heidi Pfeiffer
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
| | - Marielle Vennemann
- Institute of Legal Medicine, University of Münster, Röntgenstr. 23, 48149 Münster, Germany
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44
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Cui Y, Wang Y. Mass spectrometry-based DNA adductomics. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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45
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Yin J, Gates KS, Wang Y. N-Methyl- N-nitrosourea Induced 3'-Glutathionylated DNA-Cleavage Products in Mammalian Cells. Anal Chem 2022; 94:15595-15603. [PMID: 36332130 PMCID: PMC9869666 DOI: 10.1021/acs.analchem.2c02003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Apurinic/apyrimidinic (AP) sites, that is, abasic sites, are among the most frequently induced DNA lesions. Spontaneous or DNA glycosylase-mediated β-elimination of the 3'-phosphoryl group can lead to strand cleavages at AP sites to yield a highly reactive, electrophilic 3'-phospho-α,β-unsaturated aldehyde (3'-PUA) remnant. The latter can react with amine or thiol groups of biological small molecules, DNA, and proteins to yield various damaged 3'-end products. Considering its high intracellular concentration, glutathione (GSH) may conjugate with 3'-PUA to yield 3-glutathionyl-2,3-dideoxyribose (GS-ddR), which may constitute a significant, yet previously unrecognized endogenous lesion. Here, we developed a liquid chromatography tandem mass spectroscopy method, in combination with the use of a stable isotope-labeled internal standard, to quantify GS-ddR in genomic DNA of cultured human cells. Our results revealed the presence of GS-ddR in the DNA of untreated cells, and its level was augmented in cells upon exposure to an alkylating agent, N-methyl-N-nitrosourea (MNU). In addition, inhibition of AP endonuclease (APE1) led to an elevated level of GS-ddR in the DNA of MNU-treated cells. Together, we reported here, for the first time, the presence of appreciable levels of GS-ddR in cellular DNA, the induction of GS-ddR by a DNA alkylating agent, and the role of APE1 in modulating its level in human cells.
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Affiliation(s)
- Jiekai Yin
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
| | - Kent S Gates
- Department of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Yinsheng Wang
- Environmental Toxicology Graduate Program, University of California, Riverside, California 92521-0403, United States
- Department of Chemistry, University of California, Riverside, California 92521-0403, United States
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46
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Chiaratti MR, Chinnery PF. Modulating mitochondrial DNA mutations: factors shaping heteroplasmy in the germ line and somatic cells. Pharmacol Res 2022; 185:106466. [PMID: 36174964 DOI: 10.1016/j.phrs.2022.106466] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Until recently it was thought that most humans only harbor one type of mitochondrial DNA (mtDNA), however, deep sequencing and single-cell analysis has shown the converse - that mixed populations of mtDNA (heteroplasmy) are the norm. This is important because heteroplasmy levels can change dramatically during transmission in the female germ line, leading to high levels causing severe mitochondrial diseases. There is also emerging evidence that low level mtDNA mutations contribute to common late onset diseases such as neurodegenerative disorders and cardiometabolic diseases because the inherited mutation levels can change within developing organs and non-dividing cells over time. Initial predictions suggested that the segregation of mtDNA heteroplasmy was largely stochastic, with an equal tendency for levels to increase or decrease. However, transgenic animal work and single-cell analysis have shown this not to be the case during germ-line transmission and in somatic tissues during life. Mutation levels in specific mtDNA regions can increase or decrease in different contexts and the underlying molecular mechanisms are starting to be unraveled. In this review we provide a synthesis of recent literature on the mechanisms of selection for and against mtDNA variants. We identify the most pertinent gaps in our understanding and suggest ways these could be addressed using state of the art techniques.
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Affiliation(s)
- Marcos R Chiaratti
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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Cao Y, Oh J, Xue M, Martin AL, Song D, Crawford JM, Herzon SB, Palm NW. Commensal microbiota from patients with inflammatory bowel disease produce genotoxic metabolites. Science 2022; 378:eabm3233. [PMID: 36302024 PMCID: PMC9993714 DOI: 10.1126/science.abm3233] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Microbiota-derived metabolites that elicit DNA damage can contribute to colorectal cancer (CRC). However, the full spectrum of genotoxic chemicals produced by indigenous gut microbes remains to be defined. We established a pipeline to systematically evaluate the genotoxicity of an extensive collection of gut commensals from inflammatory bowel disease patients. We identified isolates from divergent phylogenies whose metabolites caused DNA damage and discovered a distinctive family of genotoxins-termed the indolimines-produced by the CRC-associated species Morganella morganii. A non-indolimine-producing M. morganii mutant lacked genotoxicity and failed to exacerbate colon tumorigenesis in mice. These studies reveal the existence of a previously unexplored universe of genotoxic small molecules from the microbiome that may affect host biology in homeostasis and disease.
