Peter C. Dedon

Indirect mutagenesis by oxidative DNA damage: formation of the pyrimidopurinone adduct of deoxyguanosine by base propenal.

Absence of 2'-deoxyoxanosine and presence of abasic sites in DNA exposed to nitric oxide at controlled physiological concentrations.

Analysis of 3'-phosphoglycolaldehyde residues in oxidized DNA by gas chromatography/negative chemical ionization/mass spectrometry.

Reactive nitrogen species in the chemical biology of inflammation.

Reaction of 2'-deoxyribonucleosides with cis- and trans-1,4-dioxo-2-butene.

5'-(2-phosphoryl-1,4-dioxobutane) as a product of 5'-oxidation of deoxyribose in DNA: elimination as trans-1,4-dioxo-2-butene and approaches to analysis.

Effects of peroxynitrite dose and dose rate on DNA damage and mutation in the supF shuttle vector.

Delineation of the chemical pathways underlying nitric oxide-induced homologous recombination in mammalian cells.

Chemical and biological evidence for base propenals as the major source of the endogenous M1dG adduct in cellular DNA.

Differential oxidation of deoxyribose in DNA by gamma and alpha-particle radiation.

Quantification of DNA strand breaks and abasic sites by oxime derivatization and accelerator mass spectrometry: application to gamma-radiation and peroxynitrite.

Development of enzymatic probes of oxidative and nitrosative DNA damage caused by reactive nitrogen species.

Biological role of glutathione in nitric oxide-induced toxicity in cell culture and animal models.

Relatively small increases in the steady-state levels of nucleobase deamination products in DNA from human TK6 cells exposed to toxic levels of nitric oxide.

Threshold effects of nitric oxide-induced toxicity and cellular responses in wild-type and p53-null human lymphoblastoid cells.

Paradoxical hotspots for guanine oxidation by a chemical mediator of inflammation.

Formation of 1,4-dioxo-2-butene-derived adducts of 2'-deoxyadenosine and 2'-deoxycytidine in oxidized DNA.

Rosuvastatin: an independent analysis of risks and benefits.

The DNA-damage signature in Saccharomyces cerevisiae is associated with single-strand breaks in DNA.

N-formylation of lysine in histone proteins as a secondary modification arising from oxidative DNA damage.

Lipid peroxidation dominates the chemistry of DNA adduct formation in a mouse model of inflammation.

AlkB influences the chloroacetaldehyde-induced mutation spectra and toxicity in the pSP189 supF shuttle vector.

GC/MS methods to quantify the 2-deoxypentos-4-ulose and 3'-phosphoglycolate pathways of 4' oxidation of 2-deoxyribose in DNA: application to DNA damage produced by gamma radiation and bleomycin.

The chemical toxicology of 2-deoxyribose oxidation in DNA.

Oxidation of guanine in G, GG, and GGG sequence contexts by aromatic pyrenyl radical cations and carbonate radical anions: relationship between kinetics and distribution of alkali-labile lesions.

AlkB homologue 2-mediated repair of ethenoadenine lesions in mammalian DNA.

DNA damage induced by chronic inflammation contributes to colon carcinogenesis in mice.

Surveying the damage: the challenges of developing nucleic acid biomarkers of inflammation.

Quantification of DNA damage products resulting from deamination, oxidation and reaction with products of lipid peroxidation by liquid chromatography isotope dilution tandem mass spectrometry.

Kinetic analysis of intracellular concentrations of reactive nitrogen species.

DNA sequence context as a determinant of the quantity and chemistry of guanine oxidation produced by hydroxyl radicals and one-electron oxidants.

Continuous elimination of oxidized nucleotides is necessary to prevent rapid onset of cellular senescence.

An improved method for large-scale preparation of negatively and positively supercoiled plasmid DNA.

A general method for quantifying sequence effects on nucleobase oxidation in DNA.

Recommendations for standardized description of and nomenclature concerning oxidatively damaged nucleobases in DNA.

Human AlkB homolog ABH8 Is a tRNA methyltransferase required for wobble uridine modification and DNA damage survival.

Quantification of the 2-deoxyribonolactone and nucleoside 5'-aldehyde products of 2-deoxyribose oxidation in DNA and cells by isotope-dilution gas chromatography mass spectrometry: differential effects of gamma-radiation and Fe2+-EDTA.

