Quantum Dot Fullerene-Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection

Smart Stimuli-Responsive Spherical Nucleic Acids: Cutting-Edge Platforms for Biosensing, Bioimaging, and Therapeutics

Spherical nucleic acids (SNAs) with exceptional colloidal stability, multiple modularity, and programmability are excellent candidates to address common molecular delivery-related issues. Based on this, the higher targeting accuracy and enhanced controllability of stimuli-responsive SNAs render them precise nanoplatforms with inestimable prospects for diverse biomedical applications. Therefore, tailored diagnosis and treatment with stimuli-responsive SNAs may be a robust strategy to break through the bottlenecks associated with traditional nanocarriers. Various stimuli-responsive SNAs are engineered through the incorporation of multifunctional modifications to meet biomedical demands with the development of nucleic acid functionalization. This review provides a comprehensive overview of prominent research in this area and recent advancements in the utilization of stimuli-responsive SNAs in biosensing, bioimaging, and therapeutics. For each aspect, SNA nanoplatforms that exhibit responsive behavior to both internal stimuli (including sequence, enzyme, redox reactions, and pH) and external stimuli (such as light and temperature) are highlighted. This review is expected to offer inspiration and guidance strategies for the rational design and development of stimuli-responsive SNAs in the field of biomedicine.

Zero-Dimensional Carbon Nanomaterials for Fluorescent Sensing and Imaging

Advances in nanotechnology and nanomaterials have attracted considerable interest and play key roles in scientific innovations in diverse fields. In particular, increased attention has been focused on carbon-based nanomaterials exhibiting diverse extended structures and unique properties. Among these materials, zero-dimensional structures, including fullerenes, carbon nano-onions, carbon nanodiamonds, and carbon dots, possess excellent bioaffinities and superior fluorescence properties that make these structures suitable for application to environmental and biological sensing, imaging, and therapeutics. This review provides a systematic overview of the classification and structural properties, design principles and preparation methods, and optical properties and sensing applications of zero-dimensional carbon nanomaterials. Recent interesting breakthroughs in the sensitive and selective sensing and imaging of heavy metal pollutants, hazardous substances, and bioactive molecules as well as applications in information encryption, super-resolution and photoacoustic imaging, and phototherapy and nanomedicine delivery are the main focus of this review. Finally, future challenges and prospects of these materials are highlighted and envisaged. This review presents a comprehensive basis and directions for designing, developing, and applying fascinating fluorescent sensors fabricated based on zero-dimensional carbon nanomaterials for specific requirements in numerous research fields.

Enzyme-Mimics for Sensitive and Selective Steroid Metabolite Detection

We present an enzyme-like functional polymer that recognizes nonelectroactive targets and catalyzes their redox reactions for simple, selective steroid metabolite detection. Measuring steroid metabolites, such as cortisol, has been widely adopted to diagnose stress and chronic diseases. Conventional detection method based on competitive immunoassay requires time-consuming labeling processes for signal transduction and unstable biological receptors for biorecognition yet with limited selectivity. Inspired by natural enzymes' target specificity and catalytic nature, we report an enzyme-mimic using electrocatalytic molecularly imprinted polymers (EC-MIP) to achieve label-free, external redox reagent-free, sensitive, and selective electrochemical detection of cortisol. The EC-MIP sensor contains molecularly imprinted cavities for specific cortisol binding and embedded copper phthalocyanine tetrasulfonate (CuPcTS) for electrocatalytic reduction of the ketones on the captured cortisol into alcohols. The direct sensing approach resolves the intrinsic limitations of conventional MIP-based sensors, most notably the use of external redox probes and weak sensing signals. The sensor exhibited a detection limit of 181 pM with significantly enhanced selectivity using a differential sensing mechanism. The new enzyme-like sensor can be modified to detect other targets, offering a simple, robust approach to future health monitoring technologies.

