Quick and sensitive SPR detection of prion disease-associated isoform (PrPSc) based on its self-assembling behavior on bare gold film and specific interactions with aptamer-graphene oxide (AGO)

Aptamers Targeting Hallmark Proteins of Neurodegeneration

Neurodegeneration is a progressive deterioration of neural structures leading to cognitive or motor impairment of the affected patient. There is still no effective therapy for any of the most common neurodegenerative diseases (NDs) such as Alzheimer's or Parkinson's disease. Although NDs exhibit distinct clinical characteristics, many are characterized by the accumulation of misfolded proteins or peptide fragments in the brain and/or spinal cord. The presence of similar inclusion bodies in patients with diverse NDs provides a rationale for developing therapies directed at overlapping disease mechanisms. A novel targeting strategy involves the use of aptamers for therapeutic development. Aptamers are short nucleic acid ligands able to recognize molecular targets with high specificity and high affinity. Despite the fact that several academic groups have shown that aptamers have the potential to be used in therapeutic and diagnostic applications, their clinical translation is still limited. In this study, we describe aptamers that have been developed against proteins relevant to NDs, including prion protein and amyloid beta (Aβ), cell surface receptors and other cytoplasmic proteins. This review also describes advances in the application of these aptamers in imaging, protein detection, and protein quantification, and it provides insights about their accelerated clinical use for disease diagnosis and therapy.

Recent advances in the synthesis and applications of graphene-polypeptide nanocomposites

The combination of peptides and graphene-derived materials provides a new way to prepare graphene-based nanocomposites with unique structures, properties, and functions. The modification of graphene with different polypeptides not only improves the biocompatibility and biological recognition ability of graphene-based materials, but also greatly expands their application fields. In this work, we summarize different interactions between graphene and polypeptides, and the synthesis methods of novel functional graphene-polypeptide nanocomposites based on the interactions in recent years (from 2016 to present). In addition, the potential applications of graphene-peptide hybrid nanocomposites in biomedicine, tissue engineering, biosensors, environmental science engineering, optoelectronic materials, and energy storage are introduced. We hope that this review will help readers to understand the methods and mechanisms of the modification of graphene surfaces with biomolecules, and promote readers to understand the synthesis and applications of graphene-based nanocomposites. This work may provide hints and references for the development of peptide sequence design, and biomedical and functional materials, and will help in designing and synthesizing novel graphene-based nanomaterials with unique properties and suitable for various applications in the future.

Recent Advancements in Aptamer-Based Surface Plasmon Resonance Biosensing Strategies

Surface plasmon resonance (SPR) can track molecular interactions in real time, and is a powerful as well as widely used biological and chemical sensing technique. Among the different SPR-based sensing applications, aptamer-based SPR biosensors have attracted significant attention because of their simplicity, feasibility, and low cost for target detection. Continuous developments in SPR aptasensing research have led to the emergence of abundant technical and design concepts. To understand the recent advances in SPR for biosensing, this paper reviews SPR-based research from the last seven years based on different sensing-type strategies and sub-directions. The characteristics of various SPR-based applications are introduced. We hope that this review will guide the development of SPR aptamer sensors for healthcare.

Recent Progress and Opportunities for Nucleic Acid Aptamers

Coined three decades ago, the term aptamer and directed evolution have now reached their maturity. The concept that nucleic acid could modulate the activity of target protein as ligand emerged from basic science studies of viruses. Aptamers are short nucleic acid sequences capable of specific, high-affinity molecular binding, which allow for therapeutic and diagnostic applications. Compared to traditional antibodies, aptamers have several advantages, including small size, flexible structure, good biocompatibility, and low immunogenicity. In vitro selection method is used to isolate aptamers that are specific for a desired target from a randomized oligonucleotide library. The first aptamer drug, Macugen, was approved by FDA in 2004, which was accompanied by many studies and clinical investigations on various targets and diseases. Despite much promise, most aptamers have failed to meet the requisite safety and efficacy standards in human clinical trials. Amid these setbacks, the emergence of novel technologies and recent advances in aptamer and systematic evolution of ligands by exponential enrichment (SELEX) design are fueling hope in this field. The unique properties of aptamer are gaining renewed interest in an era of COVID-19. The binding performance of an aptamer and reproducibility are still the key issues in tackling current hurdles in clinical translation. A thorough analysis of the aptamer binding under varying conditions and the conformational dynamics is warranted. Here, the challenges and opportunities of aptamers are reviewed with recent progress.

