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Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: 31 August 2025 | Viewed by 535

Special Issue Editors

Special Issue Information

Dear Colleagues,

G-quadruplexes (G4s) are one of the more stable alternative conformations that nucleic acids can adopt. G-rich nucleic acid sequences are inclined to form four-stranded structures, whose constitutive unit is the G-tetrad, a square planar arrangement of four guanosines stabilized by Hoogsteen hydrogen bonds. G4s possess a remarkable structural variability, depending on strand molecularity or arrangement, presence and type of loops, glycosidic conformation of G-residues, and groove size. The G4 biological importance is attested by their occurrence in several regions of the human genome, such as telomeres and gene promoters. In addition to endogenous G4s playing a key role in numerous biological processes, very promising exogenous G4s are known, due to their ability to modulate the activity of different protein targets. Indeed, a significant number of synthetic oligonucleotides, selected by the combinatorial technique SELEX (Systematic Evolution of Ligands by EXponential enrichment) adopt G4 structures (G4 aptamers). The notable thermal stability and structural variability of G4s constitute a valuable resource to design new aptamers with several applications in therapeutics, diagnostics, food quality control, drug development and delivery. Furthermore, suitable G4s are also endowed with catalytic properties and have proven to be able to induce enantioselectivity in several asymmetric reactions. This Special Issue aims to collect a selection of papers focused on advances in the field of G-quadruplexes, aptamers and relationships between their structural features and functionalities.

Dr. Antonella Virgilio
Dr. Veronica Esposito
Prof. Dr. Aldo Galeone
Guest Editors

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Keywords

  • G-quadruplex structure
  • aptamer
  • DNAzyme
  • catalytic G-quadruplexes

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Published Papers (1 paper)

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Research

19 pages, 6213 KiB  
Article
Studies upon Fluorescent Modulation of Silver Nanoclusters Formed on Bifunctional DNA Template
by Patrycja Filipczuk, Agnieszka Fedoruk-Wyszomirska, Joanna Nowak-Karnowska, Zuzanna Pietralik-Molińska, Ewa Banachowicz, Maciej Kozak and Anna Dembska
Int. J. Mol. Sci. 2025, 26(10), 4914; https://doi.org/10.3390/ijms26104914 - 20 May 2025
Viewed by 417
Abstract
The use of DNA as a scaffold for nanoclusters is particularly interesting due to its structural versatility and easy integration with aptamers. In their structure, aptamers often contain non-canonical forms of DNA, i.e., G-quadruplexes (GQs). Four-stranded GQs are used to construct nanomachines and [...] Read more.
The use of DNA as a scaffold for nanoclusters is particularly interesting due to its structural versatility and easy integration with aptamers. In their structure, aptamers often contain non-canonical forms of DNA, i.e., G-quadruplexes (GQs). Four-stranded GQs are used to construct nanomachines and biosensors for monitoring changes in the concentration of potassium ions. In the present study, we continue our work related to the synthesis of silver nanoclusters formed on a bifunctional DNA template. By attaching a cytosine-rich domain (C12) to a G-quadruplex-forming sequence—human telomeric (Tel22) or thrombin-binding aptamer (TBA)—we constructed bifunctional templates for fluorescent silver nanoclusters (C12) with the ability to detect potassium ions (GQs). The changing localization of the C12 domain from the 3′ to 5′ end of the oligonucleotide was a successful way to improve the fluorescence properties of the obtained fluorescent probes. The best performance as a probe for potassium ions was exhibited by C12Tel22-AgNCs, with an LOD of 0.68 mM in PBS. The introduction of the fluorescent cytosine analog tC leads to an LOD of 0.68 mM in PBS and 0.46 mM in Tris-acetate. Additionally, we performed AFM, TEM, DLS analysis, and cellular studies to further investigate the structural properties and behavior of the Tel22C12-AgNCs in biological contexts. Full article
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