DNA-Immobilized Fluorescent Polystyrene Nanoparticles as Probes with Tunable Detection Limits

DNA-immobilized nanoparticle probes show high target specificity; thus, they are employed in various bioengineering and biomedicine applications. When the nanoparticles employed are dye-loaded polymer particles, the resulting probes have the additional benefit of biocompatibility and versatile surface properties. In this study, we construct DNA-immobilized fluorescent polystyrene (PS) nanoparticles through controlled surface reactions. PS nanoparticles with surface carboxyl groups are utilized, and amine-functionalized dye molecules and capture DNAs are covalently immobilized via a one-pot reaction. We show that the surface chemistry employed allows for quantitative control over the number of fluorescent dyes and DNA strands immobilized on the PS nanoparticle surfaces. The nanoparticles thus prepared are then used for DNA detection. The off state of the nanoprobe is achieved by hybridizing quencher-functionalized DNAs (Q-DNAs) to the capture DNAs immobilized on nanoparticle surfaces. Target-DNAs (T-DNAs) are detected by the displacement of the prehybridized Q-DNAs. The nanoprobes show successful detection of T-DNAs with high sequence specificity and long-term stability. They also show excellent detection sensitivity, and the detection limit can be tuned by adjusting the capture DNA-to-dye ratio.

Nanomaterials for Cortisol Sensing

Space represents one of the most dangerous environments for humans, which can be affected by high stress levels. This can lead to severe physiological problems, such as headaches, gastrointestinal disorders, anxiety, hypertension, depression, and coronary heart diseases. During a stress condition, the human body produces specific hormones, such as dopamine, adrenaline, noradrenaline, and cortisol. In particular, the control of cortisol levels can be related to the stress level of an astronaut, particularly during a long-term space mission. The common analytical methods (HPLC, GC-MS) cannot be used in an extreme environment, such as a space station, due to the steric hindrance of the instruments and the absence of gravity. For these reasons, the development of smart sensing devices with a facile and fast analytical protocol can be extremely useful for space applications. This review summarizes the recent (from 2011) miniaturized sensoristic devices based on nanomaterials (gold and carbon nanoparticles, nanotubes, nanowires, nano-electrodes), which allow rapid and real-time analyses of cortisol levels in biological samples (such as saliva, urine, sweat, and plasma), to monitor the health conditions of humans under extreme stress conditions.

Function of Graphene Oxide as the “Nanoquencher” for Hg2+ Detection Using an Exonuclease I-Assisted Biosensor

Graphene oxide is well known for its excellent fluorescence quenching ability. In this study, positively charged graphene oxide (pGO25000) was developed as a fluorescence quencher that is water-soluble and synthesized by grafting polyetherimide onto graphene oxide nanosheets by a carbodiimide reaction. Compared to graphene oxide, the fluorescence quenching ability of pGO25000 is significantly improved by the increase in the affinity between pGO25000 and the DNA strand, which is introduced by the additional electrostatic interaction. The FAM-labeled single-stranded DNA probe can be almost completely quenched at concentrations of pGO25000 as low as 0.1 μg/mL. A simple and novel FAM-labeled single-stranded DNA sensor was designed for Hg²⁺ detection to take advantage of exonuclease I-triggered single-stranded DNA hydrolysis, and pGO25000 acted as a fluorescence quencher. The FAM-labeled single-stranded DNA probe is present as a hairpin structure by the formation of T–Hg²⁺–T when Hg²⁺ is present, and no fluorescence is observed. It is digested by exonuclease I without Hg²⁺, and fluorescence is recovered. The fluorescence intensity of the proposed biosensor was positively correlated with the Hg²⁺ concentration in the range of 0–250 nM (R² = 0.9955), with a seasonable limit of detection (3σ) cal. 3.93 nM. It was successfully applied to real samples of pond water for Hg²⁺ detection, obtaining a recovery rate from 99.6% to 101.1%.

Multifunctional carbon nanomaterials for diagnostic applications in infectious diseases and tumors

Infectious diseases (such as Corona Virus Disease 2019) and tumors pose a tremendous challenge to global public health. Early diagnosis of infectious diseases and tumors can lead to effective control and early intervention of the patient's condition. Over the past few decades, carbon nanomaterials (CNs) have attracted widespread attention in different scientific disciplines. In the field of biomedicine, carbon nanotubes, graphene, carbon quantum dots and fullerenes have the ability of improving the accuracy of the diagnosis by the improvement of the diagnostic approaches. Therefore, this review highlights their applications in the diagnosis of infectious diseases and tumors over the past five years. Recent advances in the field of biosensing, bioimaging, and nucleic acid amplification by such CNs are introduced and discussed, emphasizing the importance of their unique properties in infectious disease and tumor diagnosis and the challenges and opportunities that exist for future clinical applications. Although the application of CNs in the diagnosis of several diseases is still at a beginning stage, biosensors, bioimaging technologies and nucleic acid amplification technologies built on CNs represent a new generation of promising diagnostic tools that further support their potential application in infectious disease and tumor diagnosis.

