keyword
https://read.qxmd.com/read/38512075/comprehensive-analysis-of-intramolecular-g-quadruplex-structures-furthering-the-understanding-of-their-formalism
#21
JOURNAL ARTICLE
Marc Farag, Liliane Mouawad
G-quadruplexes (G4) are helical structures found in guanine-rich DNA or RNA sequences. Generally, their formalism is based on a few dozen structures, which can produce some inconsistencies or incompleteness. Using the website ASC-G4, we analyzed the structures of 333 intramolecular G4s, of all types, which allowed us to clarify some key concepts and present new information. To each of the eight distinguishable topologies corresponds a groove-width signature and a predominant glycosidic configuration (gc) pattern governed by the directions of the strands...
March 21, 2024: Nucleic Acids Research
https://read.qxmd.com/read/38509417/potential-protein-kinase-inhibitors-that-target-g-quadruplex-dna-structures-in-the-human-telomeric-regions
#22
JOURNAL ARTICLE
Bhavya Banjan, Abel John Koshy, Haritha Kalath, Levin John, Sowmya Soman, Rajesh Raju, Amjesh Revikumar
Telomeric regions contain Guanine-rich sequences arranged in a planar manner and connected by Hoogsteen hydrogen bonds that can fold into G-quadruplex (G4) DNA structures, and can be stabilized by monovalent metal cations. The presence of G4 DNA holds significance in cancer-related processes, especially due to their regulatory potential at transcriptional and translational levels of oncogene and tumor suppressor genes. The objective of this current research is to explore the evolving realm of FDA-approved protein kinase inhibitors, with a specific emphasis on their capacity to stabilize the G4 DNA structures formed at the human telomeric regions...
March 21, 2024: Molecular Diversity
https://read.qxmd.com/read/38505840/selective-recognition-of-c-kit-1-g-quadruplex-by-structural-tuning-of-heteroaromatic-scaffolds-and-side-chains
#23
JOURNAL ARTICLE
Khushnood Fatma, Prasanth Thumpati, Deepanjan Panda, Ravichandiran Velayutham, Jyotirmayee Dash
In this study, carbazole ( MC ) and dibenzofuran ( MD ) derivatives were synthesized to examine their effect on the biomolecular recognition of G-quadruplex (G4) targets. Biophysical studies revealed that MC-4 , a carbazole derivative, exhibits a specific affinity and effectively stabilizes the c-KIT 1 G4. Molecular modeling suggests a stable interaction of MC-4 with the terminal G-tetrad of c-KIT 1 G4. Biological studies demonstrate that MC-4 efficiently enters cells, reduces c-KIT gene expression, and induces cell cycle arrest, DNA damage, and apoptosis in cancer cells...
March 14, 2024: ACS Medicinal Chemistry Letters
https://read.qxmd.com/read/38499428/colorimetric-and-fluorescent-independent-dual-signal-on-biosensor-for-accurate-detection-of-ochratoxin-a-based-on-aptamer-triggered-biocatalytic-reactions
#24
JOURNAL ARTICLE
Hao Ding, Mingdi Zhang, Xiaochun Wang, Shuai He, Xiaokun Wang, Lingxin Chen
Ochratoxin A (OTA) is a hazardous food contaminant with significant health risks. Dual-channel OTA detection is noted for its cross-reference capability and high accuracy. Still, challenges in addressing in-system corrections and "signal off" related false positives and limited signal gains remain. Herein, we developed a dual-channel "signal on" aptasensor with one recognition process and two independent signal outputs for OTA analysis. The OTA aptamer binds to magnetic beads (MBs) and partially hybridizes with a complementary-trigger (cDNA-Trigger) sequence...
April 22, 2024: Analytica Chimica Acta
https://read.qxmd.com/read/38499092/a-supramolecular-hydrogel-dressing-with-antibacterial-immunoregulation-and-pro-regeneration-ability-for-biofilm-associated-wound-healing
#25
JOURNAL ARTICLE
Yumeng Wang, Xinghong Zhao, Xingjian Zhou, Juqin Dai, Xiaowen Hu, Yinzi Piao, Guangyue Zu, Jian Xiao, Keqing Shi, Yong Liu, Yuanfeng Li, Linqi Shi
Chronic wound treatment has emerged as a significant healthcare concern worldwide due to its substantial economic burden and the limited effectiveness of current treatments. Effective management of biofilm infections, regulation of excessive oxidative stress, and promotion of tissue regeneration are crucial for addressing chronic wounds. Hydrogel stands out as a promising candidate for chronic wound treatment. However, its clinical application is hindered by the difficulty in designing and fabricating easily and conveniently...
