Colorimetric logic response based on aptamer functionalized colloidal crystal hydrogels

Responsive photonic hydrogel for colorimetric detection of formaldehyde

Formaldehyde (FA) can damage DNA, cause liver and kidney dysfunction, and ultimately lead to malignant tumors. Therefore, it is essential to develop a method that can conveniently detect FA with high detection sensitivity. Here, a responsive photonic hydrogel was prepared by embedding three-dimensional photonic crystal (PC) into amino-functionalized hydrogel to construct a colorimetric sensing film for FA. The amino groups on the polymer chains of the photonic hydrogel reacts with FA to increase the crosslinking density of the hydrogel, resulting in its volume shrinkage and a decrease in microsphere spacing of the PC. That causes the reflectance spectra blue-shift of more than 160 nm and color change from red to cyan for the optimized photonic hydrogel, achieving the sensitive, selective and colorimetric detection of FA. The constructed photonic hydrogel shows good accuracy and reliability for practical determination of FA in air and aquatic products, providing a new strategy for designing other target analytes responsive photonic hydrogels.

Encoding microcarriers for biomedicine

High throughput biological analysis has become an important topic in modern biomedical research and clinical diagnosis. The flow encoding scheme based on the encoding microcarriers provides a feasible strategy for the multiplexed biological analysis. Different encoding characteristics invest the microcarriers with different encoding mechanisms. Biosensor analysis, drug screening, cell culture, and the construction and evaluation of bionic organ chips can be realized by decoding the microcarriers and quantifying the detection signal intensity. In this review, the encoding strategy of microcarriers was divided into the optical and non-optical encoding approaches according to their encoding elements, and the research progress of the microcarrier encoding strategy was elaborated. Finally, we summarized the biomedical applications and predicted their future prospects.

Advances in functional photonic crystal materials for the analysis of chemical hazards in food

Chemical contaminants in food generally include natural toxins (mycotoxins, animal toxins, and phytotoxins), pesticides, veterinary drugs, environmental pollutants, heavy metals, and illegal additives. Developing a low-cost, simple, and rapid detection technology for harmful substances in food is urgently needed. Analytical methods based on different advanced materials have been developed into rapid detection methods for food samples. In particular, photonic crystal (PC) materials have a unique surface periodic structure, structural color, a large surface area, easy integration with photoelectronic and magnetic devices which have great advantages in the development of rapid, low-cost, and highly sensitive analytical methods. This review focuses on the PC materials in the view of their fabrication processes, functionalized recognition components for the specific recognition of hazardous substances, and applications in the separation, enrichment, and detection of chemical hazards in real samples. Suspension array based on three-dimensional PC microspheres by droplet-based microfluidic assembly is a great promising and powerful platform for food safety detection fields. For the PCs selective analysis, biological antibodies, aptamers, and molecularly imprinted polymers (MIPs) could be modified for specific recognition of target substances, particularly MIPs because of their low-cost and easy mass production. Based on these functional PCs, various toxic and hazardous substances can be selectively enriched or recognized in real samples and further quantified in combination of liquid chromatography method or optical detection methods including fluorescence, chemiluminescence, and Raman spectroscopy.

Aptamer-functionalized 2D photonic crystal hydrogels for detection of adenosine

Aptamer-functionalized two-dimensional photonic crystal (2DPC) hydrogels are reported for the detection of adenosine (AD). As a molecular recognition group, an AD-binding aptamer was covalently attached to 2DPC hydrogels. This aptamer selectively and sensitively binds AD, changing the conformation of the aptamer from a long single-stranded structure (AD-free conformation) to a short hairpin loop structure (AD-bound conformation). The AD-binding-induced changes of aptamer conformation reduced the volume of the 2DPC hydrogels and decreased the interparticle spacing of the 2DPC embedded in the hydrogel network. The particle spacing changes being dependent on AD concentration were determined by measuring 2DPC light diffraction using a simple laser pointer. The 2DPC hydrogel sensor showed a large particle spacing decrease of ~ 110 nm in response to 1 mM AD in phosphate-buffered saline (PBS). The linear range of determination of AD was 0.1 nM to 1 mM and the limit of detection was 0.09 nM. The hydrogel sensor response for real samples was then validated in diluted fetal bovine serum (FBS) and human urine. The average % difference in particle spacing changes measured between diluted FBS and pure PBS was only 3.99%. In diluted human urine, the recoveries for the detection of AD were 95-101% and the relative standard deviations were 4.9-7.8%. The results demonstrate the potential applicability of the hydrogel sensor for real samples. This sensing concept, using the aptamer-functionalized 2DPC hydrogels, allows for a simple, sensitive, selective, and reversible detection of AD. It may enable sensor development for a wide variety of analytes by simply changing the aptamer recognition group.

