Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
9.0
4.9
Journals
IJMS
Special Issues
Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers
ijms-logo
Submit to Special Issue Submit Abstract to Special Issue Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

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: 20 February 2026 | Viewed by 2612

Special Issue Editors

Dr. Antonella Virgilio

E-Mail Website
Guest Editor
Department of Pharmacy, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
Interests: G-quadruplex; aptamers; nucleic acid chemistry; circular dichroism; electrophoresis
Special Issues, Collections and Topics in MDPI journals
Dr. Veronica Esposito

E-Mail Website
Guest Editor
Department of Pharmacy, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
Interests: G-quadruplex; aptamers; nucleic acid chemistry; nuclear magnetic resonance; electrophoretic techniques; circular dichroism; G4-catalysts
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Aldo Galeone

E-Mail Website
Guest Editor
Department of Pharmacy, Università degli Studi di Napoli Federico II, 80131 Naples, Italy
Interests: G-quadruplex; nucleic acid secondary structures; aptamers; nucleic acid chemistry
Special Issues, Collections and Topics in MDPI journals

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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

19 pages, 4688 KB  
Article
Exploring Guanidinium Group Involvement in Hordatine Interactions with the G-Quadruplex Motif Within the c-MYC Promoter Region
by Denise Dozio, Aziza Caccia, Sabrina Dallavalle, Giovanni Luca Beretta, Paola Perego, Roberto Artali, Stefania Mazzini and Salvatore Princiotto
Int. J. Mol. Sci. 2025, 26(21), 10580; https://doi.org/10.3390/ijms262110580 - 30 Oct 2025
Viewed by 103
Abstract
G-quadruplexes (G4s) are four-stranded DNA or RNA structures formed by guanine-rich sequences. They occur in functional regions of the genomic material, including the promoter part of genes, regulatory region, and telomeric threads. G4s play a key role in various biological processes, including transcription, [...] Read more.
G-quadruplexes (G4s) are four-stranded DNA or RNA structures formed by guanine-rich sequences. They occur in functional regions of the genomic material, including the promoter part of genes, regulatory region, and telomeric threads. G4s play a key role in various biological processes, including transcription, replication, and telomere maintenance. Guanidine-containing derivatives can bind to G-quadruplexes, either by intercalating into the structure or by interacting with the grooves or loops. The binding can stabilize the G-quadruplex, potentially affecting its biological function. In this paper, the ability of guanidinium-containing hordatines to interact with G4 was evaluated. Analogues lacking the guanidinium group or showing the benzofuran system instead of the dihydrobenzofuran core were prepared and tested as well. NMR titration and docking calculations were used to probe the binding of the compounds to G4 of c-MYC oncogene. Spectroscopic analyses were consistent with a significant interaction of benzofurans 3 and 4 at the 5′-end and 3′-end tetrads and with the formation of ligand/G-quadruplex complexes with a 2:1 stoichiometry. The resulting data were supported by docking simulations. Cytotoxic activity was evaluated on a model of U2OS osteosarcoma (ATCC HTB-96) and breast cancer (MDA-MB-231) cell lines, further highlighting the key role of the guanidinium fragment and the benzofuran core in the G-quadruplex stabilization. Full article
(This article belongs to the Special Issue Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers)
►▼ Show Figures

Figure 1

18 pages, 2360 KB  
Article
G4 Oligonucleotide-Based Chaperones of Heterogeneous Nuclear Ribonucleoprotein A1
by Elizaveta Malakhova, Julia Svetlova, Iuliia Pavlova, Sabina Alieva, Vyacheslav Severov, Nikolay Barinov, Dmitry Klinov, Tatiana Vedekhina and Anna Varizhuk
Int. J. Mol. Sci. 2025, 26(20), 10104; https://doi.org/10.3390/ijms262010104 - 17 Oct 2025
Viewed by 273
Abstract
Pharmacological chaperones of heterogeneous nuclear ribonucleoproteins (hnRNPs) show promise as potential neuroprotective drug candidates. They are expected to prevent the accumulation of neurotoxic hnRNP biocondensates and aggregates, which are hallmarks of severe degenerative diseases. Here, we present the first rational design of oligonucleotide [...] Read more.
Pharmacological chaperones of heterogeneous nuclear ribonucleoproteins (hnRNPs) show promise as potential neuroprotective drug candidates. They are expected to prevent the accumulation of neurotoxic hnRNP biocondensates and aggregates, which are hallmarks of severe degenerative diseases. Here, we present the first rational design of oligonucleotide chaperones of hnRNP A1. This design was inspired by previous studies on the specificity of the RNA recognition motif (RRM) and the RGG motif of hnRNP A1 for endogenous nucleic acids. To obtain robust and specific chaperones, we combined an RRM-binding sequence with an RGG-binding G-quadruplex oligonucleotide that inhibits hnRNP A1 aggregation and introduced various modifications into the sugar-phosphate backbone of the oligonucleotide. Modifications that locked the RRM-binding sequence in a conformational state characteristic of RNA improved chaperone affinity and activity. The former was assessed using microscale thermophoresis assays, while the latter was evaluated using fluorimetry and microscopy. The leading chaperone bound to hnRNP A1 at micromolar concentrations and inhibited the assembly of its condensates and amyloid-like aggregates (fibrils) by over 90%. Full article
(This article belongs to the Special Issue Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers)
►▼ Show Figures

