A facile deoxyuridine/biotin-modified molecular beacon for simultaneous detection of proteins and nucleic acids via a label-free and background-eliminated fluorescence assay

Emerging multianalyte biosensors for the simultaneous detection of protein and nucleic acid biomarkers

Traditionally, biosensors are designed to detect one specific analyte. Nevertheless, disease progression is regulated in a highly interactive way by different classes of biomolecules like proteins and nucleic acids. Therefore, a more comprehensive analysis of biomarkers from a single sample is of utmost importance to further improve both, the accuracy of diagnosis as well as the therapeutic success. This review summarizes fundamentals like biorecognition and sensing strategies for the simultaneous detection of proteins and nucleic acids and discusses challenges related to multianalyte biosensor development. We present an overview of the current state of biosensors for the combined detection of protein and nucleic acid biomarkers associated with widespread diseases, among them cancer and infectious diseases. Furthermore, we outline the multianalyte analysis in the rapidly evolving field of single-cell multiomics, to stress its significance for the future discovery and validation of biomarkers. Finally, we provide a critical perspective on the performance and translation potential of multianalyte biosensors for medical diagnostics.

DNA-Based Nanoprobes for Simultaneous Detection of Telomerase and Correlated Biomolecules

Telomerase (TE), a ribonucleoprotein reverse transcriptase, is enzymatically activated in most tumor cells and is responsible for promoting tumor progression and malignancy by enabling replicative immortality of cancer cells. TE has become an important hallmark for cancer diagnosis and a potential therapy target. Therefore, accurate and in site detection of TE activity, especially the simultaneous imaging of TE activity and its correlated biomolecules, is highly essential to medical diagnostics and therapeutics. DNA-based nanoprobes, with their effective cell penetration capability and programmability, are the most advantageous for detection of intracellular TE activity. This concept article introduces the recent strategies for in situ sensing and imaging of TE activity, with a focus on simultaneous detection of TE and related biomolecules, and provides challenges and perspectives for the development of new strategies for such correlated imaging.

Ultrasensitive fluorescent detection of telomerase activity based on tetrahedral DNA nanostructures as carriers for DNA-templated silver nanoclusters

Precise evaluation of telomerase activity is essential for the clinical diagnosis of early tumors. Herein, we have ingeniously designed a tetrahedral DNA nanostructure, with hairpin-shaped DNA probes rich in cytosine bases at four vertices for telomerase detection. The DNA-templated silver nanoclusters can be formed after the addition of Ag. Then the introduction of telomerase adds the single-strand TTAGGG extension, which can "turn on" the fluorescence of silver nanoclusters quickly by the proximity of the resulting guanine-rich sequences to silver nanoclusters and realize accurate detection of telomerase activity. In this study, integration of high stability tetrahedral DNA nanostructure and fluorescence signal amplification of four DNA-templated silver nanoclusters offers the advantage of high sensitivity, with a low detection limit of 1 cell. More than that, this method is low-cost, facile, and feasible for practical clinical applications.

Universal Nanoparticle Counting Platform for Tetraplexed Biomarkers by Integrating Immunorecognition and Nucleic Acid Hybridization in One Assay

The development of a simple and universal strategy for simultaneous quantification of proteins and nucleic acid biomarkers in one assay is valuable, particularly for disease diagnosis and pathogenesis studies. Herein, a universal and amplification-free quantum dot-doped nanoparticle counting platform was developed by integrating immunorecognition and nucleic acid hybridization in one assay. The assay can be performed at room temperature, which is friendly for routine analysis. Multiplexed biomarkers associated with Alzheimer's disease (AD) including proteins and nucleic acids were detected. For simultaneous detection of tetraplex biomarkers, the assay for amyloid β 1-42 (Aβ42), tau protein, miR-146a, and miR-138 presented limit of detection values of 250 pg/mL, 55.7 pg/mL, 52.5 pM, and 0.62 pM, respectively. By spiking all the above four biomarkers in one artificial cerebrospinal fluid sample, the recoveries were found to be 94.7-117.2%. Using tau protein as the model, four measurements in 88 days presented a coefficient of variance of 7.5%. The proposed platform for the multiplexed assay of proteins and nucleic acids presents the universality, reasonable sensitivity, and repeatability, which may open a new door for early diagnosis and pathogenesis research for AD and other diseases.