Repeatable detection of Ag+ ions using a DNA aptamer-linked hydrogel biochemical sensor integrated with microfluidic heating system

This paper describes repeatable detection of Ag⁺ ions using a DNA aptamer-linked hydrogel biochemical sensor integrated with a microfluidic heating system. Biochemical sensors that respond to chemical compounds and produce detectable signals have a critical role in many aspects of modern society. In particular, the repeatable measurement of environmental information such as toxic substances including Ag⁺ ions could be expected to improve the environment. The DNA aptamer is an attractive candidate because of the stability and the selectivity of binding to chemicals. However, previous DNA aptamer biochemical sensors could not measure repeatedly because those sensors did not have initializing functions. To overcome this challenge, we proposed a DNA aptamer-linked hydrogel biochemical sensor integrated with the microfluidic heating system enabling repeatable detection of Ag⁺ ions. The binding Ag⁺ ions are dissociated by heating and flushing through the integrated microfluidic heating device. The DNA aptamer-linked hydrogel had the capability to detect a wide range of Ag⁺ ion concentrations (10^-5-10 mM) including a toxic range for various aquatic organisms. Finally, we demonstrated the repeatable detection of the Ag⁺ ions. These results indicated that our proposed biochemical sensor is expected to use for long-term monitoring with high stability in ambient temperature and low power consumption.

DNA-Crosslinked 2D Photonic Crystal Hydrogels for Detection of Adenosine Actuated by an Adenosine-Binding Aptamer

There is a need to develop versatile sensing motifs that can be used to detect a variety of chemical targets in resource-limited settings, for example, at the point of care. While numerous sensing technologies have been developed toward this effort, these technologies can be overly complex and require a skilled technician, extensive sample preparation, or sophisticated instrumentation to use, limiting their generalizability and application in resource-limited settings. Here, we report a novel sensing motif that utilizes DNA-crosslinked two-dimensional photonic crystal (2DPC) hydrogels. These hydrogel sensors contain a DNA aptamer recognition group that binds a target analyte. As proof of concept, we fabricated 2DPC hydrogels using a well-studied adenosine-binding aptamer. This adenosine aptamer is duplexed with a partially complementary strand and forms responsive crosslinks in the hydrogel polymer network. When adenosine is introduced, aptamer-adenosine binding occurs, breaking the DNA crosslinks and causing the hydrogel to swell. This in turn increases the particle spacing of an embedded 2DPC array, shifting the 2DPC Bragg diffraction. Thus, adenosine concentration can be monitored through 2DPC Bragg diffraction measurements. A linear range of 20 μM to 2 mM was observed. The detection limits were calculated to be 13.9 μM in adenosine-binding buffer and 26.7 μM in fetal bovine serum. This reported sensing motif has a readout that is simple and rapid and requires minimal equipment. We hypothesize that this sensing motif is generalizable and that other sensors can be easily fabricated by simply exchanging the aptamer that serves as a molecular recognition group.