March 16, 2024: Journal of Controlled Release
https://read.qxmd.com/read/38498910/development-of-a-pseudocellular-system-to-quantify-specific-interactions-determining-the-g-quadruplex-function-in-cells
#26
JOURNAL ARTICLE
Hisae Tateishi-Karimata, Keiko Kawauchi, Shuntaro Takahashi, Naoki Sugimoto
Intracellular chemical microenvironments, including ion concentrations and molecular crowding, play pivotal roles in cell behaviors, such as proliferation, differentiation, and cell death via regulation of gene expression. However, there is no method for quantitative analysis of intracellular environments due to their complexity. Here, we have developed a system for highlighting the environment inside of the cell (SHELL). SHELL is a pseudocellular system, wherein small molecules are removed from the cell and a crowded intracellular environment is maintained...
March 18, 2024: Journal of the American Chemical Society
https://read.qxmd.com/read/38497675/a-ph-responsive-topological-switch-based-on-a-dna-quadruplex-duplex-hybrid
#27
JOURNAL ARTICLE
Yoanes Maria Vianney, Jagannath Jana, Klaus Weisz
A guanine-rich oligonucleotide based on a human telomeric sequence but with the first three-nucleotide intervening stretch replaced by a putative 15-nucleotide hairpin-forming sequence shows a pH-dependent folding into different quadruplex-duplex hybrids in a potassium containing buffer. At slightly acidic pH, the quadruplex domain adopts a chair-type conformation. Upon increasing the pH, a transition with a midpoint close to neutral pH to a major and minor (3+1) hybrid topology with either a coaxially stacked or orthogonally oriented duplex stem-loop occurs...
March 18, 2024: Chemistry: a European Journal
https://read.qxmd.com/read/38492541/inhibition-of-cancer-cells-by-quinoline-based-compounds-a-review-with-mechanistic-insights
#28
REVIEW
Anjali Saxena, Suman Majee, Devalina Ray, Biswajit Saha
This article includes a thorough examination of the inhibitory potential of quinoline-based drugs on cancer cells, as well as an explanation of their modes of action. Quinoline derivatives, due to their various chemical structures and biological activity, have emerged as interesting candidates in the search for new anticancer drugs. The review paper delves into the numerous effects of quinoline-based chemicals in cancer progression, including apoptosis induction, cell cycle modification, and interference with tumor-growth signaling pathways...
March 12, 2024: Bioorganic & Medicinal Chemistry
https://read.qxmd.com/read/38484151/g-quadruplex-landscape-and-its-regulation-revealed-by-a-new-antibody-capture-method
#29
JOURNAL ARTICLE
Subhamoy Datta, Manthan Patel, Chakkarai Sathyaseelan, Chandrama Ghosh, Akanksha Mudgal, Divyesh Patel, Thenmalarchelvi Rathinavelan, Umashankar Singh
Our understanding of DNA G-quadruplexes (G4s) from in vitro studies has been complemented by genome-wide G4 landscapes from cultured cells. Conventionally, the formation of G4s is accepted to depend on G-repeats such that they form tetrads. However, genome-wide G4s characterized through high-throughput sequencing suggest that these structures form at a large number of regions with no such canonical G4-forming signatures. Many G4-binding proteins have been described with no evidence for any protein that binds to and stabilizes G4s...
March 14, 2024: Oncotarget
https://read.qxmd.com/read/38482213/prediction-and-validation-of-circulating-g-quadruplexes-as-a-novel-biomarker-in-colorectal-cancer
#30
JOURNAL ARTICLE
Hui Zhang, Jing Zhou, Yingjiang Ye
BACKGROUND: There are some problems in the clinical diagnosis of colorectal cancer (CRC), such as the difficulty in saving samples, so it is the most popular research work to develop a diagnostic index and method that is easy to obtain, convenient to save and stable. G-quadruplex (G4) is a unique structure found in DNA and it plays a crucial biological role in tumor formation. G4 is derived from DNA with good stability, and the DNA of serum samples is easy to obtain. Therefore, G4 has the potential as an ideal marker for CRC diagnosis...
