Single-Molecule Identification of the Conformations of Human C-Reactive Protein and Its Aptamer Complex with Solid-State Nanopores

Enhancing RBP4 protein detection in clinical urine samples with solid-state nanopores through optimized sandwich immunoassay techniques

Nanopore technology is a promising single-molecule sensing platform that can identify substances through the precise monitoring of changes in ion currents. However, protein detection in clinical samples using solid-state nanopores remains challenging due to their heterogeneously charged spherical structure, which results in signals with extremely low signal-to-noise ratios (SNR) and low capture rates that are difficult to analyze. In this study, we employed a double-antibody sandwich technique to specifically capture and amplify the target antigen, which significantly improves the SNR and effectively distinguishes the target signal from background interference. Key factors including buffer composition, voltage, antibody concentration, and pore dimensions were systematically optimized to further improve capture efficiency. The optimized approach enabled precise and reliable detection of retinol-binding protein 4 (RBP4) with an excellent linear response within the range of 55 fM to 5.5 pM. Moreover, our method facilitates quantitative detection of RBP4 in clinical urine samples within 40 min, and achieves 100% accuracy in distinguishing between 11 urine samples from chronic kidney disease (CKD) patients and healthy donors, highlighting its robustness and specificity. Our research not only paves a new pathway for efficient RBP4 detection, but also provides valuable insights into the application of nanopore technology for the clinical diagnosis of protein biomarkers.

Regulation of Protein Transport in Functionalized PET Nanopores

Facilitated translocation is a critical mechanism for transporting substances in biological systems, where molecular and ionic species move across the biological membrane with the help of specific transmembrane protein ion channels. In this work, we systematically examined protein transport in three poly(ethylene terephthalate) (PET) nanopores modified with different types of surface functions (hydroxyl, phenyl, and amine). We found that the event signature as well as the kinetics and thermodynamics of protein movement in the PET nanopore varied significantly with the change in the surface function in the pore. In addition to the electrophoretic effect, other factors such as diffusion, electro-osmotic effect, ion selectivity of the channel, and affinity strength between the protein species and the surface functional group of the nanopore also play significant roles in the protein transport. Although properly functionalized individual PET nanopores can be used as stochastic elements for rapid protein differentiation and characterization, enhanced resolution and accuracy could be accomplished by employing an array of PET nanopores having different inner surface functional groups to characterize proteins based on their collective responses. Given the important roles proteins play in living organisms and their applications as biomarkers in early disease diagnosis and prognosis, the pattern-recognition solid-state nanopore-sensing strategy for protein detection and characterization developed in this work may find useful applications in various fields.

Research Progress of Electrochemical Biosensors for Diseases Detection in China: A Review

Disease diagnosis is not only related to individual health but is also a crucial part of public health prevention. Electrochemical biosensors combine the high sensitivity of electrochemical methods with the inherent high selectivity of biological components, offering advantages such as excellent sensitivity, fast response time, and low cost. The generated electrical signals have a linear relationship with the target analyte, allowing for identification and concentration detection. This has become a very attractive technology. This review offers a summary of recent advancements in electrochemical biosensor research for disease diagnosis in China. It systematically categorizes and summarizes biosensors developed in China for detecting cancer, infectious diseases, inflammation, and neurodegenerative disorders. Additionally, the review delves into the fundamental working principles, classifications, materials, preparation techniques, and other critical aspects of electrochemical biosensors. Finally, it addresses the key challenges impeding the advancement of electrochemical biosensors in China and examines promising future directions for their development.