Current Understanding of the Applications of Photocrosslinked Hydrogels in Biomedical Engineering

Hydrogel materials have great application value in biomedical engineering. Among them, photocrosslinked hydrogels have attracted much attention due to their variety and simple convenient preparation methods. Here, we provide a systematic review of the biomedical-engineering applications of photocrosslinked hydrogels. First, we introduce the types of photocrosslinked hydrogel monomers, and the methods for preparation of photocrosslinked hydrogels with different morphologies are summarized. Subsequently, various biomedical applications of photocrosslinked hydrogels are reviewed. Finally, some shortcomings and development directions for photocrosslinked hydrogels are considered and proposed. This paper is designed to give researchers in related fields a systematic understanding of photocrosslinked hydrogels and provide inspiration to seek new development directions for studies of photocrosslinked hydrogels or related materials.

Synthetic Biology-Empowered Hydrogels for Medical Diagnostics

Synthetic biology is strongly inspired by concepts of engineering science and aims at the design and generation of artificial biological systems in different fields of research such as diagnostics, analytics, biomedicine, or chemistry. To this aim, synthetic biology uses an engineering approach relying on a toolbox of molecular sensors and switches that endows cellular hosts with non-natural computing functions and circuits. Importantly, this concept is not only limited to cellular approaches. Synthetic biological building blocks have also conferred sensing and switching capability to otherwise inactive materials. This principle has attracted high interest for the development of biohybrid materials capable of sensing and responding to specific molecular stimuli, such as disease biomarkers, antibiotics, or heavy metals. Moreover, the interconnection of individual sense-and-respond materials to complex materials systems has enabled the processing of, for example, multiple inputs or the amplification of signals using feedback topologies. Such systems holding high potential for applications in the analytical and diagnostic sectors will be described in this chapter.

Logic Gates Based on DNA Aptamers

DNA bio-computing is an emerging trend in modern science that is based on interactions among biomolecules. Special types of DNAs are aptamers that are capable of selectively forming complexes with target compounds. This review is devoted to a discussion of logic gates based on aptamers for the purposes of medicine and analytical chemistry. The review considers different approaches to the creation of logic gates and identifies the general algorithms of their creation, as well as describes the methods of obtaining an output signal which can be divided into optical and electrochemical. Aptameric logic gates based on DNA origami and DNA nanorobots are also shown. The information presented in this article can be useful when creating new logic gates using existing aptamers and aptamers that will be selected in the future.

Design, Bioanalytical, and Biomedical Applications of Aptamer-Based Hydrogels

Aptamers are special types of single-stranded DNA generated by a process called systematic evolution of ligands by exponential enrichment (SELEX). Due to significant advances in the chemical synthesis and biotechnological production, aptamers have gained considerable attention as versatile building blocks for the next generation of soft materials. Hydrogels are high water-retainable materials with a three-dimensional (3D) polymeric network. Aptamers, as a vital element, have greatly expanded the applications of hydrogels. Due to their biocompatibility, selective binding, and molecular recognition, aptamer-based hydrogels can be utilized for bioanalytical and biomedical applications. In this review, we focus on the latest strategies of aptamer-based hydrogels in bioanalytical and biomedical applications. We begin this review with an overview of the underlying design principles for the construction of aptamer-based hydrogels. Next, we will discuss some bioanalytical and biomedical applications of aptamer-based hydrogel including biosensing, target capture and release, logic devices, gene and cancer therapy. Finally, the recent progress of aptamer-based hydrogels is discussed, along with challenges and future perspectives.

Recent advances in self-assemblies and sensing applications of colloidal photonic crystals

Colloidal photonic crystals (PCs), consisting of highly ordered monodisperse nanoparticles, have been carried out a great deal of research in recent decades due to the attributes of readable signal, easy modification and low cost. With these unique features, colloidal PCs have also gradually become a focus of candidates applied in sensing fields. In this review, an overview of recent advances in colloidal PCs including self-assemblies and sensing applications is illustrated. With respect to the development in self-assemblies of colloidal PCs, the review concentrates on the summary of responsive mechanisms, detection methods, responsive materials, unit cells and fabrication methods. In terms of advances in sensing application of colloidal PCs, various types of sensors are summarized based on the kinds and applications of target analytes. Furthermore, the current limitations and potential future directions of colloidal PCs in self-assemblies and sensing areas are also discussed.

