Luminescent lanthanide coordination polymer as a platform for DNA colorimetric detection

Biological warfare agents are infectious microorganisms or toxins capable of harming or killing humans. Francisella tularensis is a potential bioterrorism agent that is highly infectious, even at very low doses. Biosensors for biological warfare agents are simple yet reliable point-of-care analytical tools. Developing highly sensitive, reliable, and cost-effective label-free DNA biosensors poses significant challenges, particularly when utilizing traditional techniques such as fluorescence, electrochemical methods, and others. These challenges arise primarily due to the need for labeling, enzymes, or complex modifications, which can complicate the design and implementation of biosensors. In this study, we fabricated Graphene Quantum dot (GQD)-functionalized biosensors for highly sensitive label-free DNA detection. GQDs were immobilized on the surface of screen-printed gold electrodes via mercaptoacetic acid with a thiol group. The single-stranded DNA (ssDNA) probe was also immobilized on GQDs through strong π-π interactions. The ssDNA probe can hybridize with the ssDNA target and form double-stranded DNA, leading to a decrease in the effect of GQD but a positive shift associated with the increase in DNA concentration. The specificity of the developed system was observed with different microorganism target DNAs and up to three-base mismatches in the target DNA, effectively distinguishing the target DNA. The response time for the target DNA molecule is approximately 1010 s (17 min). Experimental steps were monitored using UV/Vis spectroscopy, Atomic Force Microscopy (AFM), and electrochemical techniques to confirm the successful fabrication of the biosensor. The detection limit can reach 0.1 nM, which is two-five orders of magnitude lower than previously reported methods. The biosensor also exhibits a good linear range from 105 to 0.01 nM and has good specificity. The biosensor's detection limit (LOD) was evaluated as 0.1 nM from the standard calibration curve, with a correlation coefficient of R2 = 0.9712, showing a good linear range and specificity. Here, we demonstrate a cost-effective, GQD-based SPGE/F. tularensis DNA test suitable for portable electrochemical devices. This application provides good perspectives for point-of-care portable electrochemical devices that integrate sample processing and detection into a single cartridge without requiring a PCR before detection. Based on these results, it can be concluded that this is the first enzyme-free electrochemical DNA biosensor developed for the rapid and sensitive detection of F. tularensis, leveraging the nanoenzyme and catalytic properties of GQDs.

Exploiting the size exclusion effect of protein adsorption layers for electrochemical detection of microRNA: A new mechanism for design of E-DNA sensor

Novel strategy combining SYBR Green I with carbon nanotubes for highly sensitive detection of Salmonella typhimurium DNA

As a two-dimensional (2D) ordered porous organic framework (POF), PAF-6 is demonstrated to have an extraordinarily high fluorescence quenching ability to dye-labeled single-stranded DNA (ssDNA). Based on its different affinities to ssDNA and double-stranded DNA (dsDNA), and to ssDNAs with different lengths, PAF-6 is firstly utilized as a simple, cost-efficient, sensitive and selective sensing platform for sequence-specific detection of DNA and activity analysis of exonuclease I (Exo I). In these two systems, the sensing approach is accomplished by simply mixing the dye-labeled ssDNA probe with the targets and PAF-6. The targets of DNA and Exo I are specifically and sensitively detected with detection limits of 0.6 nM and 0.03 U mL-1 (S/N = 3), respectively, by using PAF-6 as a fluorescence quencher of the dye-labeled ssDNA probe. The results of this study suggest that PAF-6 can be developed as an excellent platform for the detection of nucleic acid and nuclease activity. In addition, PAF-6 exhibits a remarkable ability to protect ssDNA probe from enzymatic digestion, which may greatly extend the applications of the proposed ssDNA probe/PAF-6 sensing system to bioanalysis and biomedicine.

Carbon/1-octadecanethiol-carboxylated multiwalled carbon nanotubes (cMWCNT) composite was used to construct a DNA sensor for detection of human bacterial meningitis caused by Neisseria meningitidis. The carbon composite electrode was used to covalently immobilize 5′-amine-labeled 19-mer single-stranded DNA (ssDNA) probe, which was hybridized with 1.35 × 102–3.44 × 104 pM (0.5–128 ng/5 μl) of single-stranded genomic DNA (ssG-DNA) of N. meningitidis for 10 min at room temperature (RT). The surface topography of the DNA sensor was characterized by using scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) while electrochemically characterized by electrochemical impedance. The immobilization of ssDNA probe and hybridization with ssG-DNA were detected electrochemically by cyclic voltammetry (CV) and differential pulse voltammetry (DPV) at RT in 30 min with a response time of 1 min. The DNA sensor showed high pathogenic specificity and can distinguish among complement, noncomplement, one base mismatch, and triple base mismatch oligomer targets. The limit of detection (LOD) and sensitivity of the sensor were approximately 68 pM and 38.095 (μA/cm2)/nM of ssG-DNA, respectively, using DPV. The improved sensitivity and LOD of the sensor can be attributed to the higher efficiency of probe immobilization due to high surface area-to-volume ratio and good electrical activity of cMWCNT.