One-electron oxidation of a pyrenyl photosensitizer covalently attached to DNA and competition between its further oxidation and DNA hole injection.

Challenges in developing DNA and RNA biomarkers of inflammation.

A quantitative systems approach reveals dynamic control of tRNA modifications during cellular stress.

The biological and metabolic fates of endogenous DNA damage products.

DNA phosphorothioation is widespread and quantized in bacterial genomes.

Reactive species and DNA damage in chronic inflammation: reconciling chemical mechanisms and biological fates.

Solvent exposure associated with single abasic sites alters the base sequence dependence of oxidation of guanine in DNA in GG sequence contexts.

Identification of N6,N6-dimethyladenosine in transfer RNA from Mycobacterium bovis Bacille Calmette-Guérin.

XRCC1 and base excision repair balance in response to nitric oxide.

Sequence-dependent variation in the reactivity of 8-Oxo-7,8-dihydro-2'-deoxyguanosine toward oxidation.

Biologically relevant oxidants and terminology, classification and nomenclature of oxidatively generated damage to nucleobases and 2-deoxyribose in nucleic acids.

Defects in purine nucleotide metabolism lead to substantial incorporation of xanthine and hypoxanthine into DNA and RNA.

2'-O methylation of internal adenosine by flavivirus NS5 methyltransferase.

Integrated molecular analysis indicates undetectable change in DNA damage in mice after continuous irradiation at ~ 400-fold natural background radiation.

Infection-induced colitis in mice causes dynamic and tissue-specific changes in stress response and DNA damage leading to colon cancer.

A system for exposing molecules and cells to biologically relevant and accurately controlled steady-state concentrations of nitric oxide and oxygen.

Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins.

Translational infidelity-induced protein stress results from a deficiency in Trm9-catalyzed tRNA modifications.

Increased tRNA modification and gene-specific codon usage regulate cell cycle progression during the DNA damage response.

In situ analysis of 8-oxo-7,8-dihydro-2'-deoxyguanosine oxidation reveals sequence- and agent-specific damage spectra.

Comparative analysis of four oxidized guanine lesions from reactions of DNA with peroxynitrite, singlet oxygen, and γ-radiation.

Quantitative analysis of histone modifications: formaldehyde is a source of pathological n(6)-formyllysine that is refractory to histone deacetylases.

Increased levels of inosine in a mouse model of inflammation.

Quantification of cellular poly(ADP-ribosyl)ation by stable isotope dilution mass spectrometry reveals tissue- and drug-dependent stress response dynamics.

An automated Fpg-based FADU method for the detection of oxidative DNA lesions and screening of antioxidants.

Chemical and cytokine features of innate immunity characterize serum and tissue profiles in inflammatory bowel disease.

DNA methylation impacts gene expression and ensures hypoxic survival of Mycobacterium tuberculosis.

A multidimensional platform for the purification of non-coding RNA species.

Chemistry meets biology in colitis-associated carcinogenesis.

Induction of functional human macrophages from bone marrow promonocytes by M-CSF in humanized mice.

Dosimetry of N⁶-formyllysine adducts following [¹³C²H₂]-formaldehyde exposures in rats.

Identification and codon reading properties of 5-cyanomethyl uridine, a new modified nucleoside found in the anticodon wobble position of mutant haloarchaeal isoleucine tRNAs.

A system of RNA modifications and biased codon use controls cellular stress response at the level of translation.

28S rRNA is inducibly pseudouridylated by the mTOR pathway translational control in CHO cell cultures.

Quantitative analysis of ribonucleoside modifications in tRNA by HPLC-coupled mass spectrometry.

Genomic mapping of phosphorothioates reveals partial modification of short consensus sequences.

Pathological phenotypes and in vivo DNA cleavage by unrestrained activity of a phosphorothioate-based restriction system in Salmonella.

tRNA modifications regulate translation during cellular stress.

Diverse cell stresses induce unique patterns of tRNA up- and down-regulation: tRNA-seq for quantifying changes in tRNA copy number.

Mycobacterial RNA isolation optimized for non-coding RNA: high fidelity isolation of 5S rRNA from Mycobacterium bovis BCG reveals novel post-transcriptional processing and a complete spectrum of modified ribonucleosides.