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Carbon nanomaterials (CNs) are systematically introduced in this review.

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This review studies the application of CNs in infectious diseases and tumors diagnosis.

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CNs act as potent nanostructures for biosensing, bioimaging, & nucleic acid amplification.

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New CN-based detection methods were introduced to detect SARS-CoV-2.

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The challenges and prospects of CN-based diagnostic assays are also discussed.

Visible-light and near-infrared fluorescence and surface-enhanced Raman scattering point-of-care sensing and bio-imaging: a review

This review article deals with the concepts, principles and applications of visible-light and near-infrared (NIR) fluorescence and surface-enhanced Raman scattering (SERS) in in vitro point-of-care testing (POCT) and in vivo bio-imaging. It has discussed how to utilize the biological transparency windows to improve the penetration depth and signal-to-noise ratio, and how to use surface plasmon resonance (SPR) to amplify fluorescence and SERS signals. This article has highlighted some plasmonic fluorescence and SERS probes. It has also reviewed the design strategies of fluorescent and SERS sensors in the detection of metal ions, small molecules, proteins and nucleic acids. Particularly, it has provided perspectives on the integration of fluorescent and SERS sensors into microfluidic chips as lab-on-chips to realize point-of-care testing. It has also discussed the design of active microfluidic devices and non-paper- or paper-based lateral flow assays for in vitro diagnostics. In addition, this article has discussed the strategies to design in vivo NIR fluorescence and SERS bio-imaging platforms for monitoring physiological processes and disease progression in live cells and tissues. Moreover, it has highlighted the applications of POCT and bio-imaging in testing toxins, heavy metals, illicit drugs, cancers, traumatic brain injuries, and infectious diseases such as COVID-19, influenza, HIV and sepsis.

Novel nucleic acid origami structures and conventional molecular beacon-based platforms: a comparison in biosensing applications

Nucleic acid nanotechnology designs and develops synthetic nucleic acid strands to fabricate nanosized functional systems. Structural properties and the conformational polymorphism of nucleic acid sequences are inherent characteristics that make nucleic acid nanostructures attractive systems in biosensing. This review critically discusses recent advances in biosensing derived from molecular beacon and DNA origami structures. Molecular beacons belong to a conventional class of nucleic acid structures used in biosensing, whereas DNA origami nanostructures are fabricated by fully exploiting possibilities offered by nucleic acid nanotechnology. We present nucleic acid scaffolds divided into conventional hairpin molecular beacons and DNA origami, and discuss some relevant examples by focusing on peculiar aspects exploited in biosensing applications. We also critically evaluate analytical uses of the synthetic nucleic acid structures in biosensing to point out similarities and differences between traditional hairpin nucleic acid sequences and DNA origami.

Label-Free Sensitive Detection of Steroid Hormone Cortisol Based on Target-Induced Fluorescence Quenching of Quantum Dots

We discovered that several types of steroid hormones quench the fluorescence of quantum dots (QDs) at close proximity. Inspired by the finding, we developed a new type of biosensor for the sensitive detection of cortisol via direct fluorescence quenching of functionalized QD probes directly induced by the capture of target cortisol without additional reporter reagents. The detection selectivity was provided by cortisol-selective aptamers or anticortisol antibodies conjugated on the QD surfaces. With the magnetic nanoparticle labeling, the new sensing method enabled rapid cortisol sensing at physiologically relevant concentrations and yielded the detection limit of ∼1 nM for aptamer-based sensors and ∼100 pM for antibody-based sensors. We also evaluated the new detection method using saliva samples with an optimized sample preparation process under the assistance of magnetic manipulation. The result showed a satisfying recovery rate for spiked saliva tests. The facile sensing technology offers an appealing approach for the detection of steroid hormones in point-of-care settings.