Sensitivity Enhancement of a Surface Plasmon Resonance Sensor with Platinum Diselenide

The extraordinary optoelectronic properties of platinum diselenide (PtSe2), whose structure is similar to graphene and phosphorene, has attracted great attention in new rapidly developed two-dimensional (2D) materials beyond the other 2D material family members. We have investigated the surface plasmon resonance (SPR) sensors through PtSe2 with the transfer matrix method. The simulation results show that the anticipated PtSe2 biochemical sensors have the ability to detect analytic. It is evident that only the sensitivities of Ag or Au film biochemical sensors were observed at 118°/RIU (refractive index unit) and 130°/RIU, whereas the sensitivities of the PtSe2-based biochemical sensors reached as high as 162°/RIU (Ag film) and 165°/RIU (Au film). The diverse biosensor sensitivities with PtSe2 suggest that this kind of 2D material can adapt SPR sensor properties.

The Response of UV/Blue Light and Ozone Sensing Using Ag-TiO2 Planar Nanocomposite Thin Film

We successfully fabricated a planar nanocomposite film that uses a composite of silver nanoparticles and titanium dioxide film (Ag-TiO₂) for ultraviolet (UV) and blue light detection and application in ozone gas sensor. Ultraviolet-visible spectra revealed that silver nanoparticles have a strong surface plasmon resonance (SPR) effect. A strong redshift of the plasmonic peak when the silver nanoparticles covered the TiO₂ thin film was observed. The value of conductivity change for the Ag-TiO₂ composite is 4–8 times greater than that of TiO₂ film under UV and blue light irradiation. The Ag-TiO₂ nanocomposite film successfully sensed 100 ppb ozone. The gas response of the composite film increased by roughly six and four times under UV and blue light irradiation, respectively. We demonstrated that a Ag-TiO₂ composite gas sensor can be used with visible light (blue). The planar composite significantly enhances photo catalysis. The composite films have practical application potential for wearable devices.

Graphene-based nanocomposites for sensitivity enhancement of surface plasmon resonance sensor for biological and chemical sensing: A review

Surface plasmon resonance (SPR) offers exceptional advantages such as label-free, in-situ and real-time measurement ability that facilitates the study of molecular or chemical binding events. Besides, SPR lacks in the detection of various binding events, particularly involving low molecular weight molecules. This drawback ultimately resulted in the development of several sensitivity enhancement methodologies and their application in the various area. Among graphene materials, graphene-based nanocomposites stands out owing to its significant properties such as strong adsorption of molecules, signal amplification by optical, high carrier mobility, electronic bridging, ease of fabrication and therefore, have established as an important sensitivity enhancement substrate for SPR. Also, graphene-based nanocomposites could amplify the signal generated by plasmon material and increase the sensitivity of molecular detection up to femto to atto molar level. This review focuses on the current important developments made in the potential research avenue of SPR and fiber optics based SPR for chemical and biological sensing. Latest trends and challenges in engineering and applications of graphene-based nanocomposites enhanced sensors for detecting minute and low concentration biological and chemical analytes are reviewed comprehensively. This review may aid in futuristic designing approaches and application of grapheneous sensor platforms for sensitive plasmonic nano-sensors.

How graphene affects the misfolding of human prion protein: A combined experimental and molecular dynamics simulation study

As the broad application of graphene in the biomedical field, it is urgent and important to evaluate how the graphene affects the structure and function of the proteins in our body, especially the amyloid-related proteins. Prion protein, as a typical amyloid protein, it misfolding and aggregation will lead to serious prion diseases. To explore if graphene promotes or inhibits the formation of amyloid, here, we combined the experimental and molecular dynamics (MD) simulation methods to study the influence of graphene on the globular domain of prion protein (PrP_117-231). The results from fluorescence quenching and circular dichroism spectrum showed that the addition of graphene changed the secondary structure of prion protein largely, mainly reflecting in the reduced α-helix structure and the increased coil structure, indicating graphene may strengthen the misfolding inclination of prion. To further uncover the mechanism of conformational change of prion under the induction of graphene, the all-atoms MD simulations in explicit solvent were performed. Our simulations suggest that prion protein can be quickly and tightly adsorbed onto graphene together with the weak conformational rearrangement and may reorient when approaching the surface. The Van der Waals' force drive the adsorption process. In the induction of graphene, H1 and S2-H2 loop regions of prion become unstable and prion begins to misfold partially. Our work shows that graphene can induce the misfolding of prion protein and may cause the potential risk to biosystems.