Highly Predictive Reprogramming of tRNA Modifications Is Linked to Selective Expression of Codon-Biased Genes.

Codon-biased translation can be regulated by wobble-base tRNA modification systems during cellular stress responses.

Alkbh8 Regulates Selenocysteine-Protein Expression to Protect against Reactive Oxygen Species Damage.

A Platform for Discovery and Quantification of Modified Ribonucleosides in RNA: Application to Stress-Induced Reprogramming of tRNA Modifications.

Metabolic fate of endogenous molecular damage: Urinary glutathione conjugates of DNA-derived base propenals as markers of inflammation.

An extensive allelic series of Drosophila kae1 mutants reveals diverse and tissue-specific requirements for t6A biogenesis.

Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation.

Novel genomic island modifies DNA with 7-deazaguanine derivatives.

Immunostimulating and Gram-negative-specific antibacterial cyclotides from the butterfly pea (Clitoria ternatea).

Gene- and genome-based analysis of significant codon patterns in yeast, rat and mice genomes with the CUT Codon UTilization tool.

The role of sequence context, nucleotide pool balance and stress in 2'-deoxynucleotide misincorporation in viral, bacterial and mammalian RNA.

Methylation at position 32 of tRNA catalyzed by TrmJ alters oxidative stress response in Pseudomonas aeruginosa.

tRNA-mediated codon-biased translation in mycobacterial hypoxic persistence.

tRNA N6-adenosine threonylcarbamoyltransferase defect due to KAE1/TCS3 (OSGEP) mutation manifest by neurodegeneration and renal tubulopathy.

Production of Superoxide in Bacteria Is Stress- and Cell State-Dependent: A Gating-Optimized Flow Cytometry Method that Minimizes ROS Measurement Artifacts with Fluorescent Dyes.

Convergence of DNA methylation and phosphorothioation epigenetics in bacterial genomes.

Oxidation of phosphorothioate DNA modifications leads to lethal genomic instability.

Three distinct 3-methylcytidine (mC) methyltransferases modify tRNA and mRNA in mice and humans.

The mA pathway facilitates sex determination in Drosophila.

N-Formyllysine as a Biomarker of Formaldehyde Exposure: Formation and Loss of N-Formyllysine in Nasal Epithelium in Long-Term, Low-Dose Inhalation Studies in Rats.

The tA modification acts as a positive determinant for the anticodon nuclease PrrC, and is distinctively nonessential in Streptococcus mutans.

Mutations in KEOPS-complex genes cause nephrotic syndrome with primary microcephaly.

Allosteric pyruvate kinase-based "logic gate" synergistically senses energy and sugar levels in Mycobacterium tuberculosis.

Transfer RNA Induces IL-12p70 via Synergistic Activation of Pattern Recognition Receptors within a Cell Network.

Phosphorylation of human TRM9L integrates multiple stress-signaling pathways for tumor growth suppression.

Identification of the minimal bacterial 2'-deoxy-7-amido-7-deazaguanine synthesis machinery.

Aristolochic Acids as Persistent Soil Pollutants: Determination of Risk for Human Exposure and Nephropathy from Plant Uptake.

tRNA epitranscriptomics and biased codon are linked to proteome expression in .

DNA phosphorothioate modification-a new multi-functional epigenetic system in bacteria.

Backbone resonance assignment for the N-terminal region of bacterial tRNA-(NG37) methyltransferase.

A Proteomics Approach to Profiling the Temporal Translational Response to Stress and Growth.

Lifestyle modifications: coordinating the tRNA epitranscriptome with codon bias to adapt translation during stress responses.

The Versatile Roles of the tRNA Epitranscriptome during Cellular Responses to Toxic Exposures and Environmental Stress.

Backbone resonance assignment for the full length tRNA-(NG37) methyltransferase of Pseudomonas aeruginosa.

The road less traveled: A new phosphorothioate antiviral defense mechanism discovered in Archaea.

Pyruvate Kinase Regulates the Pentose-Phosphate Pathway in Response to Hypoxia in Mycobacterium tuberculosis.

Transcriptome-wide dynamics of extensive mA mRNA methylation during Plasmodium falciparum blood-stage development.