Biorecognition-based electrochemical sensors for highly sensitive C-reactive protein detection: A review

Highly sensitive C-reactive protein (hsCRP) is a widely recognized biomarker for inflammation and cardiovascular diseases and plays a critical role in early diagnosis, risk assessment, and treatment monitoring. The development of sensitive and selective techniques for hsCRP detection is of paramount importance for clinical diagnostics. Electrochemical sensors have emerged as promising alternatives to traditional methods, offering rapid, cost-effective, and portable solutions for hsCRP analysis. This review comprehensively discusses advancements in biorecognition-based electrochemical sensors for hsCRP detection, focusing on label- and label-free approaches. This review highlights the sensor principles, designs, and performance, and emphasizes their advantages as well as limitations in various target applications. Recent studies have shown the potential of both label- and label-free-based sensors to achieve low detection limits and wide linear ranges comparable to traditional methods. In addition, we discuss the mechanisms, challenges, and future directions of biorecognition-based electrochemical sensors for hsCRP detection. This innovation can potentially revolutionize the diagnosis and treatment of cardiovascular and inflammatory diseases by enhancing the detection sensitivity and specificity. Ultimately, these advancements aim to improve patient outcomes by enabling earlier diagnosis, cost-effectiveness, and more precise monitoring, contributing to more effective management of cardiovascular health globally.

Nafion coated nanopore electrode for improving electrochemical aptamer-based biosensing

The transition to a personalized point-of-care model in medicine will fundamentally change the way medicine is practiced, leading to better patient care. Electrochemical biosensors based on structure-switching aptamers can contribute to this medical revolution due to the feasibility and convenience of selecting aptamers for specific targets. Recent studies have reported that nanostructured electrodes can enhance the signals of aptamer-based biosensors. However, miniaturized systems and body fluid environments pose challenges such as signal-to-noise ratio reduction and biofouling. To address these issues, researchers have proposed various electrode coating materials, including zwitterionic materials, biocompatible polymers and hybrid membranes. Nafion, a commonly used ion exchange membrane, is known for its excellent permselectivity and anti-biofouling properties, making it a suitable choice for biosensor systems. However, the performance and mechanism of Nafion-coated aptamer-based biosensor systems have not been thoroughly studied. In this work, we present a Nafion-coated gold nanoporous electrode, which excludes Nafion from the nanoporous structures and allows the aptamers immobilized inside the nanopores to freely detect chosen targets. The nanopore electrode is formed by a sputtering and dealloying process, resulting in a pore size in tens of nanometers. The biosensor is optimized by adjusting the electrochemical measurement parameters, aptamer density, Nafion thickness and nanopore size. Furthermore, we propose an explanation for the unusual signaling behavior of the aptamers confined within the nanoporous structures. This work provides a generalizable platform to investigate membrane-coated aptamer-based biosensors.

Solid-State Nanopores for Biomolecular Analysis and Detection

Advances in nanopore technology and data processing have rendered DNA sequencing highly accessible, unlocking a new realm of biotechnological opportunities. Commercially available nanopores for DNA sequencing are of biological origin and have certain disadvantages such as having specific environmental requirements to retain functionality. Solid-state nanopores have received increased attention as modular systems with controllable characteristics that enable deployment in non-physiological milieu. Thus, we focus our review on summarizing recent innovations in the field of solid-state nanopores to envision the future of this technology for biomolecular analysis and detection. We begin by introducing the physical aspects of nanopore measurements ranging from interfacial interactions at pore and electrode surfaces to mass transport of analytes and data analysis of recorded signals. Then, developments in nanopore fabrication and post-processing techniques with the pros and cons of different methodologies are examined. Subsequently, progress to facilitate DNA sequencing using solid-state nanopores is described to assess how this platform is evolving to tackle the more complex challenge of protein sequencing. Beyond sequencing, we highlight the recent developments in biosensing of nucleic acids, proteins, and sugars and conclude with an outlook on the frontiers of nanopore technologies.

