The non-coding RNAs (ncRNA) are RNA transcripts with different sizes, structures and biological functions that do not encode functional proteins. RNA G-quadruplexes (rG4s) have been found in small and long ncRNAs. The existence of an equilibrium between rG4 and stem−loop structures in ncRNAs and its effect on biological processes remains unexplored. For example, deviation from the stem−loop leads to deregulated mature miRNA levels, demonstrating that miRNA biogenesis can be modulated by ions or small molecules. In light of this, we report several examples of rG4s in certain types of ncRNAs, and the implications of G4 stabilization using small molecules, also known as G4 ligands, in the regulation of gene expression, miRNA biogenesis, and miRNA−mRNA interactions. Until now, different G4 ligands scaffolds were synthesized for these targets. The regulatory role of the above-mentioned rG4s in ncRNAs can be used as novel therapeutic approaches for adjusting miRNA levels.

Lung cancer (LC) is the leading cause of cancer-related death worldwide. Although the diagnosis and treatment of non-small cell lung cancer (NSCLC), which accounts for approximately 80% of LC cases, have greatly improved in the past decade, there is still an urgent need to find more sensitive and specific screening methods. Recently, new molecular biomarkers are emerging as potential non-invasive diagnostic agents to screen NSCLC, including multiple microRNAs (miRNAs) that show an unusual expression profile. Moreover, peripheral blood mononuclear cells’ (PBMCs) miRNA profile could be linked with NSCLC and used for diagnosis. We developed a molecular beacon (MB)-based miRNA detection strategy for NSCLC. Following PBMCs isolation and screening of the expression profile of a panel of miRNA by RT-qPCR, we designed a MB targeting of up-regulated miR-21-5p. This MB 21-5p was characterized by FRET-melting, CD, NMR and native PAGE, allowing the optimization of an in-situ approach involving miR-21-5p detection in PBMCs via MB. Data show the developed MB approach potential for miR-21-5p detection in PBMCs from clinical samples towards NSCLC.

In this work we explore the structure of a G-rich DNA aptamer termed AT11-L2 (TGGTGGTGGTTGTTGTTGGTGGTGGTGGT; derivative of AT11) by evaluating the formation and stability of G-quadruplex (G4) conformation under different experimental conditions such as KCl concentration, temperature, and upon binding with a variety of G4 ligands (360A, BRACO-19, PDS, PhenDC3, TMPyP4). We also determined whether nucleolin (NCL) can be a target of AT11-L2 G4. Firstly, we assessed by circular dichroism, UV and NMR spectroscopies the formation of G4 by AT11-L2. We observed that, for KCl concentrations of 65 mM or less, AT11-L2 adopts hybrid or multiple topologies. In contrast, a parallel topology predominates for buffer containing 100 mM of KCl. The T_m of AT11-L2 in 100 mM of KCl is 38.9 °C, proving the weak stability of this sequence. We also found that upon titration with two molar equivalents of 360A, BRACO-19 and PhenDC3, the G4 is strongly stabilized and its topology is maintained, while the addition of 3.5 molar equivalents of TMPyP4 promotes the disruption of G4. The K_D values between AT11-L2 G4, ligands and NCL were obtained by fluorescence titrations and are in the range of µM for ligand complexes and nM when adding NCL. In silico studies suggest that four ligands bind to the AT11-L2 G4 structure by stacking interactions, while the RBD1,2 domains of NCL interact preferentially with the thymines of AT11-L2 G4. Finally, AT11-L2 G4 co-localized with NCL in NCL-positive tongue squamous cell carcinoma cell line.

Lung cancer (LC) is recognized as one of the most prevalent and lethal cancers worldwide, underscoring an urgent need for innovative diagnostic and therapeutic approaches. MicroRNAs (miRNAs) have emerged as promising biomarkers for several diseases and their progression, such as LC. However, traditional methods for detecting and quantifying miRNAs, such as PCR, are time-consuming and expensive. Herein, we used a molecular beacon (MB) bead-based assay immobilized in a microfluidic device to detect miR-155-3p, which is frequently overexpressed in LC. The assay relies on the fluorescence enhancement of the MB upon binding to the target miRNA via Watson and Crick complementarity, resulting in a conformational change from a stem–loop to a linear structure, thereby bringing apart the fluorophores at each end. This assay was performed on a microfluidic platform enabling rapid and straightforward target detection. We successfully detected miR-155-3p in a saline solution, obtaining a limit of detection (LOD) of 42 nM. Furthermore, we evaluated the method’s performance in more complex biological samples, including A549 cells’ total RNA and peripheral blood mononuclear cells (PBMCs) spiked with the target miRNA. We achieved satisfactory recovery rates, especially in A549 cells’ total RNA.

Background/Objectives: Late diagnosis hampers effective treatment of non-small cell lung cancer (NSCLC). This study evaluated whether circulating microRNAs (miRs), miR-155 and miR-3196, measured in liquid biopsy peripheral blood mononuclear cells (PBMCs), can serve as potential non-invasive biomarkers for NSCLC diagnosis, patient stratification, therapy monitoring, and prognosis. Methods: RNA was isolated from PBMCs of 136 NSCLC patients and 64 healthy donors. RT–qPCR quantified miR expression in PBMCs after predefined QC filtering: miR-155-3p (NSCLC n = 63; controls n = 28), miR-3196 (NSCLC n = 55; controls n = 28), and miR-155-5p (NSCLC n = 23; controls n = 12). Diagnostic performance was assessed using receiver operating characteristic (ROC) analyses, reporting area under the curve (AUC), and threshold-dependent sensitivity/specificity. Survival was analyzed with Kaplan–Meier/Cox methods. Associations with clinicopathological variables (stage, metastasis, smoking, EGFR, and KRAS status), treatment response (chemotherapy, immunotherapy, TKIs), and survival outcomes were examined. Results: miR-155-3p was upregulated in NSCLC, whereas miR-3196 was downregulated relative to controls; AUCs were 0.881 and 0.784, respectively. At high-sensitivity operating points, specificity was lower (≈29–30%), consistent with PBMC miRs reflecting both immune activation and tumor burden. In adenocarcinoma, miR-155-3p was associated with advanced stage, metastatic disease and smoking history. miR-3196 aligned with features of metastatic progression. During systemic therapy (chemotherapy, immunotherapy, TKIs), circulating levels of both miRs tended to normalize. Notably, normalization of miR-155-3p levels was associated with improved overall survival, supporting its prognostic value and utility for treatment monitoring. Conclusions: Circulating miR-155-3p and miR-3196 in PBMCs are promising screening/monitoring non-invasive candidates rather than stand-alone NSCLC diagnostics at current thresholds. Combining these miRs with additional biomarkers and/or clinical covariates and tuning decision thresholds may enhance specificity for diagnostic use. While preliminary, these findings warrant validation in large, prospective studies with standardized protocols to enable clinical implementation.