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Article ; Online: Detection of UV-Induced Deletions in Mitochondrial DNA.

Fontana, Gabriele A / Gahlon, Hailey L

Methods in molecular biology (Clifton, N.J.)

2023 Volume 2615, Page(s) 281–292

Abstract: Mitochondrial DNA (mtDNA) mutations are found in several human pathologies and are associated with aging. Deletion mutations in mtDNA result in the loss of essential genes for mitochondrial function. Over 250 deletion mutations have been reported and the ...

Abstract	Mitochondrial DNA (mtDNA) mutations are found in several human pathologies and are associated with aging. Deletion mutations in mtDNA result in the loss of essential genes for mitochondrial function. Over 250 deletion mutations have been reported and the common deletion is the most frequent mtDNA deletion linked to disease. This deletion removes 4977 base pairs of mtDNA. It has previously been shown that exposure to UVA radiation can promote the formation of the common deletion. Furthermore, aberrations in mtDNA replication and repair are associated with formation of the common deletion. However, molecular mechanisms describing the formation of this deletion are poorly characterized. This chapter describes a method to irradiate human skin fibroblasts with physiological doses of UVA and the subsequent detection of the common deletion by quantitative PCR analysis.
MeSH term(s)	Humans ; DNA, Mitochondrial/genetics ; Sequence Deletion ; Mitochondria/genetics ; Aging/genetics ; Mutation
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2023-02-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2922-2_20
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Article: A Brief History and Practical Applications in DNA Extraction.

Gahlon, Hailey L

Chimia

2020 Volume 74, Issue 11, Page(s) 907–908

Abstract: In the late 1860s, DNA was first identified by the Swiss physician and biochemist Friedrich Miescher. Since this time, we have solved its structure, learned how DNA divides in our cells, and elucidated molecular mechanisms for the transmission of our ... ...

Abstract	In the late 1860s, DNA was first identified by the Swiss physician and biochemist Friedrich Miescher. Since this time, we have solved its structure, learned how DNA divides in our cells, and elucidated molecular mechanisms for the transmission of our hereditary information. Fundamental to all these discoveries is the ability to extract our DNA in high purity. In laboratories today, DNA extraction is a routine practice performed from readily available commercial kits. However, in the late 1800s, DNA extraction was an emerging method that required tedious laboratory approaches.
MeSH term(s)	DNA ; Laboratories
Chemical Substances	DNA (9007-49-2)
Language	English
Publishing date	2020-11-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1516-7
ISSN	0009-4293
ISSN	0009-4293
DOI	10.2533/chimia.2020.907
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Article ; Online: Mechanisms of replication and repair in mitochondrial DNA deletion formation.

Fontana, Gabriele A / Gahlon, Hailey L

Nucleic acids research

2020 Volume 48, Issue 20, Page(s) 11244–11258

Abstract: Deletions in mitochondrial DNA (mtDNA) are associated with diverse human pathologies including cancer, aging and mitochondrial disorders. Large-scale deletions span kilobases in length and the loss of these associated genes contributes to crippled ... ...

Abstract	Deletions in mitochondrial DNA (mtDNA) are associated with diverse human pathologies including cancer, aging and mitochondrial disorders. Large-scale deletions span kilobases in length and the loss of these associated genes contributes to crippled oxidative phosphorylation and overall decline in mitochondrial fitness. There is not a united view for how mtDNA deletions are generated and the molecular mechanisms underlying this process are poorly understood. This review discusses the role of replication and repair in mtDNA deletion formation as well as nucleic acid motifs such as repeats, secondary structures, and DNA damage associated with deletion formation in the mitochondrial genome. We propose that while erroneous replication and repair can separately contribute to deletion formation, crosstalk between these pathways is also involved in generating deletions.
MeSH term(s)	DNA Breaks, Double-Stranded ; DNA Mismatch Repair ; DNA Repair ; DNA Replication ; DNA, Mitochondrial/biosynthesis ; DNA, Mitochondrial/metabolism ; Genetic Diseases, Inborn/genetics ; Genetic Diseases, Inborn/metabolism ; Humans ; Mitochondria/genetics ; Mitochondria/pathology ; Mitochondrial Diseases/genetics ; Mitochondrial Diseases/metabolism ; Oxidative Phosphorylation ; Sequence Deletion
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2020-10-06
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkaa804
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Article: Molecular beacons with oxidized bases report on substrate specificity of DNA oxoguanine glycosylases.

