Theoretical and experimental study of a highly sensitive SPR biosensor based on Au grating and Au film coupling structure

A high-sensitivity surface plasmon resonance (SPR) sensor based on the coupling of Au grating and Au film is investigated through simulations and experiments. The SPR sensor is designed by using a hybrid method composed of genetic algorithm (GA) and rigorous coupled wave analysis (RCWA). The numerical results indicate the sensor has an angular sensitivity of 397.3°/RIU (refractive index unit), which is approximately 2.81 times higher than the conventional Au-based sensor and it is verified by experiments. Theoretical analysis, by finite-difference time-domain (FDTD) method, demonstrates the co-coupling between surface plasmon polaritons (SPPs) propagating on the surface of Au film and localized surface plasmons (LSPs) in the Au grating nanostructure, improving the sensitivity of the SPR sensor. According to the optimized structural parameters, the proposed sensor is fabricated using e-beam lithography and magnetron sputtering. In addition, the proposed sensor is very sensitive to the detection of small molecules. The limit of detection (LOD) for okadaic acid (OA) is 0.72 ng/mL based on an indirect competitive inhibition method, which is approximately 38 times lower than the conventional Au sensor. Such a high-sensitivity SPR biosensor has potential in the applications of immunoassays and clinical diagnosis.

Simultaneous amplification of multiple immunofluorescence signals via cyclic staining of target molecules using mutually cross-adsorbed antibodies

Amplification of immunofluorescence (IF) signals is becoming increasingly critical in cancer research and neuroscience. Recently, we put forward a new signal amplification technique, which we termed fluorescent signal amplification via cyclic staining of target molecules (FRACTAL). FRACTAL amplifies IF signals by repeatedly labeling target proteins with a pair of secondary antibodies that bind to each other. However, simultaneous amplification of multiple IF signals via FRACTAL has not yet been demonstrated because of cross-reactivity between the secondary antibodies. In this study, we show that mutual cross-adsorption between antibodies can eliminate all forms of cross-reactions between them, enabling simultaneous amplification of multiple IF signals. First, we show that a typical cross-adsorption process-in which an antibody binds to proteins with potential cross-reactivity with the antibody-cannot eliminate cross-reactions between antibodies in FRACTAL. Next, we show that all secondary antibodies used in FRACTAL need to be mutually cross-adsorbed to eliminate all forms of cross-reactivity, and then we demonstrate simultaneous amplification of multiple IF signals using these antibodies. Finally, we show that multiplexed FRACTAL can be applied to expansion microscopy to achieve higher fluorescence intensities after expansion. Multiplexed FRACTAL is a highly versatile tool for standard laboratories, as it amplifies multiple IF signals without the need for custom antibodies.

Functional nucleic acid biosensors utilizing rolling circle amplification

Functional nucleic acids regulate rolling circle amplification to produce multiple detection outputs suitable for the development of point-of-care diagnostic devices.

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.

Circular Nucleic Acids: Discovery, Functions and Applications

Circular nucleic acids (CNAs) are nucleic acid molecules with a closed-loop structure. This feature comes with a number of advantages including complete resistance to exonuclease degradation, much better thermodynamic stability, and the capability of being replicated by a DNA polymerase in a rolling circle manner. Circular functional nucleic acids, CNAs containing at least a ribozyme/DNAzyme or a DNA/RNA aptamer, not only inherit the advantages of CNAs but also offer some unique application opportunities, such as the design of topology-controlled or enabled molecular devices. This article will begin by summarizing the discovery, biogenesis, and applications of naturally occurring CNAs, followed by discussing the methods for constructing artificial CNAs. The exploitation of circular functional nucleic acids for applications in nanodevice engineering, biosensing, and drug delivery will be reviewed next. Finally, the efforts to couple functional nucleic acids with rolling circle amplification for ultra-sensitive biosensing and for synthesizing multivalent molecular scaffolds for unique applications in biosensing and drug delivery will be recapitulated.

In situ generated nanozyme-initiated cascade reaction for amplified surface plasmon resonance sensing

A novel nanozyme-amplified surface plasmon resonance (SPR) sensor was successfully developed based on target-induced in situ generation of AuNPs and a AuNP-guided cascade amplification reaction, with Hg²⁺ as the target analyte.

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.

Sensitive determination of DNA based on phosphate-dye interaction using photothermal lens technique

Photothermal lens spectrometry is a powerful optical detection technique that can be used to investigate biomolecules. In this work, for the first time to our knowledge, photothermal lens spectrometry was used for determination of nanomolar concentrations of three distinct deoxyribonucleic acid (DNA) strands using methylene blue as a labeling dye. Methylene blue interacts with phosphate groups of the DNA in lower DNA concentrations. It was observed that phosphate-methylene blue interaction had no obvious effect on methylene blue absorption and fluorescence spectra, but the photothermal lens spectrometry signal of methylene blue increased with DNA concentration. For this purpose, to evaluate the performance of the presented method, herring sperm DNA, Escherichia coli bacteria DNA, and partial 16S rRNA genes were examined. Under optimum conditions, photothermal lens spectrometry intensity of methylene blue increased linearly with DNA concentration when herring sperm DNA, Escherichia coli DNA, and 16S rRNA gene concentrations increased in the ranges of 0.1-250, 1-700, and 1-800  nmol L^-1, respectively. The corresponding detection limits were found to be 0.07, 0.71, and 0.56  nmol L^-1, respectively, and relative standard deviations for 50  nmol L^-1 of the tested samples were 2.59%, 4.95%, and 4.57%, respectively.

Label-free imaging of epidermal growth factor receptor-induced response in single living cells

Epidermal growth factor receptor (EGFR), which belongs to the second-largest protein family for cell signal transduction, plays crucial roles in homeostasis, cellular organized patterns and most human cancers. In EGFR-activated signaling networks, the detection of the spatial and temporal dynamics of cascades that encode the many cell fates is still a challenge. Here, we report real-time imaging of epidermal growth factor (EGF)-induced EGFR activation and its signaling cascade in single A431 cells using surface plasmon resonance (SPR) microscopy. A two-phase SPR response pattern was observed within 30 min after EGF treatment, including a positive SPR response that was related to the EGFR-activated mass redistribution in the first 600 s, and a subsequent negative SPR signal caused by the morphological change of the cells. Furthermore, the inhibitor analysis verified that AG1478 inhibited the response from the whole the cell, whereas cytochalasin B strongly inhibited the response from the cell edge region.

A new electrochemical aptasensor for sensitive assay of a protein based on the dual-signaling electrochemical ratiometric method and DNA walker strategy

Herein, a new electrochemical aptamer-based biosensor for highly sensitive assay of thrombin has been developed based on the dual-signaling electrochemical ratiometric method and the DNA walker strategy, and shows a low detection limit of about 56 fM.

Plasmonic molecular assays: Recent advances and applications for mobile health

Plasmonics-based biosensing assays have been extensively employed for biomedical applications. Significant advancements in use of plasmonic assays for the construction of point-of-care (POC) diagnostic methods have been made to provide effective and urgent health care of patients, especially in resourcelimited settings. This rapidly progressive research area, centered on the unique surface plasmon resonance (SPR) properties of metallic nanostructures with exceptional absorption and scattering abilities, has greatly facilitated the development of cost-effective, sensitive, and rapid strategies for disease diagnostics and improving patient healthcare in both developed and developing worlds. This review highlights the recent advances and applications of plasmonic technologies for highly sensitive protein and nucleic acid biomarker detection. In particular, we focus on the implementation and penetration of various plasmonic technologies in conventional molecular diagnostic assays, and discuss how such modification has resulted in simpler, faster, and more sensitive alternatives that are suited for point-of-use. Finally, integration of plasmonic molecular assays with various portable POC platforms for mobile health applications are highlighted.

An enzyme-free and label-free surface plasmon resonance biosensor for ultrasensitive detection of fusion gene based on DNA self-assembly hydrogel with streptavidin encapsulation

In this research, an enzyme-free and label-free surface plasmon resonance (SPR) biosensing strategy has been developed for ultrasensitive detection of fusion gene based on the heterogeneous target-triggered DNA self-assembly aptamer-based hydrogel with streptavidin (SA) encapsulation. In the presence of target, the capture probes (Cp) immobilized on the chip surface can capture the PML/RARα, forming a Cp-PML/RARα duplex. After that, the aptamer-based network hydrogel nanostructure is formed on the gold surface via target-triggered self-assembly of X shaped polymers. Subsequently, the SA can be encapsulated into hydrogel by the specific binding of SA aptamer, forming the complex with super molecular weight. Thus, the developed strategy achieves dramatic enhancement of the SPR signal. Using PML/RARα "S" subtype as model analyte, the developed biosensing method can detect target down to 45.22 fM with a wide linear range from 100 fM to 10 nM. Moreover, the high efficiency biosensing method shows excellent practical ability to identify the clinical PCR products of PML/RARα. Thus, this proposed strategy presents a powerful platform for ultrasensitive detection of fusion gene and early diagnosis and monitoring of disease.

Specific detection of cancer cells through aggregation-induced emission of a light-up bioprobe

A cancer cell specific aptamer was labeled with an aggregation-induced emission (AIE) probe for the first time. Using it as a light-up bioprobe, a specific cancer cell detection method is developed.

Optical nano-biosensing interface via nucleic acid amplification strategy: construction and application

Modern optical detection technology plays a critical role in current clinical detection due to its high sensitivity and accuracy. However, higher requirements such as extremely high detection sensitivity have been put forward due to the clinical needs for the early finding and diagnosing of malignant tumors which are significant for tumor therapy. The technology of isothermal amplification with nucleic acids opens up avenues for meeting this requirement. Recent reports have shown that a nucleic acid amplification-assisted modern optical sensing interface has achieved satisfactory sensitivity and accuracy, high speed and specificity. Compared with isothermal amplification technology designed to work completely in a solution system, solid biosensing interfaces demonstrated better performances in stability and sensitivity due to their ease of separation from the reaction mixture and the better signal transduction on these optical nano-biosensing interfaces. Also the flexibility and designability during the construction of these nano-biosensing interfaces provided a promising research topic for the ultrasensitive detection of cancer diseases. In this review, we describe the construction of the burgeoning number of optical nano-biosensing interfaces assisted by a nucleic acid amplification strategy, and provide insightful views on: (1) approaches to the smart fabrication of an optical nano-biosensing interface, (2) biosensing mechanisms via the nucleic acid amplification method, (3) the newest strategies and future perspectives.

Homogeneous enzyme-free and entropy-driven isothermal fluorescent assay for nucleic acids based on a dual-signal output amplification strategy

The proposed fluorescent biosensor improves the reaction rate, has excellent analytical performance (LOD 15.6 fM) and shows outstanding recognition toward mismatched DNA strands. This approach provides a potential universal platform for the determination of other nucleic acids.

Y-Shaped DNA Duplex Structure-Triggered Gold Nanoparticle Dimers for Ultrasensitive Colorimetric Detection of Nucleic Acid with the Dark-Field Microscope

Herein, we present a novel gold nanoparticle (AuNP) enumeration-based colorimetric aptamer biosensor for ultrasensitive detection of nucleic acid. This AuNP enumeration-based colorimetric method takes advantages of the distinctive and strong localized surface plasmon resonance light scattering with the dark-field microscope. In our model system, first, cost-effective DNA1 instead of expensive 2-thioethyl ether acetic acid was capped on the surface of AuNPs to form a dense DNA1 layer. Then, two DNA strands (DNA2 and DNA3) in two different solutions were separately asymmetrically functionalized on the AuNPs capped dense DNA1 layer. The subsequent binding of the target DNA could trigger the formation of perfect complementary DNA with a Y shape and adjust the distance between nanoparticles to form AuNP dimers, accompanied by a color change from green to yellow as observed, and thereby modulated the performance of the sensor, which resulted in the ultrahigh sensitivity. With this design, a 43 aM limit of detection was obtained, which exhibited an increase of at least 5-9 orders of magnitude in sensitivity over other colorimetric sensors fabricated using conventional strategies.

Quantitative control of CaCO3 growth on quartz crystal microbalance sensors as a signal amplification method

Quantitative control of mass growth on QCM sensor surfaces was realized, providing a potential signal amplification method.

Surface plasmon resonance biosensor for sensitive detection of microRNA and cancer cell using multiple signal amplification strategy

A sensitive and versatile surface plasmon resonance (SPR) biosensor was proposed for the detection of microRNA (miRNA) and cancer cell based on multiple signal amplification strategy. Thiol-modified hairpin probe, including a sequence complementary to the target miRNA, was first immobilized on the Au film. In the presence of target miRNA, the stem-loop structure of hairpin probe was unfolded, and then DNA-linked Au nanoparticles (AuNPs) were hybridized with the terminus of the unfolded hairpin probe. Subsequently, DNA-linked AuNPs initiated the formation of DNA supersandwich structure through the addition of two report DNA sequences. Owing to the electronic coupling between localized plasmon of the AuNPs and the surface plasmon wave, as well as the enhancement of the refractive index of the medium over the Au film induced by DNA supersandwich structure, the SPR response was significantly enhanced. Next, numerous positively charged silver nanoparticles (AgNPs) were absorbed onto the long-range DNA surpersandwich equably, resulting in a further increase of SPR response. Due to the enzyme-free multiple signal amplification strategy, as low as ca. 0.6 fM miRNA-21 could be detected. In addition, this biosensor showed high selectivity toward single-base mismatch. More importantly, this SPR biosensor was also used for cancer cell detection coupled with the cell-specific aptamer modified magnetic nanoparticles. Given that the biosensor avoided enzyme introduction, the limitation of the enzyme was overcome. The versatile biosensor has great potential for the broad applications in the field of clinical analysis.