Ultrasensitive Detection of Bacterial Protein Toxins on Patterned Microarray via Surface Plasmon Resonance Imaging with Signal Amplification by Conjugate Nanoparticle Clusters

Sensitive detection and monitoring of biological interactions in a high throughput, multiplexed array format has numerous advantages. We report here a method to enhance detection sensitivity in surface plasmon resonance (SPR) spectroscopy and SPR imaging via the effect of accumulation of conjugated nanoparticles of varying sizes. Bacterial cholera toxin (CT) was chosen for the demonstration of enhanced immunoassay by SPR. After immobilization of CT on a gold surface, specific recognition is achieved by biotinylated anti-CT. The signal is amplified by the attachment of biotinylated 20 nm AuNP via streptavidin bridge, followed by attachment of 5 nm streptavidin-functionalized Fe₃O₄NP to the AuNP-biotin surface. The continuous surface binding of two differently sized conjugated nanoparticles effectively increases their packing density on surface and significantly improves SPR detection sensitivity, allowing quantitative measurement of CT at very low concentration. The dense packing of conjugated nanoparticles on the surface was confirmed by atomic force microscopy characterization. SPR imaging of the immunoassay for high-throughput analysis utilized an Au-well microarray that attenuated the background resonance interference on the resulting images. A calibration curve of conjugated nanoparticle binding signal amplification for CT detection based on surface coverage has been obtained that shows a correlation in a range from 6.31 × 10^-16 to 2.51 × 10^-13 mol/cm² with the limit of detection of 5.01 × 10^-16 mol/cm². The absolute quantity of detection limit using SPR imaging was 0.25 fmol. The versatile nanoparticles and biotin-streptavidin interaction used here should allow adaptation of this enhancement method to many other systems that include DNA, RNA, peptides, and carbohydrates, opening new avenues for ultrasensitive analysis of biomolecules.

Ultra-sensitive detection by metal nanoparticles-mediated enhanced SPR biosensors

Surface plasmon resonance (SPR), as an optical technique, has widely been used for the detection of biomarkers. Various investigations have been conducted to address the impacts of SPR on the kinetics of biological interactions between the ligand and its cognate bio-element. Up until now, different biofunctionalized metal nanoparticles (NPs) have been used for the ultrasensitive detection of biomarkers in the enhanced SPR. The enhancement of plasmonic properties and refractive index by means of metal NPs in SPR-based biosensors have significantly improved the diagnosis and monitoring of molecular markers in different disesaes including malignancies. In all the enhanced SPR systems utilized for the direct/sandwich assay, each NP is covalently modified with the analyte molecules like antibody (Ab) or a nucleic acid such as DNA/RNA aptamer (Ap) capable of interaction with the related biomarker(s). The increasing of density near the gold surface and plasmonic coupling of gold film and NPs can provide a large shift in the refractive index enhancing the plasmonic resonance because the SPR response unit is sensitive to alteration of the refractive index and the mass shifting onto the chip surface. In this study, we review the potential applications of two major NPs for enhancing the SPR signals for the detection of molecular biomarkers, including gold and magnetic NPs.

Fabrication of Magnetic Conjugation Clusters via Intermolecular Assembling for Ultrasensitive Surface Plasmon Resonance (SPR) Detection in a Wide Range of Concentrations

Herein, a novel sandwich surface plasmon resonance (SPR) detection assay, which utilizes prion disease-associated isoform (PrP^Sc) conjugating magnetic nanoparticle clusters (nanoparticle-organic clusters, NOCs) as signal amplification reagents, is constructed for the ultrasensitive detection of PrP^Sc. Due to the highly specific affinity of aptamer-Fe₃O₄ nanoparticles (AMNPs) toward PrP^Sc and the intermolecular assembly behaviors among PrP^Sc, PrP^Sc conjugating magnetic nanoparticle clusters were obtained after the incubation of AMNPs and PrP^Sc and the subsequent concentration processes in an external magnetic field. The conjugation clusters were further injected into the SPR cuvette and captured by the gold sensing film via the Au-S bonding interaction, inducing intense SPR responses. Meanwhile, a traditional sandwich SPR detection format using a gold/PrPSc/AMNPs amplification mode was conducted for the detection of PrP^Sc as comparison. The results reveal that the synthesized NOCs permitted a 215-fold increase of the SPR signal, while the sandwich format permitted only a 65-fold increase. Moreover, a lower detection limit (1 × 10^-4 ng/mL) and a wider quantitation range (1 × 10^-4-1 × 10⁵ ng/mL) were demonstrated. The formation of the conjugation clusters and the capture of these clusters were confirmed by high-resolution AFM imaging and molecular simulations. This conjugation-cluster-induced signal amplification strategy has great potential for the detection of small analytes with similar structural characteristics in trace level concentrations with high selectivity and sensitivity by altering the corresponding aptamer labeled to magnetic particles.