Crystal structure and catalytic mechanism of the essential mG37 tRNA methyltransferase TrmD from .

Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.

Discovery of novel bacterial queuine salvage enzymes and pathways in human pathogens.

Quantifying the RNA cap epitranscriptome reveals novel caps in cellular and viral RNA.

Discovery of a new predominant cytosine DNA modification that is linked to gene expression in malaria parasites.

7-Deazaguanine modifications protect phage DNA from host restriction systems.

Irp2 regulates insulin production through iron-mediated Cdkal1-catalyzed tRNA modification.

Loss of Elongator- and KEOPS-Dependent tRNA Modifications Leads to Severe Growth Phenotypes and Protein Aggregation in Yeast.

SspABCD-SspE is a phosphorothioation-sensing bacterial defence system with broad anti-phage activities.

The epitranscriptomic writer ALKBH8 drives tolerance and protects mouse lungs from the environmental pollutant naphthalene.

Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage.

Epigenetic competition reveals density-dependent regulation and target site plasticity of phosphorothioate epigenetics in bacteria.

DNA Phosphorothioate Modifications Are Widely Distributed in the Human Microbiome.

Exploring the virulence gene interactome with CRISPR/dCas9 in the human malaria parasite.

Pyruvate kinase from Plasmodium falciparum: Structural and kinetic insights into the allosteric mechanism.

Crystal structure of the periplasmic sensor domain of histidine kinase VbrK suggests indirect sensing of β-lactam antibiotics.

tRNA-modifying enzyme mutations induce codon-specific mistranslation and protein aggregation in yeast.

Detection of preQ0 deazaguanine modifications in bacteriophage CAjan DNA using Nanopore sequencing reveals same hypermodification at two distinct DNA motifs.

Illuminating Host-Mycobacterial Interactions with Genome-wide CRISPR Knockout and CRISPRi Screens.

Development of Methods Derived from Iodine-Induced Specific Cleavage for Identification and Quantitation of DNA Phosphorothioate Modifications.

Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator.

Quantitative mapping of the cellular small RNA landscape with AQRNA-seq.

Functional Characterization of the mA-Dependent Translational Modulator PfYTH.2 in the Human Malaria Parasite.

Detecting the epitranscriptome.

Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA.

Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses.

Crystal structure and functional analysis of mycobacterial erythromycin resistance methyltransferase Erm38 reveals its RNA-binding site.

Nanopore Sequencing for Detection and Characterization of Phosphorothioate Modifications in Native DNA Sequences.

Queuine Salvaging in the Human Parasite .

The absence of the queuosine tRNA modification leads to pleiotropic phenotypes revealing perturbations of metal and oxidative stress homeostasis in Escherichia coli K12.

Arsenite toxicity is regulated by queuine availability and oxidation-induced reprogramming of the human tRNA epitranscriptome.

Dysfunctional tRNA reprogramming and codon-biased translation in cancer.

DNA Modifications Enabling Proximity Biotinylation.

Accumulation of mA exhibits stronger correlation with MAPT than β-amyloid pathology in an APP /MAPT mouse model of Alzheimer's disease.

Rifaximin potentiates clarithromycin against and in zebrafish.

Accumulation of mA exhibits stronger correlation with MAPT than β-amyloid pathology in an APP /MAPT mouse model of Alzheimer's disease.

An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis.

A systems-level mass spectrometry-based technique for accurate and sensitive quantification of the RNA cap epitranscriptome.

Four additional natural 7-deazaguanine derivatives in phages and how to make them.

Cohesin contributes to transcriptional repression of stage-specific genes in the human malaria parasite.

Nanopore-based direct sequencing of RNA transcripts with 10 different modified nucleotides reveals gaps in existing technology.

Discovery adductomics provides a comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans.

Dengue virus exploits the host tRNA epitranscriptome to promote viral replication.

Molecular Coping Mechanisms: Reprogramming tRNAs To Regulate Codon-Biased Translation of Stress Response Proteins.

The Greatwall-Endosulfine-PP2A/B55 pathway controls entry into quiescence by promoting translation of Elongator-tuneable transcripts.

Queuosine Salvage in Houston 1: A Unique Evolutionary Path.