An enzyme-free surface plasmon resonance biosensing strategy for detection of DNA and small molecule based on nonlinear hybridization chain reaction

A label-free and enzyme-free surface plasmon resonance (SPR) biosensing strategy has been developed for highly sensitive and specific detection of target DNA by employing the nonlinear hybridization chain reaction (HCR) amplification. Nonlinear HCR is a hairpin-free system in which double-stranded DNA monomers could dendritically assemble into highly branched nanostructure upon introducing a trigger sequence. The target DNA partly hybridizes with capture probe on the gold sensing chip and the unpaired fragment of target DNA works as a trigger to initiate the nonlinear HCR, forming a chain-branching growth of DNA dendrimer by self-assembly. Real-time amplified SPR response is observed upon the introduction of nonlinear HCR system. The method is capable of detecting target DNA at the concentration down to 0.85 pM in 60min with a dynamic range from 1 pM to 1000 pM, and could discriminate target DNA from mismatched sequences. This biosensing strategy exhibits good reproducibility and precision, and has been successfully applied for detection of target DNA in complex sample matrices. In addition, the nonlinear HCR based SPR biosensing methodology is extended to the detection of adenosine triphosphate (ATP) by aptamer recognition. Thus, the versatile method might become a potential alternative tool for biomolecule detection in medical research and early clinical diagnosis.

Human serum biomarker detection based on a cascade signal amplification strategy by a DNA molecule machine

A convenient method is presented that employs a DNA machine for protein biomarker detection. The detection limit is 400 times lower compared to the method without a DNA machine. This study provides a promising method that could realize most protein biomarker detections without the corresponding aptamers, using a DNA machine for signal amplification.

A signal-on split aptasensor for highly sensitive and specific detection of tumor cells based on FRET

The split aptasensor for highly sensitive and specific detection of tumor cells based on FRET.

Cross-triggered and cascaded recycling amplification for ultrasensitive electrochemical sensing of the mutant human p53 gene

Cross-triggered and cascaded recycling amplification enables the highly sensitive electrochemical detection of the mutant p53 gene in human serum.

A visible light induced photoelectrochemical aptsensor constructed by aligned ZnO@CdTe core shell nanocable arrays/carboxylated g-C3N4 for the detection of Proprotein convertase subtilisin/kexin type 6 gene

It was reported that Proprotein convertase subtilisin/kexin type 6 (PCSK6) can promote the progression of rheumatoid arthritis to a higher aggressive status. In this work, a novel visible light induced photoelectrochemical (PEC) platform was designed to detect PCSK6 gene. ZnO@CdTe nanocable arrays/carboxylated g-C3N4 used as the PEC signal generator. Hexagonal ZnO nanorods grew on ITO electrode firstly. CdTe were then electrodeposited on the ZnO nanorods surface to enhance the photogenerated h(+)/e(-) separation efficiency. Carboxylated g-C3N4 was utilized to improve h(+)/e(-) separation efficiency and anchor the capture probes of PCSK6 gene by the covalent bonding effect. The 5' and 3' primers captured PCSK6 ssDNA by the specific recognition. The linear range was 10 pg/mL to 20.0 ng/mL with a detection limit of 2 pg/mL.

Optimal DNA templates for rolling circle amplification revealed by in vitro selection

Rolling circle amplification (RCA) has been widely used as an isothermal DNA amplification technique for diagnostic and bioanalytical applications. Because RCA involves repeated copying of the same circular DNA template by a DNA polymerase thousands of times, we hypothesized there exist DNA sequences that can function as optimal templates and produce more DNA amplicons within an allocated time. Herein we describe an in vitro selection effort conducted to search from a random sequence DNA pool for such templates for phi29 DNA polymerase, a frequently used polymerase for RCA. Diverse DNA molecules were isolated and they were characterized by richness in adenosine (A) and cytidine (C) nucleotides. The top ranked sequences exhibit superior RCA efficiency and the use of these templates for RCA results in significantly improved detection sensitivity. AC-rich sequences are expected to find useful applications for setting up effective RCA assays for biological sensing.

A novel electrochemical biosensor for DNA detection based on exonuclease III-assisted target recycling and rolling circle amplification

A strategy for electrochemical detection of DNA by exonuclease III-assisted DNA recycling and the rolling circle amplification was developed.

DNA methylation detection with end-to-end nanorod assembly-enhanced surface plasmon resonance

The Au nanorod (AuNR) assembly-enhanced SPR system coupling with polymerization and nicking reactions was developed for amplified detection of DNA methylation and Dam MTase activity assay.