Immuno-cytometric detection of circulating cell free methylated DNA, post-translationally modified histones and micro RNAs using semi-conducting nanocrystals

Cardiovascular disease risk assessment through sensing the circulating microbiome with perovskite quantum dots leveraging deep learning models for bacterial species selection

Perovskite quantum dots (PQDs) are novel nanomaterials wherein perovskites are used to formulate quantum dots (QDs). The present study utilizes the excellent fluorescence quantum yields of these nanomaterials to detect 16S rRNA of circulating microbiome for risk assessment of cardiovascular diseases (CVDs). A long short-term memory (LSTM) deep learning model was used to find the association of the circulating bacterial species with CVD risk, which showed the abundance of three different bacterial species (Bauldia litoralis (BL), Hymenobacter properus (HYM), and Virgisporangium myanmarense (VIG)). The observations suggested that the developed nano-sensor provides high sensitivity, selectivity, and applicability. The observed sensitivities for Bauldia litoralis, Hymenobacter properus, and Virgisporangium myanmarense were 0.606, 0.300, and 0.281 fg, respectively. The developed sensor eliminates the need for labelling, amplification, quantification, and biochemical assessments, which are more labour-intensive, time-consuming, and less reliable. Due to the rapid detection time, user-friendly nature, and stability, the proposed method has a significant advantage in facilitating point-of-care testing of CVDs in the future. This may also facilitate easy integration of the approach into various healthcare settings, making it accessible and valuable for resource-constrained environments.

Quantum Dots-Based Protocols for the Detection of RNAs

RNA (ribonucleic acid) plays a crucial role in various cellular processes and is involved in the development and progression of several diseases. RNA molecules have gained considerable attention as potential biomarkers for various ailments, as they reflect the activity of genes in a particular cell or tissue. By measuring the levels of specific RNA molecules, such as messenger RNA (mRNA), noncoding RNAs, including microRNAs (miRNAs), and long noncoding RNAs (lncRNAs), researchers can infer the expression patterns of genes associated with a particular disease. Aberrant expression of specific miRNAs or lncRNAs has been associated with conditions such as cancer, cardiovascular diseases, neurodegenerative disorders, and more. Detection and quantification of these RNAs in biological samples, such as blood or tissue, can provide valuable diagnostic or prognostic information. Yet their analysis is a challenging endeavor due to their length, sequence similarity across family members, sensitivity to disintegration, and low quantity in total samples. New advances in nanophotonics have provided novel options for fabrication of quantum dots (QDs)-based biosensing devices capable of detecting a variety of disease-specific RNAs. Thus, we proposed and designed a nanophotonic method employing oligonucleotide-conjugated quantum dot nanoconjugates for the rapid and accurate detection of RNAs. Despite the abundance of other molecules in the sample, the approach delivers highly selective, precise identification of the target RNAs. The data also indicated the method's great practicality and simplicity in determining RNAs selectively. Overall, the approach enables the evaluation of RNA expression in relation to the initial onset and progression of a human health disorder.

Design and Fabrication of a Nanobiosensor for the Detection of Cell-Free Circulating miRNAS-LncRNAS-mRNAS Triad Grid

The increased understanding of the competitive endogenous RNA (ceRNA) network in the onset and development of breast cancers has suggested their use as promising disease biomarkers. Keeping these RNAs as molecular targets, we designed and developed an optical nanobiosensor for specific detection of the miRNAs-LncRNAs-mRNAs triad grid in circulation. The sensor was formulated using three quantum dots (QDs), i.e., QD-705, QD-525, and GQDs. These QDs were surface-activated and modified with a target-specific probe. The results suggested the significant ability of the developed nanobiosensor to identify target RNAs in both isolated and plasma samples. Apart from the higher specificity and applicability, the assessment of the detection limit showed that the sensor could detect the target up to 1 fg concentration. After appropriate validation, the developed nanobiosensor might prove beneficial to characterizing and detecting aberrant disease-specific cell-free circulating miRNAs-lncRNAs-mRNAs.