Figure 1

22 pages, 2326 KB  
Article
Stabilization of G-Quadruplexes Modulates the Expression of DNA Damage and Unfolded Protein Response Genes in Canine Lymphoma/Leukemia Cells
by Beatriz Hernández-Suárez, David A. Gillespie, Ewa Dejnaka, Bożena Obmińska-Mrukowicz and Aleksandra Pawlak
Int. J. Mol. Sci. 2025, 26(20), 9928; https://doi.org/10.3390/ijms26209928 - 12 Oct 2025
Viewed by 395
Abstract
G-quadruplexes have been identified as a promising anti-cancer target because of their ability to modulate the stability of mRNAs encoding oncogenes, tumor suppressor genes, and other potential therapeutic targets. Deregulation of DNA damage and Unfolded Protein Response pathways in cancer cells may create [...] Read more.
G-quadruplexes have been identified as a promising anti-cancer target because of their ability to modulate the stability of mRNAs encoding oncogenes, tumor suppressor genes, and other potential therapeutic targets. Deregulation of DNA damage and Unfolded Protein Response pathways in cancer cells may create vulnerabilities that can be exploited therapeutically. Previous studies have shown variations in the relative expression of DDR and UPR components in canine lymphoma and leukemia cell lines CLBL-1, CLB70, and GL-1. In the present study, we report the presence of G-quadruplex structures in these canine cell lines. Downregulation of the expression of DDR and UPR components at the mRNA level was observed in the CLBL-1 and CLB70 cell lines after stabilization of G4 structures using the ligand PhenDC3. In contrast, in GL-1 cells, important components of the DDR pathway, such as PARP1, GADD45A, and PIK3CB were upregulated in response to PhenDC3 treatment. Downregulation of DDIT4 mRNA expression, which encodes an important UPR component, was detected in the CLBL-1 and GL-1 cell lines after PhenDC3 exposure. These results suggest that G4 structures can be used to manipulate the expression of potential targets to treat lymphoma in dogs. A substantial enrichment of DNA replication and pyrimidine metabolism pathways was found in the GL-1 cell line after G4 stabilization. This finding suggests that PhenDC3 may induce DNA replication stress in this cell line. Collectively, these results support the feasibility of employing canine cancer cells as a model system to investigate the role of G-quadruplex structures in cancer. Full article
(This article belongs to the Special Issue Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers)
►▼ Show Figures

Figure 1

14 pages, 4041 KB  
Article
Comparative Analysis of Crystal Violet-Binding Aptamers as Potential Cores for Binary Sensors
by Gleb A. Bobkov, Gleb S. Yushkov, Andrei D. Kuzmin, Tatiana D. Popysheva, Elena I. Stepchenkova and Maria S. Rubel
Int. J. Mol. Sci. 2025, 26(19), 9833; https://doi.org/10.3390/ijms26199833 - 9 Oct 2025
Viewed by 512
Abstract
‘Light-up’ aptamers are short oligonucleotides that can induce fluorescence of certain organic compounds upon binding. In this study, we compared three crystal violet (CV) aptamers—CV30S, parallel G-quadruplex (G4), and antiparallel G4—regarding their absolute fluorescence intensity, signal-to-background ratio (S/B), and potential as a core [...] Read more.
‘Light-up’ aptamers are short oligonucleotides that can induce fluorescence of certain organic compounds upon binding. In this study, we compared three crystal violet (CV) aptamers—CV30S, parallel G-quadruplex (G4), and antiparallel G4—regarding their absolute fluorescence intensity, signal-to-background ratio (S/B), and potential as a core component in binary sensors for nucleic acid detection. The G4 antiparallel aptamer exhibited the highest fluorescence intensity and a robust S/B ratio, indicating its effectiveness in stabilizing the CV binding and enhancing fluorescence. In contrast, the G4 parallel aptamer demonstrated poorer performance, suggesting that its structural topology is less suitable for interactions with CV. The CV30S aptamer showed distinct advantages in binary sensor configurations, achieving the best limit of detection at 6 nM. Full article
(This article belongs to the Special Issue Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers)
►▼ Show Figures

Graphical abstract

19 pages, 6213 KB  
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 917
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
(This article belongs to the Special Issue Advances in Structural and Functional Properties of G-Quadruplexes and Aptamers)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop