Colorimetric detection of single-nucleotide mutations based on rolling circle amplification and G-quadruplex-based DNAzyme

In this work, we proposed a sensitive and selective colorimetric assay for single nucleotide mutation (SNM) detection combining rolling circle amplification (RCA) and G-quadruplex/hemin DNAzyme complex formation. In the detection principle, the first step involves ssDNA hybridization with a padlock probe (PLP) DNA, which can discriminate a single base mismatch. The successful ligation is followed by an RCA event to generate an abundance of G-quadruplexes (GQ-RCA) which are then transformed into a DNAzyme (G-quadruplex/hemin complex) by the addition of hemin. The color change from colorless 3,3',5,5'-tetramethylbenzidine (TMB) into colored oxTMB when hydrogen peroxide (H2O2) is added indicated the presence of a mutation. The assay had a limit of detection (LOD) of 2.14 pM. Mutations in samples from breast cancer patients were successfully detected with an accuracy of 100% when compared to Sanger sequencing results. The method is easily applicable even in resource poor setting regions given that it doesn't require any sophisticated or expensive instruments, and the signal readout is detectable simply by the naked eye. Our assay might be a useful tool for genetic analysis and clinical molecular diagnosis for breast cancer risk assessment and early detection.

T790M mutation upconversion fluorescence biosensor via mild ATRP strategy and site-specific DNA cleavage of restriction endonuclease

A unique combination of a specific nucleic acid restriction endonuclease (REase) and atom transfer radical polymerization (ATRP) signal amplification strategy was employed for the detection of T790M mutations prevalent in the adjuvant diagnosis of lung cancer. REase selectively recognizes and cleaves T790M mutation sites on double-stranded DNA formed by hybridization of a capture sequence and a target sequence. At the same time, the ATRP strategy resulted in the massive aggregation of upconverted nanoparticles (UCNPs), which significantly improved the sensitivity of the biosensor. In addition, the UCNPs have excellent optical properties and can eliminate the interference of autofluorescence in the samples, thus further improving the detection sensitivity. The proposed upconversion fluorescent biosensor is characterized by high specificity, high sensitivity, mild reaction conditions, fast response time, and a detection limit as low as 0.14 fM. The performance of the proposed biosensor is comparable to that of clinical PCR methods when applied to clinical samples. This work presents a new perspective for assisted diagnosis in the pre-intervention stage of tumor diagnostics in the early stage of precision oncology treatments.

Dual amplification-based ultrasensitive and highly selective colorimetric detection of miRNA

In this study, we combined a Pradeep Kumar (PK)-probe with a ligation-transcription-ramified RCA (LTR) dual-amplification system for the isothermal colorimetric detection of miRNA 25-3P, where the PK-probe transformed from its pink color to colorless in the presence of the amplification byproduct pyrophosphate (PPi), thereby allowing the simple naked-eye qualitative detection of the miRNA. Through this double-amplification strategy, the limit of detection reached as low as 91.4 aM-quite extraordinary sensitivity for a colorimetric miRNA detection system based on absorbance readings. Our detection system also operated with high specificity, the result of using two different target-selective ligation steps (linear DNA ligation and circular DNA ligation) mediated by SplintR ligase, and so could discriminate single-mismatched from perfectly matched target sequences. We suspect that this ultrasensitive and selective PK-probe/LTR dual-amplification system should be a great colorimetric diagnostic for the detection of any miRNA with high efficiency.

