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Quadruplex DNA and Its Ligands for Disease Treatment
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Quadruplex DNA and Its Ligands for Disease Treatment

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: 20 September 2025 | Viewed by 2642

Special Issue Editor

Prof. Dr. Ding Li

E-Mail Website
Guest Editor
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
Interests: quadruplex; i-motif; transcriptional regulation; apoptosis; cancer

Special Issue Information

Dear Colleagues,

Quadruplex DNA including G-quadruplex and i-motif structures are formed from guanine- or cytosine-rich nucleotides, respectively, which mainly exist in the regulatory regions of the genome. These special secondary structures play important regulatory roles, which have attracted significant attention as potential drug targets in recent decades. The purpose of this Special Issue is to report the recent progress achieved in quadruplex DNA and its binding ligands developed for monitoring or treating selected diseases. These binding ligands can serve as both molecular tools to tease out these nuclear functions and potential new therapeutics for drug development. This Special Issue includes but is not limited to the following topics: relevant new methods or techniques to synthesize and screen for identified interactive agents, the development of fluorescent binding ligands, biological and biophysical characterizations, mechanistic studies at molecular and cellular levels, and animal studies.

Prof. Dr. Ding Li
Guest Editor

Manuscript Submission Information

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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.

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Keywords

  • quadruplex
  • i-motif
  • transcriptional regulation
  • apoptosis
  • cancer

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Published Papers (3 papers)

