4.0 Article

Promoters vs. telomeres: AP-endonuclease 1 interactions with abasic sites in G-quadruplex folds depend on topology

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Telomeric 8-oxo-guanine drives rapid premature senescence in the absence of telomere shortening

Ryan P. Barnes et al.

Summary: This study reveals how oxidative stress induces significant cellular aging by generating oxidative damage at telomeres. The mechanism through which oxidative damage triggers cellular senescence is not through telomere shortening, but through inducing telomere fragility, leading to accelerated cellular aging.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2022)

Review Chemistry, Multidisciplinary

G-quadruplex DNA: A Longer Story

Robert C. Monsen et al.

Summary: G-quadruplexes (G4s) are unique four-stranded DNA or RNA structures found within cells, which are involved in gene regulation, transcription, recombination, and DNA damage/repair. Unimolecular G4 structures are the most common form and are highly conserved and specifically located in genomes. G4 structures are composed of guanine tetrads and loop sequences connecting the guanine bases. In longer sequences, adjacent G4 units can combine to form more complex multimeric G4 structures. Using an integrated structural biology approach, researchers have discovered the diversity of multimeric G4 structures.

ACCOUNTS OF CHEMICAL RESEARCH (2022)

Review Chemistry, Multidisciplinary

DNA G-Quadruplex in Human Telomeres and Oncogene Promoters: Structures, Functions, and Small Molecule Targeting

Luying Chen et al.

Summary: DNA G-quadruplexes formed in human telomeres and oncogene promoters are functionally important and have emerged as a promising class of cancer-specific drug targets. In this article, the authors discuss their efforts to understand the structures and functions of these DNA G-quadruplexes and their interactions with small molecules. They have determined the high-resolution structures of telomeric G-quadruplexes and studied G-quadruplexes formed in key oncogene promoters. The authors also highlight the potential of G-quadruplexes as selectively targetable drug receptors and discuss their recent discoveries of small molecules that specifically recognize these G-quadruplexes. Overall, this work provides a strong foundation for future research on G-quadruplexes and the design of G-quadruplex-targeted drugs.

ACCOUNTS OF CHEMICAL RESEARCH (2022)

Article Biochemistry & Molecular Biology

Cysteine Oxidation to Sulfenic Acid in APE1 Aids G-Quadruplex Binding While Compromising DNA Repair

Shereen A. Howpay Manage et al.

Summary: This study provides a quantitative survey of cysteine oxidation to sulfenic acid in APE1 and demonstrates how this modification affects APE1's function towards the NEIL3 gene promoter G4. The research suggests that cysteine oxidation to sulfenic acid enhances APE1's affinity for G4 during oxidative stress, but attenuates its endonuclease activity.

ACS CHEMICAL BIOLOGY (2022)

Article Chemistry, Analytical

Second Harmonic Generation Interrogation of the Endonuclease APE1 Binding Interaction with G-Quadruplex DNA

Aaron M. Fleming et al.

Summary: This study used SHG to measure the binding interaction between the DNA repair enzyme APE1 and the VEGF promoter G4 folds with AP sites, demonstrating that the interaction is ordered and specific. This resolves the question of how APE1 engages G4 folds with gene regulatory features.

ANALYTICAL CHEMISTRY (2022)

Review Biochemistry & Molecular Biology

The Relevance of G-Quadruplexes for DNA Repair

Rebecca Linke et al.

Summary: In summary, G-quadruplex DNA structures play important roles in cellular function, but can also induce genome instability leading to tumorigenesis and genetic disorders. By interacting with DNA repair proteins and ligands, G4 structures can block specific DNA repair pathways.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Biochemistry & Molecular Biology

Genome-wide analysis of 8-oxo-7,8-dihydro-2′-deoxyguanosine at single-nucleotide resolution unveils reduced occurrence of oxidative damage at G-quadruplex sites

Jiao An et al.

Summary: A method called CLAPS-seq was developed to accurately map the distribution of OGs in the genome. The study revealed decreased occurrence of OGs in G-quadruplexes and in promoters with high GC content. Additionally, potential quadruplex sequences were identified as hotspots of OGs, suggesting a role of non-G4 quadruplex sequences in the oxidative stress response mediated by OG.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

DNA G-quadruplex structures: more than simple roadblocks to transcription?

Jenna Robinson et al.

Summary: The relationship between G-quadruplex (G4) secondary structures in gene promoters and gene expression regulation has been studied for over 20 years. While originally thought to act as transcriptional repressors, recent research has challenged this simplistic model by suggesting that G4 formation can alter gene expression at various levels, serving as key regulatory elements disrupting epigenetic marks and chromatin architecture.

NUCLEIC ACIDS RESEARCH (2021)

Article Biochemistry & Molecular Biology

Binding of AP Endonuclease-1 to G-Quadruplex DNA Depends on the N-Terminal Domain, Mg2+, and Ionic Strength

Aaron M. Fleming et al.

Summary: APE1, a base excision repair enzyme, is involved in transcriptional regulation by binding to promoter G-quadruplex structures with abasic sites, leading to recruitment of activating transcription factors. This study found that APE1's binding and cleavage activity on VEGF promoter G4 structures is dependent on cation concentrations and the N-terminal domain of the protein. Furthermore, APE1 can remodel F-containing VEGF promoter DNA structures and is inhibited by the G4 ligand pyridostatin.

ACS BIO & MED CHEM AU (2021)

Article Biotechnology & Applied Microbiology

G-quadruplexes are transcription factor binding hubs in human chromatin

Jochen Spiegel et al.