Development of a Portable SPR Sensor for Nucleic Acid Detection

Nucleic acid detection is of great significance in clinical diagnosis, environmental monitoring and food safety. Compared with the traditional nucleic acid amplification detection method, surface plasmon resonance (SPR) sensing technology has the advantages of being label-free, having simple operation, and providing real-time detection. However, the angle scanning system in many SPR angle modulation detection applications usually requires a high-resolution stepper motor and complex mechanical structure to adjust the angle. In this paper, a portable multi-angle scanning SPR sensor was designed. The sensor only uses one stepping motor to rotate a belt, and the belt pulls the mechanical linkages of incident light and reflected light to move in opposite directions for achieving the SPR angle scanning mode that keeps the incident angle and reflected angle equal. The sensor has an angle scanning accuracy of 0.002°, response sensitivity of 3.72 × 10⁻⁶ RIU (refractive index unit), and an angle scanning range of 30°–74°. The overall size of the system is only 480 mm × 150 mm × 180 mm. The portable SPR sensor was used to detect nucleic acid hybridization on a gold film chip modified with bovine serum albumin (BSA). The result revealed that the sensor had high sensitivity and fast response, and could successfully accomplish the hybridization detection of target DNA solution of 0.01 μmol/mL.

Rolling Circle Amplification-Based Polyvalent Molecular Beacon Probe-Assisted Signal Amplification Strategies for Sensitive Detection of B16 Cells

We developed a simple and sensitive signal amplification method for the detection of B16 cells based on the combination of rolling circle amplification (RCA) and molecular beacons (MBs). A long-chain structure of DNA synthesized by RCA was used to turn on aptamer-based MBs. Because of the multiple complementary repeat units, the RCA scaffold hybridized tens or hundreds of MBs to form polyvalent aptamer probes. The unfold ability and the fluorescence intensity of MBs were both improved by RCA, as compared to short single chains. The cell experiment results demonstrated that RCA-based polyvalent MBs were significantly more effective than monovalent MBs in targeting B16 cells and signal sensitivity because of their multivalent effects. The establishment of this strategy would provide a powerful platform for early clinical diagnostics of cancer cells.

Engineering Cellular Signal Sensors based on CRISPR-sgRNA Reconstruction Approaches

The discovery of the CRISPR systems has enriched the application of gene therapy and biotechnology. As a type of robust and simple toolbox, the CRISPR system has greatly promoted the development of cellular signal sensors at the genomic level. Although CRISPR systems have demonstrated that they can be used in eukaryotic and even mammalian cells after extraction from prokaryotic cells, controlling their gene-editing activity remains a challenge. Here we summarize the advantages and disadvantages of building a CRIRPR-based signal sensor through sgRNA reconstruction, as well as possible ways to reprogram the signal network of cells. We also propose how to further improve the design of the current signal sensors based on sgRNA-riboswitch. We believe that the development of these technologies and the construction of platforms can further promote the development of environment detection, disease diagnosis, and gene therapy by means of synthetic biology.

Single-Step FRET-Based Detection of Femtomoles DNA

Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), we show that these sensors can be regenerated in situ, and they allow detection of femtomoles DNA without the need for target amplification while still using a dramatically small sample size (fewer than three orders of magnitude compared to the typical sample size of bulk fluorescence). In addition, these single-molecule sensors exhibit a dynamic range of approximately two orders of magnitude. Using one of the sensors, we demonstrate that the single-base mismatch sequence can be discriminated from a fully matched DNA target, showing a high specificity of the method. These sensors with simple and recyclable design, sensitive detection of DNA, and the ability to discriminate single-base mismatch sequences may find applications in quantitative analysis of nucleic acid biomarkers.

Advances in DNA/RNA detection using nanotechnology

Specific nucleic acid detection in vitro or in vivo has become increasingly important in the discovery of genetic diseases, diagnosing pathogen infection and monitoring disease treatment. One challenge, however, is that the amount of target nucleic acid in specimens is limited. Furthermore, direct sensing methods are also unable to provide sufficient sensitivity and specificity. Fortunately, due to advances in nanotechnology and nanomaterials, nanotechnology-based bioassays have emerged as powerful and promising approaches providing ultra-high sensitivity and specificity in nucleic acid detection. This chapter presents an overview of strategies used in the development and integration of nanotechnology for nucleic acid detection, including optical and electrical detection methods, and nucleic acid assistant recycling amplification strategies. Recent 5 years representative examples are reviewed to demonstrate the proof-of-concept with promising applications for DNA/RNA detection and the underlying mechanism for detection of DNA/RNA with the higher sensitivity and selectivity. Furthermore, a brief discussion of common unresolved issues and future trends in this field is provided both from fundamental and practical point of view.