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Research

20 pages, 9377 KiB  
Article
Tandemly Repeated G-Quadruplex Structures in the Pseudorabies Virus Genome: Implications for Epiberberine-Based Antiviral Therapy
by Songjie Fan, Xiaotian Chang, Yan Qiao, Xiaoxiao Zhao, Jiafu Zhao, Heshui Zhu, Yingqian Han and Chao Zhang
Int. J. Mol. Sci. 2025, 26(8), 3764; https://doi.org/10.3390/ijms26083764 - 16 Apr 2025
Viewed by 367
Abstract
G-quadruplex (G4) structures have emerged as critical regulatory elements in viral genomes and represent potential targets for antiviral intervention. In this study, we identified and characterized G4 structures in the unique long (UL) region of the Pseudorabies virus (PRV) genome, highlighting their role [...] Read more.
G-quadruplex (G4) structures have emerged as critical regulatory elements in viral genomes and represent potential targets for antiviral intervention. In this study, we identified and characterized G4 structures in the unique long (UL) region of the Pseudorabies virus (PRV) genome, highlighting their role as novel antiviral targets. Bioinformatic analysis revealed two guanine-rich regions (R1 and R2) that form stable G4 structures, as confirmed by fluorescence assays, circular dichroism (CD) spectroscopy, and immunofluorescence staining. Notably, these G4 structures exhibit a tandem repeat arrangement, a previously unreported feature in the PRV genome. Epiberberine (EPI), a natural G4-stabilizing ligand, bound to and stabilized these structures, leading to the inhibition of Taq polymerase progression. Functional assays demonstrated that EPI effectively suppressed PRV replication in vitro while having no significant impact on viral entry or release. In vivo, EPI treatment significantly improved survival rates and reduced viral loads in multiple organs, including the brain, heart, lungs, and kidneys of infected mice. These findings provide new insights into the role of G4 structures in PRV replication and demonstrate that EPI exhibits potential antiviral activity by targeting G4 structures. Full article
(This article belongs to the Special Issue Quadruplex DNA and Its Ligands for Disease Treatment)
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17 pages, 2993 KiB  
Article
Evaluating the Performance of Peak Calling Algorithms Available for Intracellular G-Quadruplex Sequencing
by Yuqi Wang, Ke Xiao, Tiantong Tao, Rongxin Zhang, Huiling Shu and Xiao Sun
Int. J. Mol. Sci. 2025, 26(3), 1268; https://doi.org/10.3390/ijms26031268 - 31 Jan 2025
Viewed by 735
Abstract
DNA G-quadruplexes (G4) are non-canonical DNA structures that play key roles in various biological processes. Antibody-dependent sequencing is an important tool for identifying intracellularly formed DNA G4s, and peak calling is a crucial step in processing the sequencing data. As the applicability of [...] Read more.
DNA G-quadruplexes (G4) are non-canonical DNA structures that play key roles in various biological processes. Antibody-dependent sequencing is an important tool for identifying intracellularly formed DNA G4s, and peak calling is a crucial step in processing the sequencing data. As the applicability of existing peak calling algorithms to intracellular G4 data has not been previously assessed, we systematically compared and evaluated these algorithms to determine those best suited for G4 detection. We selected seven representative candidates from 43 published peak calling algorithms for detailed evaluation. The performance of each candidate on six published intracellular G4 sequencing datasets (GSE107690, GSE145090, GSE133379, GSE178668ChIP-seq, GSE178668CUT&Tag, GSE221437) were assessed by precision and recall against customized benchmarks integrating results from multiple algorithms, as well as consistency with known G4 information (pG4 predicted by pqsfinder, oG4 from GSE63874, and multi-cell-line conserved G4s) and epigenetic signals. We identified MACS2, PeakRanger, and GoPeaks as the most effective algorithms for analyzing intracellular G4 sequencing data, and attributed their superior performance partially to the distribution model of sequencing reads/fragments used in the hypothesis testing step of the peak calling procedures. These findings provide guidance and rationale for selecting peak callers appropriate for intracellular G4 data. Full article
(This article belongs to the Special Issue Quadruplex DNA and Its Ligands for Disease Treatment)
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20 pages, 5664 KiB  
Article
New Therapeutic Method for Alleviating Damage of Acute Kidney Injury Through BCL-2 Gene Promoter I-Motif
by Dongsheng Ji, Jiahui Zhang, Jihai Liang, Jing Wang, Xiaoya Li, Zhi-Shu Huang and Ding Li
Int. J. Mol. Sci. 2024, 25(22), 12028; https://doi.org/10.3390/ijms252212028 - 8 Nov 2024
Viewed by 1141
Abstract
Acute kidney injury (AKI) is a global public health problem with its pathogenesis not fully understood. Excessive apoptosis of renal tubular epithelial cells is an important feature of AKI patients, and therefore an anti-apoptotic approach could be used in the treatment for AKI. [...] Read more.
Acute kidney injury (AKI) is a global public health problem with its pathogenesis not fully understood. Excessive apoptosis of renal tubular epithelial cells is an important feature of AKI patients, and therefore an anti-apoptotic approach could be used in the treatment for AKI. Up-regulation of B-cell lymphoma-2 (BCL-2) gene and protein has been found to be correlated with anti-apoptosis of cells. It has been found that the presence of the C-rich sequence on the upstream region of the BCL-2 gene promoter could form DNA secondary i-motif structure, and its stabilization by small molecules could up-regulate gene transcription and translation. In the present study, we constructed AKI models through folic acid (FA) induction. With these in vitro and in vivo models, we demonstrated that the acridone derivative A22 could up-regulate the expression of BCL-2 by targeting its gene promoter i-motif to reduce renal tubular epithelial cell apoptosis and improve renal function in many ways. A22 could alleviate FA-induced oxidative stress injury, inflammatory response, and endoplasmic reticulum stress in mouse kidneys. Our results provided a potentially new anti-apoptotic approach for the treatment of early stages of AKI. Our employed model focused on its short-term effect on AKI, while its long-term efficacy and safety, particularly regarding the regeneration of renal tubular epithelial cells, require further investigation before clinical application. This study further demonstrated that promoter i-motif could be targeted for up-regulating BCL-2 expression for the treatment of important diseases caused by excessive apoptosis. Full article
(This article belongs to the Special Issue Quadruplex DNA and Its Ligands for Disease Treatment)
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