February 29, 2024: Journal of Gastrointestinal Oncology
https://read.qxmd.com/read/38481135/structural-motifs-at-the-telomeres-and-their-role-in-regulatory-pathways
#31
REVIEW
Abeer F R Alanazi, Gary N Parkinson, Shozeb Haider
Telomeres are specialized structures, found at the ends of linear chromosomes in eukaryotic cells, that play a crucial role in maintaining the stability and integrity of genomes. They are composed of repetitive DNA sequences, ssDNA overhangs, and several associated proteins. The length of telomeres is linked to cellular aging in humans, and deficiencies in their maintenance are associated with various diseases. Key structural motifs at the telomeres serve to protect vulnerable chromosomal ends. Telomeric DNA also has the ability to form diverse complex DNA higher-order structures, including T-loops, D-loops, R-loops, G-loops, G-quadruplexes, and i-motifs, in the complementary C-rich strand...
March 14, 2024: Biochemistry
https://read.qxmd.com/read/38477716/why-are-left-handed-g-quadruplexes-scarce
#32
JOURNAL ARTICLE
Michał Jurkowski, Mateusz Kogut, Subrahmanyam Sappati, Jacek Czub
G-quadruplexes (G4s) are nucleic acid structures crucial for the regulation of gene expression and genome maintenance. While they hold promise as nanodevice components, achieving desired G4 folds requires understanding the interplay between stability and structural properties, like helicity. Although right-handed G4 structures dominate the experimental data, the molecular basis for this preference over left-handed helicity is unclear. To address this, we employ all-atom molecular dynamics simulations and quantum chemical methods...
March 13, 2024: Journal of Physical Chemistry Letters
https://read.qxmd.com/read/38477454/structural-differences-at-quadruplex-duplex-interfaces-enable-ligand-induced-topological-transitions
#33
JOURNAL ARTICLE
Yoanes Maria Vianney, Dorothea Dierks, Klaus Weisz
Quadruplex-duplex (QD) junctions, which represent unique structural motifs of both biological and technological significance, have been shown to constitute high-affinity binding sites for various ligands. A QD hybrid construct based on a human telomeric sequence, which harbors a duplex stem-loop in place of a short lateral loop, is structurally characterized by NMR. It folds into two major species with a (3+1) hybrid and a chair-type (2+2) antiparallel quadruplex domain coexisting in a K+ buffer solution. The antiparallel species is stabilized by an unusual capping structure involving a thymine and protonated adenine base AH+ of the lateral loop facing the hairpin duplex to form a T·AH+ ·G·C quartet with the interfacial G·C base pair at neutral pH...
March 13, 2024: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://read.qxmd.com/read/38473730/stabilization-of-g-quadruplex-structures-of-the-sars-cov-2-genome-by-tmpyp4-braco19-and-phendc3
#34
JOURNAL ARTICLE
Miklós Cervenak, Orsolya Réka Molnár, Péter Horváth, László Smeller
The G-quadruplex is one of the non-canonical structures formed by nucleic acids, which can be formed by guanine-rich sequences. They became the focus of much research when they were found in several oncogene promoter regions and also in the telomeres. Later on, they were discovered in viruses as well. Various ligands have been developed in order to stabilize DNA G-quadruplexes, which were believed to have an anti-cancer or antiviral effect. We investigated three of these ligands, and whether they can also affect the stability of the G-quadruplex-forming sequences of the RNA genome of SARS-CoV-2...
February 20, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38471837/insights-into-the-g-quadruplex-dna-interaction-landscape-comparative-analysis-of-anionic-zn-ii-and-co-ii-phthalocyanine-tetrasulfonate-complexes
#35
JOURNAL ARTICLE
Efkan Bağda
G-quadruplexes play a pivotal role in regulating various cellular processes, including gene expression and replication, making them essential structures in understanding, and manipulating cellular functions. The development of G-quadruplex ligands holds significant promise in therapeutic and research applications, offering targeted tools to modulate G-quadruplex structures and potentially influence critical biological pathways. An exciting frontier in G-quadruplex research lies in the exploration of anionic ligands, and their profound impact on stabilizing and modulating G-quadruplex DNA...