Bioanalytical Applications of Graphene Quantum Dots for Circulating Cell-Free Nucleic Acids: A Review

Graphene quantum dots (GQDs) are carbonaceous nanodots that are natural crystalline semiconductors and range from 1 to 20 nm. The broad range of applications for GQDs is based on their unique physical and chemical properties. Compared to inorganic quantum dots, GQDs possess numerous advantages, including formidable biocompatibility, low intrinsic toxicity, excellent dispensability, hydrophilicity, and surface grating, thus making them promising materials for nanophotonic applications. Owing to their unique photonic compliant properties, such as superb solubility, robust chemical inertness, large specific surface area, superabundant surface conjugation sites, superior photostability, resistance to photobleaching, and nonblinking, GQDs have emerged as a novel class of probes for the detection of biomolecules and study of their molecular interactions. Here, we present a brief overview of GQDs, their advantages over quantum dots (QDs), various synthesis procedures, and different surface conjugation chemistries for detecting cell-free circulating nucleic acids (CNAs). With the prominent rise of liquid biopsy-based approaches for real-time detection of CNAs, GQDs-based strategies might be a step toward early diagnosis, prognosis, treatment monitoring, and outcome prediction of various non-communicable diseases, including cancers.

Graphene Quantum-Dot-Based Nanophotonic Approach for Targeted Detection of Long Noncoding RNAs in Circulation

Recent progress in the field of nanophotonics has opened up novel avenues for developing nanomaterial-based biosensing systems, which can detect various disease-specific biomarkers, including long noncoding RNAs (lncRNAs) known to circulate in biological fluids. Herein, we designed and developed a nanophotonic approach for rapid and specific capture of lncRNAs using oligonucleotide-conjugated graphene quantum-dot-nanoconjugates. The method offers accurate identification of the target lncRNAs with high selectivity, despite the presence of other molecules in the given sample. The observations also pointed toward the high feasibility and simplicity of the method in the selective determination of lncRNAs. Overall, the approach has the potential of assessing lncRNA expression as a function of disease initiation and progression.

Surface-enhanced Raman scattering biosensors for detection of oncomiRs in breast cancer

Surface-enhanced Raman scattering (SERS) has emerged as one of the most promising platforms for various biosensing applications. These sensing systems encompass the advantages of specificity, ultra-high sensitivity, stability, low cost, repeatability, and easy-to-use methods. Moreover, their ability to offer a molecular fingerprint and identify the target analyte at low levels make SERS a promising technique for detecting circulating cancer biomarkers with greater sensitivity and reliability. Among the various circulating biomolecules, oncomiRs are emerging as prominent biomarkers for the early screening of breast cancers (BCs). In this review, we provide a comprehensive understanding of different SERS-based biosensors and their application to identify BC-specific oncomiRs. We also discuss different SERS-based sensing strategies, nano-analytical frameworks, and challenges to be addressed for effective clinical translation.

A fluorescent biosensor based on quantum dot-labeled streptavidin and poly-l-lysine for the rapid detection of Salmonella in milk

Salmonella, as a common foodborne pathogen in dairy products, poses a great threat to human health. We studied a new detection method based on quantum dots (QD). A fluorescent biosensor with multiple fluorescent signal amplification based on a streptavidin (SA) biotin system and the polyamino linear polymer poly-l-lysine (PLL) were established to detect Salmonella in milk. First, Salmonella was captured on a black 96-well plate with paired Salmonella mAb to form a double-antibody sandwich. Second, SA was immobilized on biotin-modified mAb by SA-biotin specific bond. Then, the biotin-modified polylysine (BT-PLL) was bound on SA and specifically bonded again through the SA-biotin system. Finally, water-soluble CdSe/ZnS QD-labeled SA was added to a black 96-well plate for covalent coupling with BT-PLL. The fluorescent signal was amplified in a dendritic manner by the layer-by-layer overlap of SA and biotin and the covalent coupling of biotinylated PLL. Under optimal conditions, the detection limit was 4.9 × 10³ cfu/mL in PBS. The detection limit was 10 times better than that of the conventional sandwich ELISA. In addition, the proposed biosensor was well specific and could be used for detecting Salmonella in milk samples.