MNAzyme probes mediated DNA logic platform for microRNAs logic detection and cancer cell identification

Here, a MNAzyme probes mediated DNA logic platform was developed for microRNAs (miRNAs) logic detection and cancer cells identification. A series of MNAzyme probes containing the cleavage active center were designed. Four types of logic gates were constructed, including YES, AND, XOR and NOR gate. These logic gates used miRNAs that were high expression in cancer cells as logic inputs and used MNAzyme cleavage amplification reaction to output signals. For the construction of intracellular logic gates, MnO₂ nanosheets were used as carriers and cofactor providers. When MnO₂ nanoprobes entered the cells through endocytosis, the intracellular glutathione degraded the MnO₂ nanosheets to release the cofactor Mn²⁺ and MNAzyme probes. The MNAzyme probes bound to the miRNAs and catalyze the MNAzyme cleavage amplification reaction, producing enhanced fluorescent signal with "true" output. The logic detection of miRNAs was achieved by integrating information from the AND, XOR and NOR logic gates. Moreover, through the construction of intracellular YES and AND logic gates, the cancer cells identification, especially the identification of same type of cancer cells with different phenotypes was achieved. These experimental results showed that this platform held great promise in accurate diagnosis and treatment of cancer.

A DNA Based Biosensor Amplified With ZIF-8/Ionic Liquid Composite for Determination of Mitoxantrone Anticancer Drug: An Experimental/Docking Investigation

An ultrasensitive DNA electrochemical biosensor based on the carbon paste electrode (CPE) amplified with ZIF-8 and 1-butyl-3-methylimidazolium methanesulfonate (BMIMS) was fabricated in this research. The DNA/BMIMS/ZIF-8/CPE was used for the selective determination of a mitoxantrone anticancer drug in aqueous solution, resulting in a good catalytic effect and a powerful ability for determining mitoxantrone. Also, the interaction of the mitoxantrone anticancer drug with guanine bases of ds-DNA was used as a powerful strategy in the suggested biosensor, which was confirmed with docking investigation. Docking study of mitoxantrone into the ds-DNA sequence showed the intercalative binding mode of mitoxantrone into the nitrogenous-based pairs of ds-DNA. The effective factors such as ds-DNA concentration, temperature, buffer types, and incubation time were also optimized for the fabricated mitoxantrone biosensor. The results showed that, under optimum conditions (T = 25°C; incubation time=12 min; pH= 4.8 acetate buffer solution and [DNA] = 50 mg/L), the DNA/BMIMS/ZIF-8/CPE could be used in mitoxantrone assay in a concentration ranging from 8.0 nM to 110 μM with a detection limit of 3.0 nM. In addition, recovery data between 99.18 and 102.08% were obtained for the determination of mitoxantrone in the injection samples using DNA/ZIF-8/BMIMF/CPE as powerful biosensors.

Simultaneous detection of small molecules, proteins and microRNAs using single molecule arrays

Biological samples such as blood, urine, cerebrospinal fluid and saliva contain a large variety of proteins, nucleic acids, and small molecules. These molecules can serve as potential biomarkers of disease and therefore, it is desirable to simultaneously detect multiple biomarkers in one sample. Current detection techniques suffer from various limitations including low analytical sensitivity and complex sample processing. In this work, we present an ultrasensitive method for simultaneous detection of small molecules, proteins and microRNAs using single molecule arrays (Simoa). Dye-encoded beads modified with specific capture probes were used to quantify each analyte. Multiplex competitive Simoa assays were established for simultaneous detection of cortisol and prostaglandin E2. In addition, competitive and sandwich immunoassays were combined with a direct nucleic acid hybridization assay for simultaneous detection of cortisol, interleukin 6 and microRNA 141. The multi-analyte Simoa assay shows high sensitivity and specificity, which provides a powerful tool for the analysis of many different samples.