Sun, Jingjing / Antczak, Nicole M / Gahlon, Hailey L / Sturla, Shana J

Chemical science

2022 Volume 13, Issue 15, Page(s) 4295–4302

Abstract: DNA glycosylase enzymes recognize and remove structurally distinct modified forms of DNA bases, thereby repairing genomic DNA from chemically induced damage or erasing epigenetic marks. However, these enzymes are often promiscuous, and advanced tools are ...

Abstract	DNA glycosylase enzymes recognize and remove structurally distinct modified forms of DNA bases, thereby repairing genomic DNA from chemically induced damage or erasing epigenetic marks. However, these enzymes are often promiscuous, and advanced tools are needed to evaluate and engineer their substrate specificity. Thus, in the present study, we developed a new strategy to rapidly profile the substrate specificity of 8-oxoguanine glycosylases, which cleave biologically relevant oxidized forms of guanine. We monitored the enzymatic excision of fluorophore-labeled oligonucleotides containing synthetic modifications 8-oxoG and FapyG, or G. Using this molecular beacon approach, we identified several hOGG1 mutants with higher specificity for FapyG than 8-oxoG. This approach and the newly synthesized probes will be useful for the characterization of glycosylase substrate specificity and damage excision mechanisms, as well as for evaluating engineered enzymes with altered reactivities.
Language	English
Publishing date	2022-02-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2559110-1
ISSN	2041-6539 ; 2041-6520
ISSN (online)	2041-6539
ISSN	2041-6520
DOI	10.1039/d1sc05648d
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Article ; Online: Hair Dye Ingredients and Potential Health Risks from Exposure to Hair Dyeing.

He, Lin / Michailidou, Freideriki / Gahlon, Hailey L / Zeng, Weibin

Chemical research in toxicology

2022 Volume 35, Issue 6, Page(s) 901–915

Abstract: Given the worldwide popularity of hair dyeing, there is an urgent need to understand the toxicities and risks associated with exposure to chemicals found in hair dye formulations. Hair dyes are categorized as oxidative and nonoxidative in terms of their ... ...

Abstract	Given the worldwide popularity of hair dyeing, there is an urgent need to understand the toxicities and risks associated with exposure to chemicals found in hair dye formulations. Hair dyes are categorized as oxidative and nonoxidative in terms of their chemical composition and ingredients. For several decades, the expert panel's Cosmetic Ingredient Review (CIR) has assessed the safety of many of the chemicals used in hair dyes; however, a comprehensive review of hair dye ingredients and the risk of exposure to hair dyeing has not been documented. Herein, we review the safety of the various chemicals in oxidative and nonoxidative hair dyes, toxicities associated with hair dyeing, and the carcinogenic risks related to hair dyeing. While many compounds are considered safe for users at the concentrations in hair dyes, there are conflicting data about a large number of hair dye formulations. The CIR expert panel has ratified a number of coloring ingredients for hair dyes and banned a series of chemicals as carcinogenic to animals and unsafe for this application. The use of these chemicals as raw materials for producing hair dyes may result in the synthesis of other contaminants with potential toxicities and increased risk of carcinogenesis. It is an open question whether personal or occupational hair dyeing increases the risk of cancer; however, in specific subpopulations, a positive association between hair dye use and cancer occurrence has been reported. To address this question, a better understanding of the chemical and mechanistic basis of the reported toxicities of hair dye mixtures and individual hair dye ingredients is needed. It is anticipated that in-depth chemical and systems toxicology studies harnessing modern and emerging techniques can shed light on this public health concern in the future.
MeSH term(s)	Allergens ; Animals ; Consumer Product Safety ; Cosmetics/toxicity ; Hair ; Hair Dyes/chemistry ; Hair Dyes/toxicity
Chemical Substances	Allergens ; Cosmetics ; Hair Dyes
Language	English
Publishing date	2022-06-06
Publishing country	United States
Document type	Journal Article ; Review
ZDB-ID	639353-6
ISSN	1520-5010 ; 0893-228X
ISSN (online)	1520-5010
ISSN	0893-228X
DOI	10.1021/acs.chemrestox.1c00427
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Article ; Online: The mitochondrial DNA common deletion as a potential biomarker of cancer-associated fibroblasts from skin basal and squamous cell carcinomas.