Solid-State Nanopore Distinguishes Ferritin and Apo-Ferritin with Identical Exteriors through Amplified Flexibility at Single-Molecule Level

Protein identification and discrimination at the single-molecule level are big challenges. Solid-state nanopores as a sensitive biosensor have been used for protein analysis, although it is difficult to discriminate proteins with similar structures in the traditional discrimination method based on the current blockage fraction. Here, we select ferritin and apo-ferritin as the model proteins that exhibit identical exterior and different interior structures and verify the practicability of their discrimination with flexibility features by the strategy of gradually decreasing the nanopore size. We show that the larger nanopore (relative to the protein size) has no obvious effect on discriminating two proteins. Then, the comparable-sized nanopore plays a key role in discriminating two proteins based on the dwell time and fraction distribution, and the conformational changes of both proteins are also studied with this nanopore. Finally, in the smaller nanopore, the protein molecules are trapped rather than translocated, where two proteins are obviously discriminated through the current fluctuation caused by the vibration of proteins. This strategy has potential in the discrimination of other important similar proteins.

Nanopore Single-molecule Analysis of Biomarkers: Providing Possible Clues to Disease Diagnosis

Biomarker detection has attracted increasing interest in recent years due to the minimally or non-invasive sampling process. Single entity analysis of biomarkers is expected to provide real-time and accurate biological information for early disease diagnosis and prognosis, which is critical to the effective disease treatment and is also important in personalized medicine. As an innovative single entity analysis method, nanopore sensing is a pioneering single-molecule detection technique that is widely used in analytical bioanalytical fields. In this review, we overview the recent progress of nanopore biomarker detection as new approaches to disease diagnosis. In highlighted studies, nanopore was focusing on detecting biomarkers of different categories of communicable and noncommunicable diseases, such as pandemic Covid-19, AIDS, cancers, neurologic diseases, etc. Various sensitive and selective nanopore detecting strategies for different types of biomarkers are summarized. In addition, the challenges, opportunities, and direction for future development of nanopore-based biomarker sensors are also discussed.

Procedural Data Processing for Single-Molecule Identification by Nanopore Sensors

Nanopores are promising single-molecule sensing devices that have been successfully used for DNA sequencing, protein identification, as well as virus/particles detection. It is important to understand and characterize the current pulses collected by nanopore sensors, which imply the associated information of the analytes, including the size, structure, and surface charge. Therefore, a signal processing program, based on the MATLAB platform, was designed to characterize the ionic current signals of nanopore measurements. In a movable data window, the selected current segment was analyzed by the adaptive thresholds and corrected by multi-functions to reduce the noise obstruction of pulse signals. Accordingly, a set of single molecular events was identified, and the abundant information of current signals with the dwell time, amplitude, and current pulse area was exported for quantitative analysis. The program contributes to the efficient and fast processing of nanopore signals with a high signal-to-noise ratio, which promotes the development of the nanopore sensing devices in various fields of diagnosis systems and precision medicine.

Metal-Organic Cage as Single-Molecule Carrier for Solid-State Nanopore Analysis

The ability to detect biomolecules at the single-molecule level is at the forefront of biological research, precision medicine, and early diagnosis. Recently, solid-state nanopore sensors have emerged as a promising technique for label-free and precise diagnosis assay. However, insufficient sensitivity and selectivity for small analytes are a great challenge for clinical diagnosis applications via solid-state nanopores. Here, for the first time, a metal-organic cage, PCC-57, is employed as a carrier to increase the sensitivity and selectivity of solid-state nanopores based on the intrinsic interaction of the nanocage with biomolecules. Firstly, it is found that the carrier itself is undetectable unless bound with the target analytes and used oligonucleotides as linkers to attach PCC-57 and target analytes. Secondly, two small analytes, oligonucleotide conjugated angiopep-2 and polyphosphoric acid, are successfully distinguished using the molecular carrier. Finally, selectivity of nanopore detection is achieved by attaching PCC-57 to oligonucleotide-tailed aptamers, and the human alpha-thrombin sample is successfully detected. It is believed that the highly designable metal-organic cage could serve as a rich carrier repository for a variety of biomolecules, facilitating single-molecule screening of clinically relevant biomolecules based on solid-state nanopores in the future.