Photolithographic shape control of DNA hydrogels by photo-activated self-assembly of DNA nanostructures

We report a photolithographic method for the shape control of DNA hydrogels based on photo-activated self-assembly of Y-shaped DNA nanostructures (Y-motifs). To date, various methods to control the shape of DNA hydrogels have been developed to enhance the functions of the DNA hydrogel system. However, photolithographic production of shape-controlled DNA hydrogels formed through the self-assembly of DNA nanostructures without the use of radical polymerizations has never been demonstrated, although such a method is expected to be applied for the shape-control of DNA hydrogels encapsulating sensitive biomolecules, such as proteins. In this study, we used a photo-activated linker to initiate the self-assembly of Y-motifs, where the cross-linker DNA was at first inactive but was activated after UV light irradiation, resulting in the formation of shape-controlled DNA hydrogels only at the UV-exposed area produced by photomasks. We believe that this method will be applied for the construction of biohybrid machines, such as molecular robots and artificial cells that contain intelligent biomolecular devices, such as molecular sensors and computers.

Upgrading biomaterials with synthetic biological modules for advanced medical applications

One key aspect of synthetic biology is the development and characterization of modular biological building blocks that can be assembled to construct integrated cell-based circuits performing computational functions. Likewise, the idea of extracting biological modules from the cellular context has led to the development of in vitro operating systems. This principle has attracted substantial interest to extend the repertoire of functional materials by connecting them with modules derived from synthetic biology. In this respect, synthetic biological switches and sensors, as well as biological targeting or structure modules, have been employed to upgrade functions of polymers and solid inorganic material. The resulting systems hold great promise for a variety of applications in diagnosis, tissue engineering, and drug delivery. This review reflects on the most recent developments and critically discusses challenges concerning in vivo functionality and tolerance that must be addressed to allow the future translation of such synthetic biology-upgraded materials from the bench to the bedside.

Label-Free Photonic Crystal-Based β-Lactamase Biosensor for β-Lactam Antibiotic and β-Lactamase Inhibitor

A simple, label-free, and visual photonic crystal-based β-lactamase biosensor was developed for β-lactam antibiotic and β-lactamase inhibitor in which the penicillinase (a β-lactamase) was immobilized on the pH-sensitive colloidal crystal hydrogel (CCH) film to form penicillinase colloidal crystal hydrogel (PCCH) biosensing film. The hydrolysis of penicillin G (a β-lactam antibiotic) can be catalyzed by penicillinase to produce penicilloic acid, leading to a pH decrease in the microenvironment of PCCH film, which causes the shrink of pH-sensitive CCH film and triggers a blue-shift of the diffraction wavelength. Upon the addition of β-lactamase inhibitor, the hydrolysis reaction is suppressed and no clear blue-shift is observed. The concentrations of β-lactam antibiotic and β-lactamase inhibitor can be sensitively evaluated by measuring the diffraction shifts. The minimum detectable concentrations for penicillin G and clavulanate potassium (a β-lactamase inhibitor) can reach 1 and 0.1 μM, respectively. Furthermore, the proposed method is highly reversible and selective, and it allows determination of penicillin G in fish pond water samples.

Free-Standing Photonic Crystal Films with Gradient Structural Colors

Hydrogel colloidal crystal composite materials have a demonstrated value in responsive photonic crystals (PhCs) via controllable stimuli. Although they have been successfully exploited to generate a gradient of color distribution, the soft hydrogels have limitations in terms of stability and storage caused by dependence on environment. Here, we present a practical strategy to fabricate free-standing PhC films with a stable gradient of structural colors using binary polymer networks. A colloidal crystal hydrogel film was prepared for this purpose, with continuously varying photonic band gaps corresponding to the gradient of the press. Then, a second polymer network was used to lock the inside non-close-packed PhC structures and color distribution of the hydrogel film. It was demonstrated that our strategy could bring about a solution to the angle-dependent structural colors of the PhC films by coating the surface with special microstructures.