Summary: This study reveals the important role of DNA secondary structures in transcription factor binding, with G-quadruplex secondary structures being prevalent binding sites for many transcription factors in human chromatin, promoting increased transcription of genes.

GENOME BIOLOGY (2021)

Article Biochemistry & Molecular Biology

Genome-Wide Mapping of Oxidative DNA Damage via Engineering of 8-Oxoguanine DNA Glycosylase

Yuxin Fang et al.

BIOCHEMISTRY (2020)

Review Chemistry, Multidisciplinary

Interplay of Guanine Oxidation and G-Quadruplex Folding in Gene Promoters

Aaron M. Fleming et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2020)

Article Multidisciplinary Sciences

Endogenous oxidized DNA bases and APE1 regulate the formation of G-quadruplex structures in the genome

Shrabasti Roychoudhury et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)

Article Cell Biology

Activity of Human Apurinic/Apyrimidinic Endonuclease APE1 Toward Damaged DNA and Native RNA With Non-canonical Structures

Anastasia T. Davletgildeeva et al.

FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY (2020)

Review Chemistry, Multidisciplinary

On the irrelevancy of hydroxyl radical to DNA damage from oxidative stress and implications for epigenetics

Aaron M. Fleming et al.

CHEMICAL SOCIETY REVIEWS (2020)

Article Biochemistry & Molecular Biology

Generation of 8-oxo-7,8-dihydroguanine in G-Quadruplexes Models of Human Telomere Sequences by One-electron Oxidation

Tomasz J. Merta et al.

PHOTOCHEMISTRY AND PHOTOBIOLOGY (2019)

Article Biochemistry & Molecular Biology

Location dependence of the transcriptional response of a potential G-quadruplex in gene promoters under oxidative stress

Aaron M. Fleming et al.

NUCLEIC ACIDS RESEARCH (2019)

Article Chemistry, Multidisciplinary

Human NEIL3 Gene Expression Regulated by Epigenetic-Like Oxidative DNA Modification

Aaron M. Fleming et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Review Chemistry, Multidisciplinary

DNA Quadruple Helices in Nanotechnology

Jean-Louis Mergny et al.

CHEMICAL REVIEWS (2019)

Article Biochemistry & Molecular Biology

The regulatory G4 motif of the Kirsten ras (KRAS) gene is sensitive to guanine oxidation: implications on transcription

Susanna Cogoi et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Chemistry, Multidisciplinary

G-Quadruplex Secondary Structure Obtained from Circular Dichroism Spectroscopy

Rafael del Villar-Guerra et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2018)

Article Chemistry, Multidisciplinary

Nucleotide-Resolution Genome-Wide Mapping of Oxidative DNA Damage by Click-Code-Seq

Junzhou Wu et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2018)

Article Biochemistry & Molecular Biology

DNA G-quadruplex structures mold the DNA methylome

Shi-Qing Mao et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2018)

Review Biochemistry & Molecular Biology

Zinc Finger Readers of Methylated DNA

Nicholas O. Hudson et al.

MOLECULES (2018)

Article Biotechnology & Applied Microbiology

Genomic landscape of oxidative DNA damage and repair reveals regioselective protection from mutagenesis

Anna R. Poetsch et al.

GENOME BIOLOGY (2018)

Article Chemistry, Multidisciplinary

Sequencing the Mouse Genome for the Oxidatively Modified Base 8-Oxo-7,8-dihydroguanine by OG-Seq

Yun Ding et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Article Multidisciplinary Sciences

Oxidative DNA damage is epigenetic by regulating gene transcription via base excision repair

Aaron M. Fleming et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Chemistry, Multidisciplinary

Sequencing of DNA Lesions Facilitated by Site-Specific Excision via Base Excision Repair DNA Glycosylases Yielding Ligatable Gaps

Jan Riedl et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2016)

Review Chemistry, Multidisciplinary

Metal Cations in G-Quadruplex Folding and Stability

Debmalya Bhattacharyya et al.

FRONTIERS IN CHEMISTRY (2016)

Article Biochemistry & Molecular Biology

The NEIL glycosylases remove oxidized guanine lesions from telomeric and promoter quadruplex DNA structures

Jia Zhou et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Cell Biology

SIRT1 gene expression upon genotoxic damage is regulated by APE1 through nCaRE-promoter elements

Giulia Antoniali et al.

MOLECULAR BIOLOGY OF THE CELL (2014)

Article Biochemistry & Molecular Biology

Human AP endonuclease inefficiently removes abasic sites within G4 structures compared to duplex DNA

Christopher Broxson et al.

NUCLEIC ACIDS RESEARCH (2014)

Review Biochemistry & Molecular Biology

The Intertwined Roles of Transcription and Repair Proteins

Yick W. Fong et al.

MOLECULAR CELL (2013)

Article Biochemistry & Molecular Biology

Promoter G-quadruplex sequences are targets for base oxidation and strand cleavage during hypoxia-induced transcription

David W. Clark et al.

FREE RADICAL BIOLOGY AND MEDICINE (2012)

Review Chemistry, Multidisciplinary

Mechanisms for DNA Charge Transport

Joseph C. Genereux et al.

CHEMICAL REVIEWS (2010)

Article Biochemistry & Molecular Biology

Structure of two intramolecular G-quadruplexes formed by natural human telomere sequences in K+ solution

Anh Tuan Phan et al.

NUCLEIC ACIDS RESEARCH (2007)

Review Multidisciplinary Sciences

Base-excision repair of oxidative DNA damage

Sheila S. David et al.

NATURE (2007)