Fontana, Gabriele A / MacArthur, Michael R / Rotankova, Nadezhda / Di Filippo, Michela / Beer, Hans-Dietmar / Gahlon, Hailey L

Scientific reports

2024 Volume 14, Issue 1, Page(s) 553

Abstract: Cancer-associated fibroblasts (CAFs) are components of the tumor microenvironment and represent appealing therapeutic targets for translational studies. Conventional protein-based biomarkers for CAFs have been reported to be limited in their specificity, ...

Abstract	Cancer-associated fibroblasts (CAFs) are components of the tumor microenvironment and represent appealing therapeutic targets for translational studies. Conventional protein-based biomarkers for CAFs have been reported to be limited in their specificity, rendering difficult the identification of CAFs from normal fibroblasts (NFs) in clinical samples and dampening the development of CAF-targeted therapies to treat cancer. In this study, we propose the mitochondrial RNA and the mitochondrial DNA (mtDNA) common deletion (CD) as novel indicators of CAF identity. We found that cancer-activation correlated with decreased levels of the mtDNA CD, a condition not due to altered mitochondria count or cellular redox state, but potentially linked to the generalized overexpression of mtDNA maintenance genes in CAFs. Decreased mtDNA CD content in CAFs was associated with moderate to strong overexpression of mtDNA-encoded genes and to slightly improved mitochondrial function. We identified similar patterns of upregulation of mtDNA-encoded genes in independent single-cell RNA seq data obtained from squamous cell carcinoma (SCC) patients. By using the identified nucleic acids-based indicators, identification of CAFs from NFs could be improved, leading to potential therapeutic benefits in advancing translational and clinical studies.
MeSH term(s)	Humans ; Cancer-Associated Fibroblasts/pathology ; Carcinoma, Squamous Cell/pathology ; Fibroblasts/pathology ; Skin/pathology ; DNA, Mitochondrial/genetics ; Tumor Microenvironment/genetics
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2024-01-04
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-50213-1
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Article ; Online: Determining Steady-State Kinetics of DNA Polymerase Nucleotide Incorporation.

Gahlon, Hailey L / Sturla, Shana J

Methods in molecular biology (Clifton, N.J.)

2019 Volume 1973, Page(s) 299–311

Abstract: Polymerase enzymes catalyze the replication of DNA by incorporating deoxynucleoside monophosphates (dNMPs) into a primer strand in a 5' to 3' direction. Monitoring kinetic aspects of this catalytic process provides mechanistic information regarding ... ...

Abstract	Polymerase enzymes catalyze the replication of DNA by incorporating deoxynucleoside monophosphates (dNMPs) into a primer strand in a 5' to 3' direction. Monitoring kinetic aspects of this catalytic process provides mechanistic information regarding polymerase-mediated DNA synthesis and the influences of nucleobase structure. For example, a range of polymerases have different capacities to synthesize DNA depending on the structure of the inserted dNMP (natural or synthetic) and also depending on the templating DNA base (modified vs. unmodified). Under steady-state conditions, relative rates depend on the deoxynucleoside triphosphate (dNTP) residence times in the ternary (polymerase-DNA-dNTP) complex. This chapter describes a method to measure steady-state incorporation efficiencies by which polymerase enzymes insert dNMPs into primer-template (P/T) oligonucleotides. The method described involves the use of a primer oligonucleotide 5' radiolabeled with [γ-
MeSH term(s)	DNA Primers/chemistry ; DNA Replication ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; Kinetics ; Nucleotides/chemistry ; Templates, Genetic
Chemical Substances	DNA Primers ; Nucleotides ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2019-04-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9216-4_19
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Article ; Online: A gene-targeted polymerase-mediated strategy to identify O

Aloisi, Claudia M N / Sturla, Shana J / Gahlon, Hailey L

Chemical communications (Cambridge, England)

2019 Volume 55, Issue 27, Page(s) 3895–3898

Abstract: Detecting DNA adducts in cancer genes is important for understanding cancer etiology. This study reports a strategy to identify the mutagenic DNA adduct ... ...