March 12, 2024: Journal of Molecular Recognition: JMR
https://read.qxmd.com/read/38461301/terra-lsd1-phase-separation-promotes-r-loop-formation-for-telomere-maintenance-in-alt-cancer-cells
#36
JOURNAL ARTICLE
Meng Xu, Dulmi Senanayaka, Rongwei Zhao, Tafadzwa Chigumira, Astha Tripathi, Jason Tones, Rachel M Lackner, Anne R Wondisford, Laurel N Moneysmith, Alexander Hirschi, Sara Craig, Sahar Alishiri, Roderick J O'Sullivan, David M Chenoweth, Nicholas J Reiter, Huaiying Zhang
The telomere repeat-containing RNA (TERRA) forms R-loops to promote homology-directed DNA synthesis in the alternative lengthening of telomere (ALT) pathway. Here we report that TERRA contributes to ALT via interacting with the lysine-specific demethylase 1A (LSD1 or KDM1A). We show that LSD1 localizes to ALT telomeres in a TERRA dependent manner and LSD1 function in ALT is largely independent of its demethylase activity. Instead, LSD1 promotes TERRA recruitment to ALT telomeres via RNA binding. In addition, LSD1 and TERRA undergo phase separation, driven by interactions between the RNA binding properties of LSD1 and the G-quadruplex structure of TERRA...
March 9, 2024: Nature Communications
https://read.qxmd.com/read/38456425/negative-electron-transfer-collision-induced-dissociation-of-g-quadruplexes-uncovering-the-guanine-radical-anion-loss-pathway
#37
JOURNAL ARTICLE
Nicole M Brundridge, Jordan M Fritz, Jonathan Dickerhoff, Danzhou Yang, Scott A McLuckey
G-quadruplex (G4) DNA can form highly stable secondary structures in the presence of metal cations, and research has shown its potential as a transcriptional regulator for oncogenes in the human genome. In order to explore the interactions of DNA with metal cations using mass spectrometry, employing complementary fragmentation methods can enhance structural information. This study explores the use of ion-ion reactions for sequential negative electron transfer collision-induced dissociation (nET-CID) as a complement to traditional ion-trap CID (IT-CID)...
March 8, 2024: Journal of the American Society for Mass Spectrometry
https://read.qxmd.com/read/38456368/synthetic-peptides-promising-modalities-for-the-targeting-of-disease-related-nucleic-acids
#38
JOURNAL ARTICLE
Brecht Ellenbroek, Jan Pascal Kahler, Sophie R Evers, Sebastian J Pomplun
DNA and RNA play pivotal roles in life processes by storing and transferring genetic information, modulating gene expression, and contributing to essential cellular machinery such as ribosomes. Dysregulation and mutations in nucleic acid-related processes are implicated in numerous diseases. Despite the critical impact on health of nucleic acid mutations or dysregulation, therapeutic compounds addressing these biomolecules remain limited. Peptides have emerged as a promising class of molecules for biomedical research, offering potential solutions for challenging drug targets...
March 8, 2024: Angewandte Chemie
https://read.qxmd.com/read/38454599/hydration-water-drives-the-self-assembly-of-guanosine-monophosphate
#39
JOURNAL ARTICLE
Yu Heng Tao, Simon Schulke, Gerhard Schwaab, Gareth L Nealon, Simone Pezzotti, Stuart I Hodgetts, Alan R Harvey, Vincent P Wallace, Martina Havenith
Guanosine monophosphate (GMP) is a nucleotide that can self-assemble in aqueous solution under certain conditions. An understanding of the process at the molecular level is an essential step to comprehend the involvement of DNA substructures in transcription and replication, as well as their relationship to genetic diseases, such as cancer. We present the temperature-dependent terahertz (1.5-12 THz, 50-400 cm-1 ) absorptivity spectra of aqueous Na2 GMP solution (GMP) in comparison with the aqueous solutions of other RNA nucleotides...
March 7, 2024: Biophysical Journal
https://read.qxmd.com/read/38452213/dna-fragility-at-topologically-associated-domain-boundaries-is-promoted-by-alternative-dna-secondary-structure-and-topoisomerase-ii-activity
#40
JOURNAL ARTICLE
Heather M Raimer Young, Pei-Chi Hou, Anna R Bartosik, Naomi D Atkin, Lixin Wang, Zhenjia Wang, Aakrosh Ratan, Chongzhi Zang, Yuh-Hwa Wang
CCCTC-binding factor (CTCF) binding sites are hotspots of genome instability. Although many factors have been associated with CTCF binding site fragility, no study has integrated all fragility-related factors to understand the mechanism(s) of how they work together. Using an unbiased, genome-wide approach, we found that DNA double-strand breaks (DSBs) are enriched at strong, but not weak, CTCF binding sites in five human cell types. Energetically favorable alternative DNA secondary structures underlie strong CTCF binding sites...
March 7, 2024: Nucleic Acids Research
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