A photonic dual nano-hybrid assay for detection of cell-free circulating mitochondrial DNA

Circulating cell free mitochondrial DNA (ccf-mtDNA) has emerged as a potential marker for diagnosis and prognosis of different chronic and age associated non-communicable diseases. Therefore, owing to its biomarker potential, we herein assessed a novel nano-photonic dual hybrid assay system for rapid and specific detection of ccf-mtDNA. The assay comprised of two systems, i.e. a capture and screen facet containing aminopyrene tethered carbon quantum dots for effective screening of circulating cell free nucleic acids (ccf-NAs) and a quantum dot conjugated probe for precise detection of ccf-mtDNA in the screened ccf-NAs. Our observations suggested that the developed dual-assay system possesses high feasibility and selectivity in screening of ccf-NAs and estimation of ccfmtDNA in a given sample. It also offers high versatility of measurement in different analytical platforms, indicating the translational potential of the method for possible disease risk assessment in control and field settings.

Lateral flow assay-based detection of long non-coding RNAs: A point-of-care platform for cancer diagnosis

Lateral flow assay (LFA) is a flexible, simple, low-costpoint-of-care platform for rapid detection of disease-specific biomarkers. Importantly, the ability of the assay to capture the circulating bio-molecules has gained significant attention, as it offers a potential minimal invasive system for early disease diagnosis and prognosis. In the present article, we review an innovative concept of LFA-based detection of circulating long non-coding RNAs (lncRNAs), one of the key regulators of fundamental biological processes. In addition, their disease-specific expression pattern and presence in biological fluids at differential levels make them excellent biomarker candidates for cancer detection. Our article also provides an update on the requirements for developing and improving such systems and discusses the key aspects of material selection, operational concepts, principles and conceptual design. We assume that the reviewed points will be helpful to improve the diagnostic applicability of LFA based lncRNA detection in cancer diagnosis.

Gold based nano-photonic approach for point-of-care detection of circulating long non-coding RNAs

Development of a rapid, sensitive and easy to use point of care assay for detection of circulating long non-coding RNAs (lncRNAs) is of great importance. These biomolecules possess the ability to regulate vital cellular processes and act as biomarkers for various human non-communicable diseases. The present work aimed to develop a simplified and reliable cytometric fluorescence-based approach for precise recognition of circulating lncRNAs in a given sample using biotinylated uracil-modified oligonucleotide tethered AlexaFluor488-labeled streptavidin gold colloidal (BiO-StrAG) nano-conjugates. The fluorophores in close proximity to the gold nanoparticles result in quenching of fluorescence; however, specific recognition of target lncRNAs increases this distance which causes plasmonic enhancement of fluorescence. As per the flow cytometry and fluorometry investigations, the developed methodology provides a precise and sensitive approach for detection of the target lncRNAs (up to 5 nM in any given sample). With advantages of high selectivity and feasibility, our strategy offers great potential of being developed as a promising tool for interrogating aberrant regulation of lncRNAs functions, especially indicated in various diseased states.

Point-of-care diagnostics approaches for detection of lung cancer-associated circulating miRNAs

Circulating cell-free miRNAs (ccf-miRs) have gained significant interest as biomarkers for lung cancer (LC) diagnosis. However, the clinical application of ccf-miRs is mainly limited by time, cost, and expertise-related problems of existing detection strategies. Recently, the development of different point-of-care (POC) approaches offers useful on-site platforms, because these technologies have important features such as portability, rapid turnaround time, minimal sample requirement, and cost-effectiveness. In this review, we discuss different POC approaches for detecting ccf-miRs and highlight the utility of incorporating nanomaterials for enhanced biorecognition and signal transduction, further improving their diagnostic applicability in LC settings.