In this communication, we report on the use of tetracyanoquinodimethane nanoparticles (TNs) as an effective fluorescent sensing platform for nucleic acid detection for the first time. The general concept used in this approach is based on adsorption of fluorescently labeled single-stranded DNA (ssDNA) probe by TN, due to the strong π–π stacking between unpaired DNA bases and TN. As a result, the fluorophor is brought into close proximity of TN, leading to substantial fluorescence quenching via photoinduced electron transfer between fluorescent dye and TN. Upon presence of the target ssDNA, specific hybridization with the target takes place to form a double-stranded DNA (dsDNA). The helix cannot be adsorbed by TN due to its rigid conformation and the absence of unpaired DNA bases. Thus, the fluorophor is seperated from TN accompanied by fluorescence recovery. This fluorescence enhancement signals completion of the assay. It also suggests that this sensing platform can well differentiate perfect complementary and mismatched sequences. A detection limit as low as 1.5 nM was obtained.

In this article, we report on the use of multi-walled carbon nanotubes (MWCNTs) as an effective fluorescent sensing platform for nucleic acid detection with selectivity down to single-base mismatch. The detection is accomplished with two steps: (1) MWCNTs adsorb and quench the fluorescence of the dye-labeled single-stranded DNA (ssDNA) probe; (2) in the presence of the target, a hybridization event occurs, which produces a double-stranded DNA (dsDNA) that detaches from the MWCNT surface, leading to the restoration of the dye fluorescence. We also compared the sensing responses of MWCNTs and single-walled carbon nanotubes (SWCNTs) under the same experimental conditions.

DNA hybridization based on Trichoderma harzianum gene probe immobilization on self-assembled monolayers on a modified gold electrode

Dragging it out: The first direct quantitative analysis of multiple miRNAs (DQAMmiR) uses miRNAs directly, without chemical or enzymatic modification, and accurately determines concentrations of multiple miRNAs without the need for calibration curves. This method involves a capillary-electrophoresis-based hybridization assay with a combination of two separation-enhancement approaches: drag tags and single strand DNA binding protein (SSB). Detailed facts of importance to specialist readers are published as "Supporting Information". Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.

Two novel lanthanide (Nd, Gd) coordination polymers with chromate anion as building block of the 2D metal oxide

DNA biosensors are now recognized as unvaluable tools for detecting target genes responsible for diseases, or pollution, in various fields (Fodor et al., 1991; DeRisi et al., 1997; Landegren et al., 1998). Therefore, detection of DNA hybridisation is of significant scientific and technological importance, as manifest, for example, from the growing interest in chip-based characterisation of gene expression pattern and detection of pathogens. DNA biosensors technologies are currently under intense investigation owing to their great promise for rapid and low-cost detection of specific DNA sequences. These technologies commonly rely on the immobilisation of a single-strand (ss) DNA probe onto optical, electrochemical, or mass-sensitive transducers (Xu et al., 1995; Mikkelsen et al., 1996; Okahata et al., 1992). There is still a crucial need to improve the sensitivity, selectivity and rapidity of the DNA hybridisation detection. Among the possible strategies, a new artificial Peptide Nucleic Acid (PNA), a highly specific probe, combined with the use of surface science techniques to optimise the sensing layer as well as to detect biomolecular recognition, open promising ways to win this biotechnological challenge. This chapter will focus on these two novel aspects of DNA biosensors.

The application of solid-state nanopore technology for biosensing is a rapidly developing area of research with high commercial potential. Different synthetic materials, including silicon nitride, alumina, and polymers, are employed to fabricate single and multiple pores and offer a good platform for selective biomolecule detection. Two solid-state pore arrays, one with integrated silicon microfluidic system, were considered and an immobilization strategy suitable for detecting a single-stranded DNA (ssDNA) sequence was investigated. For the silicon nitride pores, a modification method based on the use of 3-aminopropyltriethoxysilane for silanization and 1,4-phenylene diisothiocyanate for amine crosslinking was applied to immobilize 100-nM ssDNA (amine C6) and a 100-nM limit of detection for complementary to probe ssDNA (Cy5) was estimated. The polycarbonate pores (the second type of the pore arrays) underwent surface modification based on an oxidation reduction reaction using sodium periodate and sodium borohydride and was used to immobilize 10-nM ssDNA and an estimated 100-nM limit of detection was also achieved. Linear sweep voltammetry was used to characterize the pores and a current potential profile was obtained after both immobilization of probe ssDNA and hybridization of complementary to probe ssDNA on the modified pore array surface. A decrease in current amplitude was measured after surface modification of both pore arrays, and this was attributed to the appearance of an additional layer on the pore surface reducing the pore opening and hindering the current flow. The hybridization event was also supported by contact angle measurements, where an increase in hydrophilicity was recorded at the different surface modification steps that were applied to produce the biofunctionalized nanopore. In addition, fluorescence was observed on the surfaces after hybridization, through incorporation of a CY5 fluorescent tag attached on the 5' end of the complementary to probe DNA. These results show the potential to use both silicon nitride and polycarbonate nanopores in DNA detection applications.

