Cluster-Enhanced Nanopore Sensing of Ovarian Cancer Marker Peptides in Urine

Empowering protein single-molecule sequencing: nanopore technology toward sensing gene sequences

The investigation of proteins at the single-molecule level is urgent to reveal the relationship between their structure and function. Unlike traditional techniques for attaining the overall average effect of group systems, nanopore sensing mode can provide information on the characteristics of proteins at the single-molecule level. Assisting with the intensity, frequency, and period of current changes, nanopore sequencing technology is rapidly advancing due to its merits, including fast readout, high accuracy, low cost, and portability. In particular, the single-molecule nanopore sequencing mode enables in-depth studies of DNA-protein interactions, protein conformation, DNA sequencing, and microbial assay, including genome sequencing of new species. This review summarizes the sensing mechanisms of nanopore sequencing technology in DNA damage, DNA methylation, RNA sequencing, and protein post-translational modifications and unfolding, covering both biological and solid-state nanopores. Due to these significant advantages, nanopore sequencing provides new insights into complex biological processes and enables more precise real-time monitoring of molecular changes. Its applications extend to clinical diagnostics, environmental monitoring, food safety, and forensic analysis. Moreover, the review outlines the present challenges faced by nanopore sequencing patterns, such as the choice of raw reagents and the design of special construction, offering a deep understanding of nanoporous single-molecule sensing toward protein sequence information and structure prediction.

Body fluid diagnostics using activatable optical probes

In vitro diagnostics often detects biomarkers in body fluids (such as blood, urine, sputum, and cerebrospinal fluids) to identify life-threatening diseases at an early stage, monitor overall health, or provide information to help cure, treat, or prevent diseases. Most clinically used optical in vitro diagnostic tests utilize dye-labeled biomolecules for biomarker recognition and signal readout, which typically involve complex steps and long processing times. Activatable optical probes (AOPs), which spontaneously activate their optical signals only in the presence of disease biomarkers, offer higher signal-to-background ratios and improved detection specificity. They also have the potential to simplify detection procedures by eliminating multiple washing steps. In this review, we summarize recent advances in the use of AOPs for pre-clinical and clinical body fluid diagnostics across various diseases, including cancer, nephro-urological disorders, infectious diseases, and digestive diseases. We begin by discussing the molecular design strategies of AOPs to achieve different optical signal readouts and biomarker specificity. We then highlight their diagnostic applications in various disease models and body fluids. Finally, we address the challenges and future perspectives of AOPs in enhancing body fluid diagnostics and advancing precision medicine.

Nanopore sensing of protein and peptide conformation for point-of-care applications

The global population's aging and growth will likely result in an increase in chronic aging-related diseases. Early diagnosis could improve the medical care and quality of life. Many diseases are linked to misfolding or conformational changes in biomarker peptides and proteins, which affect their function and binding properties. Current clinical methods struggle to detect and quantify these changes. Therefore, there is a need for sensitive conformational sensors that can detect low-concentration analytes in biofluids. Nanopore electrical detection has shown potential in sensing subtle protein and peptide conformation changes. This technique can detect single molecules label-free while distinguishing shape or physicochemical property changes. Its proven sensitivity makes nanopore sensing technology promising for ultra-sensitive, personalized point-of-care devices. We focus on the capability of nanopore sensing for detecting and quantifying conformational modifications and enantiomers in biomarker proteins and peptides and discuss this technology as a solution to future societal health challenges.

A Patient-Centered Approach in Sensor Science: Embracing Patient Engagement for Translational Clinical Technologies

With the goal of impacting patient quality of life and outcomes, sensor science offers significant potential to revolutionize healthcare by providing advances in the detection of molecular biomarkers for personalized clinical technologies. The sensor community has achieved significant technical advancements that can impact diagnostics, health monitoring, and disease treatment; however, many sensor innovations remain confined to the laboratory, failing to bridge the translational gap between research and real-world clinical applications. This perspective presents a new direction for the sensor community, where sensor development centers on the needs and experiences of the primary beneficiaries: the patients. We provide guidelines and resources for researchers to engage with patients early and continuously throughout the research process to inform sensor specifications and better align sensor technologies with real-world clinical needs, improving their adoption and impact. We also present examples for implementing a patient-centered approach in sensor development and planning for patient engagement in sensor research. In the design of impactful sensors for patients, researchers must expand focus beyond technical specifications to embrace a patient-centered approach, which will likely lead to new opportunities for collaboration and evolution in the sensor science community.

