ArticleNucleic acids research2022
High-affinity binding at quadruplex-duplex junctions: rather the rule than the exception.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Structural insights into the binding of CX-5461 and MTR-106 to G-quadruplex DNA.Nucleic acids research · 2026Article
- In Search of the Most Significant Potential G-Quadruplexes in SARS-CoV-2 RNA: Genomic Analysis.Viruses · 2026Article
- Structural basis of bis-quinolinium ligands binding to quadruplex-duplex hybrids from PIM1 oncogene.Nucleic acids research · 2025Article
- Bridged Azobenzene Exhibits Fully Reversible Photocontrolled Binding to a G‑Quadruplex DNA/Duplex Junction.JACS Au · 2025Article
- Targeting the G-quadruplex as a novel strategy for developing antibiotics against hypervirulent drug-resistant Staphylococcus aureus.Journal of biomedical science · 2025Article
- Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Structural elucidation of HIV-1 G-quadruplexes in a cellular environment and their ligand binding using responsiveChemical science · 2024Article
- Base pair dynamics, electrostatics, and thermodynamics at the LTR-III quadruplex:duplex junction.Biophysical journal · 2024Article
- Quadruplex-duplex junction in LTR-III: A molecular insight into the complexes with BMH-21, namitecan and doxorubicin.PloS one · 2024Article
- Steric hindrance and structural flexibility shape the functional properties of a guanine-rich oligonucleotide.Nucleic acids research · 2023Article
- WebTetrado: a webserver to explore quadruplexes in nucleic acid 3D structures.Nucleic acids research · 2023Article
- Probing juxtaposed G-quadruplex and hairpin motifs using a responsive nucleoside probe: a unique scaffold for chemotherapy.Chemical science · 2023Article
- Taq-Polymerase Stop Assay to Determine Target Selectivity of G4 Ligands in Native Promoter Sequences ofPharmaceuticals (Basel, Switzerland) · 2023Article
- The Potent G-Quadruplex-Binding Compound QN-302 Downregulates S100P Gene Expression in Cells and in an In Vivo Model of Pancreatic Cancer.Molecules (Basel, Switzerland) · 2023Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Quadruplex-duplex (Q-D) junctions constitute unique structural motifs in genomic sequences. Through comprehensive calorimetric as well as high-resolution NMR structural studies, Q-D junctions with a hairpin-type snapback loop coaxially stacked onto an outer G-tetrad were identified to be most effective binding sites for various polycyclic quadruplex ligands. The Q-D interface is readily recognized by intercalation of the ligand aromatic core structure between G-tetrad and the neighboring base pair. Based on the thermodynamic and structural data, guidelines for the design of ligands with enhanced selectivity towards a Q-D interface emerge. Whereas intercalation at Q-D junctions mostly outcompete stacking at the quadruplex free outer tetrad or intercalation between duplex base pairs to varying degrees, ligand side chains considerably contribute to the selectivity for a Q-D target over other binding sites. In contrast to common perceptions, an appended side chain that additionally interacts within the duplex minor groove may confer only poor selectivity. Rather, the Q-D selectivity is suggested to benefit from an extension of the side chain towards the exposed part of the G-tetrad at the junction. The presented results will support the design of selective high-affinity binding ligands for targeting Q-D interfaces in medicinal but also technological applications.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the Socratic graph.