Recent Progress in Single-Nucleotide Polymorphism Biosensors

Single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in the human genome, are the main cause of individual differences. Furthermore, such attractive genetic markers are emerging as important hallmarks in clinical diagnosis and treatment. A variety of destructive abnormalities, such as malignancy, cardiovascular disease, inherited metabolic disease, and autoimmune disease, are associated with single-nucleotide variants. Therefore, identification of SNPs is necessary for better understanding of the gene function and health of an individual. SNP detection with simple preparation and operational procedures, high affinity and specificity, and cost-effectiveness have been the key challenge for years. Although biosensing methods offer high specificity and sensitivity, as well, they suffer drawbacks, such as complicated designs, complicated optimization procedures, and the use of complicated chemistry designs and expensive reagents, as well as toxic chemical compounds, for signal detection and amplifications. This review aims to provide an overview on improvements for SNP biosensing based on fluorescent and electrochemical methods. Very recently, novel designs in each category have been presented in detail. Furthermore, detection limitations, advantages and disadvantages, and challenges have also been presented for each type.

Recent advances in plasmon-enhanced luminescence for biosensing and bioimaging

Plasmon-enhanced luminescence (PEL) is a unique photophysical phenomenon in which the interaction between luminescent moieties and metal nanostructures results in a marked luminescence enhancement. PEL offers several advantages and has been extensively used to design robust biosensing platforms for luminescence-based detection and diagnostics applications, as well as for the development of many efficient bioimaging platforms, enabling high-contrast non-invasive real-time optical imaging of biological tissues, cells, and organelles with high spatial and temporal resolution. This review summarizes recent progress in the development of various PEL-based biosensors and bioimaging platforms for diverse biological and biomedical applications. Specifically, we comprehensively assessed rationally designed PEL-based biosensors that can efficiently detect biomarkers (proteins and nucleic acids) in point-of-care tests, highlighting significant improvements in the sensing performance upon the integration of PEL. In addition to discussing the merits and demerits of recently developed PEL-based biosensors on substrates or in solutions, we include a brief discussion on integrating PEL-based biosensing platforms into microfluidic devices as a promising multi-responsive detection method. The review also presents comprehensive details about the recent advances in the development of various PEL-based multi-functional (passive targeting, active targeting, and stimuli-responsive) bioimaging probes, highlighting the scope of future improvements in devising robust PEL-based nanosystems to achieve more effective diagnostic and therapeutic insights by enabling imaging-guided therapy.

Target-triggered hybridization chain reaction for ultrasensitive dual-signal miRNA detection

A signal amplification sensing system with target-triggered DNA cascade reaction combined with dual-signal readout technology was designed for ultrasensitive analysis of miRNA. The highly conductive metal organic frameworks (MOFs) derivative, N-doped carbon dodecahedron (N-PCD) was deposited with gold nanoparticles as the electrode substrate, which could assist the electron transfer between the molecular probe and the electrode surface, and could remarkably enhance electrochemical response. Tetrahedral DNA nanostructure (T4-DNA) with high structural stability and mechanical stiffness was designed to improve the loading capacity and binding efficiency of the target, thus increasing the sensitivity of the system. The non-enzymatic amplification method based on the DNA cascade reaction allows the electrochemical responses from dual signal DNA probes labeled with ferrocene (Fc) and methylene blue (MB), respectively in turn to improve the reliability of detection. Under optimal conditions, the sensor has a linear range of 5-1.0 × 10⁴ fM, and the limit of detection is as low as 1.92 fM and 3.74 fM for Fc and MB labeled probe, respectively. This strategy raises the promising application for the rapid detection of miRNA targets with low abundance in complex biological systems.

Near-Infrared-Fluorescent Probe for Turn-On Lipopolysaccharide Analysis Based on PEG-Modified Gold Nanorods with Plasmon-Enhanced Fluorescence

Lipopolysaccharide (LPS), as the major component of the outer membrane of Gram-negative bacteria, can trigger a variety of biological effects such as sepsis, septic shock, and even multiorgan failure. Herein, we developed a near-infrared-fluorescent probe for fluorescent turn-on analysis of LPS based on plasmon-enhanced fluorescence (PEF). Gold nanorods (Au NRs) modified polyethylene glycol (PEG) was used as PEF materials. Au NRs were prepared with different longitudinal surface plasmon resonance (LSPR), and their fluorescence enhancement was investigated. Three kinds of molecular weights (1000, 5000, and 10000) of polyethylene glycol (PEG) were employed to control the distance between the Au NRs and the fluorescence substances of cyanine 7 (Cy7). Experimental analysis showed that the enhancement was related to the spectral overlap between the plasmon resonance of Au NRs and the extinction/emission of fluorophore. The three-dimensional finite-difference time-domain (3D-FDTD) simulation further revealed that the enhancement was caused by local electric field enhancement. Furthermore, the probe was used for the ultrasensitive analysis of LPS with a detection limit of 3.85 ng/mL and could quickly distinguish the Gram-negative bacterium-Escherichia coli (E. coli) (with LPS in the membrane) from Gram-positive bacterium-Staphylococcus aureus (S. aureus) (without LPS), as well as quantitative determination of E. coli with a detection limit of 1.0 × 10⁶ cfu/mL. These results suggested that the prepared probe has great potential for biomedical diagnosis and selective detection of LPS from different bacterial strains.

Metal Nanoparticles-Enhanced Biosensors: Synthesis, Design and Applications in Fluorescence Enhancement and Surface-enhanced Raman Scattering

Metal nanoparticles (NP) that exhibit localized surface plasmon resonance play an important role in metal-enhanced fluorescence (MEF) and surface-enhanced Raman scattering (SERS). Among the optical biosensors, MEF and SERS stand out to be the most sensitive techniques to detect a wide range of analytes from ions, biomolecules to macromolecules and microorganisms. Particularly, anisotropic metal NPs with strongly enhanced electric field at their sharp corners/edges under a wide range of excitation wavelengths are highly suitable for developing the ultrasensitive plasmon-enhanced biosensors. In this review, we first highlight the reliable methods for the synthesis of anisotropic gold NPs and silver NPs in high yield, as well as their alloys and composites with good control of size and shape. It is followed by the discussion of different sensing mechanisms and recent advances in the MEF and SERS biosensor designs. This includes the review of surface functionalization, bioconjugation and (directed/self) assembly methods as well as the selection/screening of specific biorecognition elements such as aptamers or antibodies for the highly selective bio-detection. The right combinations of metal nanoparticles, biorecognition element and assay design will lead to the successful development of MEF and SERS biosensors targeting different analytes both in-vitro and in-vivo. Finally, the prospects and challenges of metal-enhanced biosensors for future nanomedicine in achieving ultrasensitive and fast medical diagnostics, high-throughput drug discovery as well as effective and reliable theranostic treatment are discussed.

Hybrid Silver Nanocubes for Improved Plasmon-Enhanced Singlet Oxygen Production and Inactivation of Bacteria

Plasmonic nanoparticles can strongly interact with adjacent photosensitizer molecules, resulting in a significant alteration of their singlet oxygen (¹O₂) production. In this work, we report the next generation of metal-enhanced ¹O₂ nanoplatforms exploiting the lightning rod effect, or plasmon hot spots, in anisotropic (nonspherical) metal nanoparticles. We describe the synthesis of Rose Bengal-decorated silica-coated silver nanocubes (Ag@SiO₂-RB NCs) with silica shell thicknesses ranging from 5 to 50 nm based on an optimized protocol yielding highly homogeneous Ag NCs. Steady-state and time-resolved ¹O₂ measurements demonstrate not only the silica shell thickness dependence on the metal-enhanced ¹O₂ production phenomenon but also the superiority of this next generation of nanoplatforms. A maximum enhancement of ¹O₂ of approximately 12-fold is observed with a 10 nm silica shell, which is among the largest ¹O₂ production metal enhancement factors ever reported for a colloidal suspension of nanoparticles. Finally, the Ag@SiO₂-RB NCs were benchmarked against the Ag@SiO₂-RB nanospheres previously reported by our group, and the superior ¹O₂ production of Ag@SiO₂-RB NCs resulted in improved antimicrobial activities in photodynamic inactivation experiments using both Gram-positive and -negative bacteria model strains.