Evolving landscape of detection and targeting miRNA/epigenetics for therapeutic strategies in ovarian cancer

Ovarian cancer (OC) accounts for the highest mortality rates among all gynecologic malignancies. The high mortality of OC is often associated with delayed detection, prolonged latency, enhanced metastatic potential, acquired drug resistance, and frequent recurrence. This review comprehensively explores key aspects of OC, including cancer diagnosis, mechanisms of disease resistance, and the pivotal role of epigenetic regulation, particularly by microRNAs (miRs) in cancer progression. We highlight the intricate regulatory mechanisms governing miR expression within the context of OC and the current status of epigenetic advancement in the therapeutic development and clinical trial progression. Through network analysis we elucidate the regulatory interactions between dysregulated miRs in OC and their targets which are involved in different signaling pathways. By exploring these interconnected facets and critical analysis, we endeavor to provide a nuanced understanding of the molecular dynamics underlying OC, its detection and shedding light on potential avenues for miRs and epigenetics-based therapeutic intervention and management strategies.

DNA Origami Incorporated into Solid-State Nanopores Enables Enhanced Sensitivity for Precise Analysis of Protein Translocations

The rapidly advancing field of nanotechnology is driving the development of precise sensing methods at the nanoscale, with solid-state nanopores emerging as promising tools for biomolecular sensing. This study investigates the increased sensitivity of solid-state nanopores achieved by integrating DNA origami structures, leading to the improved analysis of protein translocations. Using holo human serum transferrin (holo-hSTf) as a model protein, we compared hybrid nanopores incorporating DNA origami with open solid-state nanopores. Results show a significant enhancement in holo-hSTf detection sensitivity with DNA origami integration, suggesting a unique role of DNA interactions beyond confinement. This approach holds potential for ultrasensitive protein detection in biosensing applications, offering advancements in biomedical research and diagnostic tool development for diseases with low-abundance protein biomarkers. Further exploration of origami designs and nanopore configurations promises even greater sensitivity and versatility in the detection of a wider range of proteins, paving the way for advanced biosensing technologies.

Exploring single-molecule interactions: heparin and FGF-1 proteins through solid-state nanopores

Detection and characterization of protein-protein interactions are essential for many cellular processes, such as cell growth, tissue repair, drug delivery, and other physiological functions. In our research, we have utilized emerging solid-state nanopore sensing technology, which is highly sensitive to better understand heparin and fibroblast growth factor 1 (FGF-1) protein interactions at a single-molecule level without any modifications. Understanding the structure and behavior of heparin-FGF-1 complexes at the single-molecule level is very important. An abnormality in their formation can lead to life-threatening conditions like tumor growth, fibrosis, and neurological disorders. Using a controlled dielectric breakdown pore fabrication approach, we have characterized individual heparin and FGF-1 (one of the 22 known FGFs in humans) proteins through the fabrication of 17 ± 1 nm nanopores. Compared to heparin, the positively charged heparin-binding domains of some FGF-1 proteins translocationally react with the pore walls, giving rise to a distinguishable second peak with higher current blockade. Additionally, we have confirmed that the dynamic FGF-1 is stabilized upon binding with heparin-FGF-1 at the single-molecule level. The larger current blockades from the complexes relative to individual heparin and the FGF-1 recorded during the translocation ensure the binding of heparin-FGF-1 proteins, forming binding complexes with higher excluded volumes. Taken together, we demonstrate that solid-state nanopores can be employed to investigate the properties of individual proteins and their complex interactions, potentially paving the way for innovative medical therapies and advancements.