RecQ helicases maintain chromosome stability by resolving a number of highly specific DNA structures that would otherwise impede the correct transmission of genetic information. Previous studies have shown that two human RecQ helicases, BLM and WRN, have very similar substrate specificities and preferentially unwind noncanonical DNA structures, such as synthetic Holliday junctions and G-quadruplex DNA. Here, we extend this analysis of BLM to include new substrates and have compared the substrate specificity of BLM with that of another human RecQ helicase, RECQ1. Our findings show that RECQ1 has a distinct substrate specificity compared with BLM. In particular, RECQ1 cannot unwind G-quadruplexes or RNA-DNA hybrid structures, even in the presence of the single-stranded binding protein, human replication protein A, that stimulates its DNA helicase activity. Moreover, RECQ1 cannot substitute for BLM in the regression of a model replication fork and is very inefficient in displacing plasmid D-loops lacking a 3'-tail. Conversely, RECQ1, but not BLM, is able to resolve immobile Holliday junction structures lacking an homologous core, even in the absence of human replication protein A. Mutagenesis studies show that the N-terminal region (residues 1-56) of RECQ1 is necessary both for protein oligomerization and for this Holliday junction disruption activity. These results suggest that the N-terminal domain or the higher order oligomer formation promoted by the N terminus is essential for the ability of RECQ1 to disrupt Holliday junctions. Collectively, our findings highlight several differences between the substrate specificities of RECQ1 and BLM (and by inference WRN) and suggest that these enzymes play nonoverlapping functions in cells.

Lanthanide coordination polymers (LnCPs), [Eu(HL)3(CH3OH)2]n (1) and [Tb(HL)3(CH3OH)(H2O)]n·H2O (2) (H2L = 3-(picolinamido)benzoic acid)), have been synthesized and characterized. Single crystal analyses of both LnCPs display that HL ligands not only coordinate to Ln ions but also act as the bridge between them generating one-dimensional (1D) chains. Such 1D chains further pack into three-dimensional (3D) architectures by the mediation of H-bonding interactions. Both LnCPs offer strategically placed exposed Lewis basic sites, which potentially interact with the electron-deficient nitroaromatics, whereas H-bonded 3D architecture having hydrophobic channels allows their facile inclusion within the network. A notable feature is the size-dependent sensing of nitroaromatics potentially governed by the packing of 1D chains into a 3D architecture. Both LnCPs act as the fluorescent sensor for quick, sensitive, and selective detection of nitrobenzene not only in solution but also in the vapor phase suggesting pote...

Background: Carbon-based nanoparticle classes consisting of various subgroups based on morphology and crystallinity are called carbon dots (CQDs). The physical, chemical, and optical properties of CQDs can be modified using the simple pot synthesis technique. Additionally, its non-toxic nature, biocompatibility, physical and chemical responsiveness, resistance to chemical and photo bleaching, and low cost make it suitable for various purposes, such as biomedical imaging applications. Biomass waste, which has been widely discarded without economic utilization and potential, can surprisingly be used as a precursor for CQDs. Method: The literature was systematically collected from major databases. Studies from 2017–2025 were analyzed based on synthesis strategies, surface functionalization, and biological performance. Its potential in the medical field is highly advantageous. CQDs have fluorescence that is useful for biomedical imaging both in vivo and in vitro. The hydrothermal carbonization approach is also discussed in more detail, highlighting its green and sustainable synthesis, as well as the ease of the synthesis process. Finding: It was found that CQDs have compatibility and adjustable optical properties. Its fluorescence can clearly record tissues, body care, aging, and living cells. Utilizing renewable biomass precursors offers an environmentally friendly and cost-effective route for synthesizing fluorescent nanoprobes with excellent water solubility, tunable emission, and low cytotoxicity. Additionally, in vitro studies reinforce CQDs as multicolor fluorescent probes, and in vivo studies demonstrate that CQDs have low toxicity, rapid clearance, are safe, and biocompatible. Conclusion: This paper delves into the remarkable potential of CQDs to provide insights into how fluorescent inks are truly essential in biomedical imaging. Novelty/Originality of this article: This study provides a comprehensive and updated synthesis of CQD research spanning up to 2025, specifically focusing on the transition from "waste to nanoprobe."