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Affiliation(s)
- Yiyun Cao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Joonseok Oh
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
| | - Mengzhao Xue
- Laboratory of Genetically Encoded Small Molecules, The Rockefeller University, New York, NY 10065, USA
| | - Anjelica L. Martin
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Deguang Song
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
| | - Jason M. Crawford
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT 06516, USA
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06536, USA
| | - Seth B. Herzon
- Department of Chemistry, Yale University, New Haven, CT 06520, USA
- Department of Pharmacology, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Noah W. Palm
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06519, USA
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Amin SM, Islam T, Price NE, Wallace A, Guo X, Gomina A, Heidari M, Johnson KM, Lewis CD, Yang Z, Gates KS. Effects of Local Sequence, Reaction Conditions, and Various Additives on the Formation and Stability of Interstrand Cross-Links Derived from the Reaction of an Abasic Site with an Adenine Residue in Duplex DNA. ACS OMEGA 2022; 7:36888-36901. [PMID: 36278095 PMCID: PMC9583646 DOI: 10.1021/acsomega.2c05736] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
The experiments described here examined the effects of reaction conditions, various additives, and local sequence on the formation and stability interstrand cross-links (ICLs) derived from the reaction of an apurinic/apyrimidinic (AP) site with the exocyclic amino group of an adenine residue on the opposing strand in duplex DNA. Cross-link formation was observed in a range of different buffers, with faster formation rates observed at pH 5. Inclusion of the base excision repair enzyme alkyladenine DNA glycosylase (hAAG) which binds tightly to AP-containing duplexes decreased, but did not completely prevent, formation of the dA-AP ICL. Formation of the dA-AP ICL was not altered by the presence of the biological metal ion Mg2+ or the biological thiol, glutathione. Several organocatalysts of imine formation did not enhance the rate of dA-AP ICL formation. Duplex length did not have a large effect on dA-AP yield, so long as the melting temperature of the duplex was not significantly below the reaction temperature (the duplex must remain hybridized for efficient ICL formation). Formation of the dA-AP ICL was examined in over 40 different sequences that varied the neighboring and opposing bases at the cross-linking site. The results indicate that ICL formation can occur in a wide variety of sequence contexts under physiological conditions. Formation of the dA-AP ICL was strongly inhibited by the aldehyde-trapping agents methoxyamine and hydralazine, by NaBH3CN, by the intercalator ethidium bromide, and by the minor groove-binding agent netropsin. ICL formation was inhibited to some extent in bicarbonate and Tris buffers. The dA-AP ICL showed substantial inherent stability under a variety of conditions and was not a substrate for AP-processing enzymes APE1 or Endo IV. Finally, we characterized cross-link formation in a small (11 bp) stem-loop (hairpin) structure and in DNA-RNA hybrid duplexes.
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Affiliation(s)
- Saosan
Binth Md. Amin
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Tanhaul Islam
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Nathan E. Price
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Amanda Wallace
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Xu Guo
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Anuoluwapo Gomina
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Marjan Heidari
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kevin M. Johnson
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Calvin D. Lewis
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Zhiyu Yang
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
| | - Kent S. Gates
- Department
of Chemistry, University of Missouri, Columbia, Missouri 65211, United States
- Department
of Biochemistry, University of Missouri, Columbia, Missouri 65211, United States
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49
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Ulhusna A, Murata A, Nakatani K. Inhibitory Effects of Mismatch Binding Molecules on the Repair Reaction of Uracil-Containing DNA. Biochemistry 2022; 61:2522-2530. [PMID: 36250600 DOI: 10.1021/acs.biochem.2c00344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The stable R-loop formed during transcription induces enzyme-mediated deamination of cytosine, and the uracil in the DNA produced activates the base excision repair (BER) pathway. DNA cleavage involved in the BER pathway is thought to be one of the possible causes of trinucleotide repeat instability. Here, we performed an in vitro assay to investigate the effect of a DNA-binding small molecule, naphthyridine carbamate dimer (NCD), on BER enzyme reactions. The gel electrophoretic mobility shift assay (EMSA) and thermal melting analysis revealed the binding of NCD to a 5'-XGG-3'/5'-XGG-3' triad (X = C or U or apurinic/apyrimidinic site), which is a mimic of a BER enzyme substrate. Polyacrylamide gel electrophoresis (PAGE) of the reaction products of these substrates with hSMUG1 and APE1 enzymes in the presence of NCD showed that NCD interfered with the repair reaction in the 5'-XGG-3'/5'-XGG-3' triad. These findings would broaden the potential of small molecules in modulating trinucleotide repeat instability.
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Affiliation(s)
- Anisa Ulhusna
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, SANKEN (The Institute of Scientific and Industrial Research), Osaka University, Mihogaoka 8-1, Ibaraki, Osaka 567-0047, Japan
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50
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Abstract
DNA damage by chemicals, radiation, or oxidative stress leads to a mutational spectrum, which is complex because it is determined in part by lesion structure, the DNA sequence context of the lesion, lesion repair kinetics, and the type of cells in which the lesion is replicated. Accumulation of mutations may give rise to genetic diseases such as cancer and therefore understanding the process underlying mutagenesis is of immense importance to preserve human health. Chemical or physical agents that cause cancer often leave their mutational fingerprints, which can be used to back-calculate the molecular events that led to disease. To make a clear link between DNA lesion structure and the mutations a given lesion induces, the field of single-lesion mutagenesis was developed. In the last three decades this area of research has seen much growth in several directions, which we attempt to describe in this Perspective.
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Affiliation(s)
- Ashis K Basu
- Department of Chemistry, The University of Connecticut Storrs, Storrs, Connecticut 06269, United States
| | - John M Essigmann
- Departments of Chemistry, Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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