Abstract	Detecting DNA adducts in cancer genes is important for understanding cancer etiology. This study reports a strategy to identify the mutagenic DNA adduct O
Language	English
Publishing date	2019-03-12
Publishing country	England
Document type	Journal Article
ZDB-ID	1472881-3
ISSN	1364-548X ; 1359-7345 ; 0009-241X
ISSN (online)	1364-548X
ISSN	1359-7345 ; 0009-241X
DOI	10.1039/c9cc00278b
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Article ; Online: Hydrogen-Bonding Interactions at the DNA Terminus Promote Extension from Methylguanine Lesions by Human Extender DNA Polymerase ζ.

Räz, Michael H / Sturla, Shana J / Gahlon, Hailey L

Biochemistry

2018 Volume 57, Issue 41, Page(s) 5978–5988

Abstract: Chemically induced DNA lesions can become DNA replication substrates that are bypassed by low-fidelity DNA polymerases. Following nucleotide misinsertion opposite a DNA lesion, the extension step can contribute to preserving such errors and lead to ... ...

Abstract	Chemically induced DNA lesions can become DNA replication substrates that are bypassed by low-fidelity DNA polymerases. Following nucleotide misinsertion opposite a DNA lesion, the extension step can contribute to preserving such errors and lead to genomic instability and cancer. DNA polymerase ζ, a B-family polymerase, is proficient as an extender polymerase that catalyzes elongation; however, the chemical factors that impact its DNA replication are not understood. This study addresses the question of how DNA polymerase ζ achieves extension by examining the ability of recombinant human DNA polymerase ζ to extend from a series of methylated guanine lesions. The influence of H-bonding was examined by placing structurally altered nucleoside analogues and canonical bases opposite G, O
MeSH term(s)	Computer Simulation ; DNA/chemistry ; DNA/metabolism ; DNA Repair ; DNA-Directed DNA Polymerase/chemistry ; DNA-Directed DNA Polymerase/metabolism ; Humans ; Methylguanidine/chemistry ; Methylguanidine/metabolism ; Models, Chemical
Chemical Substances	Methylguanidine (5L0H5Q9VAG) ; DNA (9007-49-2) ; DNA polymerase zeta (EC 2.7.7.-) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2018-09-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1108-3
ISSN	1520-4995 ; 0006-2960
ISSN (online)	1520-4995
ISSN	0006-2960
DOI	10.1021/acs.biochem.8b00861
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Article ; Online: Influence of DNA Lesions on Polymerase-Mediated DNA Replication at Single-Molecule Resolution.

Gahlon, Hailey L / Romano, Louis J / Rueda, David

Chemical research in toxicology

2017 Volume 30, Issue 11, Page(s) 1972–1983

Abstract: Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous ... ...

Abstract	Faithful replication of DNA is a critical aspect in maintaining genome integrity. DNA polymerases are responsible for replicating DNA, and high-fidelity polymerases do this rapidly and at low error rates. Upon exposure to exogenous or endogenous substances, DNA can become damaged and this can alter the speed and fidelity of a DNA polymerase. In this instance, DNA polymerases are confronted with an obstacle that can result in genomic instability during replication, for example, by nucleotide misinsertion or replication fork collapse. It is important to know how DNA polymerases respond to damaged DNA substrates to understand the mechanism of mutagenesis and chemical carcinogenesis. Single-molecule techniques have helped to improve our current understanding of DNA polymerase-mediated DNA replication, as they enable the dissection of mechanistic details that can otherwise be lost in ensemble-averaged experiments. These techniques have also been used to gain a deeper understanding of how single DNA polymerases behave at the site of the damage in a DNA substrate. In this review, we evaluate single-molecule studies that have examined the interaction between DNA polymerases and damaged sites on a DNA template.
MeSH term(s)	Animals ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; DNA Damage ; DNA Repair ; DNA Replication ; DNA-Directed DNA Polymerase/metabolism ; Humans ; Models, Molecular ; Optical Tweezers ; Spectrometry, Fluorescence/methods
Chemical Substances	DNA (9007-49-2) ; DNA-Directed DNA Polymerase (EC 2.7.7.7)
Language	English
Publishing date	2017-10-23
Publishing country	United States
Document type	Journal Article ; Review ; Research Support, Non-U.S. Gov't
ZDB-ID	639353-6
ISSN	1520-5010 ; 0893-228X
ISSN (online)	1520-5010
ISSN	0893-228X
DOI	10.1021/acs.chemrestox.7b00224
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