Structural and evolutionary approaches to the design and optimization of fluorescence-based small molecule biosensors

Smart genetically-encoded biosensors for the chemical monitoring of living systems

Genetically-encoded biosensors provide the all-optical and non-invasive visualization of dynamic biochemical events within living systems, which has allowed the discovery of profound new insights. Twenty-five years of biosensor development has steadily improved their performance and has provided us with an ever increasing biosensor repertoire. In this feature article, we present recent advances made in biosensor development and provide a perspective on the future direction of the field.

Confocal imaging of biomarkers at a single-cell resolution: quantifying 'living' in 3D-printable engineered living material based on Pluronic F-127 and yeast Saccharomyces cerevisiae

BACKGROUND

Engineered living materials (ELMs) combine living cells with non-living scaffolds to obtain life-like characteristics, such as biosensing, growth, and self-repair. Some ELMs can be 3D-printed and are called bioinks, and their scaffolds are mostly hydrogel-based. One such scaffold is polymer Pluronic F127, a liquid at 4 °C but a biocompatible hydrogel at room temperature. In such thermally-reversible hydrogel, the microorganism-hydrogel interactions remain uncharacterized, making truly durable 3D-bioprinted ELMs elusive.

METHODS

We demonstrate the methodology to assess cell-scaffold interactions by characterizing intact alive yeast cells in cross-linked F127-based hydrogels, using genetically encoded ratiometric biosensors to measure intracellular ATP and cytosolic pH at a single-cell level through confocal imaging.

RESULTS

When embedded in hydrogel, cells were ATP-rich, in exponential or stationary phase, and assembled into microcolonies, which sometimes merged into larger superstructures. The hydrogels supported (micro)aerobic conditions and induced a nutrient gradient that limited microcolony size. External compounds could diffuse at least 2.7 mm into the hydrogels, although for optimal yeast growth bioprinted structures should be thinner than 0.6 mm. Moreover, the hydrogels could carry whole-cell copper biosensors, shielding them from contaminations and providing them with nutrients.

CONCLUSIONS

F127-based hydrogels are promising scaffolds for 3D-bioprinted ELMs, supporting a heterogeneous cell population primarily shaped by nutrient availability.

Two-Dimensional Graphitic Carbon Nitride (g-C3N4) Nanosheets and Their Derivatives for Diagnosis and Detection Applications

The early diagnosis of certain fatal diseases is vital for preventing severe consequences and contributes to a more effective treatment. Despite numerous conventional methods to realize this goal, employing nanobiosensors is a novel approach that provides a fast and precise detection. Recently, nanomaterials have been widely applied as biosensors with distinctive features. Graphite phase carbon nitride (g-C₃N₄) is a two-dimensional (2D) carbon-based nanostructure that has received attention in biosensing. Biocompatibility, biodegradability, semiconductivity, high photoluminescence yield, low-cost synthesis, easy production process, antimicrobial activity, and high stability are prominent properties that have rendered g-C₃N₄ a promising candidate to be used in electrochemical, optical, and other kinds of biosensors. This review presents the g-C₃N₄ unique features, synthesis methods, and g-C₃N₄-based nanomaterials. In addition, recent relevant studies on using g-C₃N₄ in biosensors in regard to improving treatment pathways are reviewed.

A novel AIE fluorescent probe for the monitoring of aluminum ions in living cells and zebrafish

A novel fluorescent probe BTD with aggregation induced emission (AIE) characteristics for the monitoring of Al³⁺ was developed. This fluorescent probe could be used to detect Al³⁺ in aqueous solution under mild conditions, along with high sensitivity and high selectivity. The detection limit of the probe BTD for Al³⁺ is as low as 3.25 nM, which is below the WHO recommendation concentration (7.41 μM) for drinking water. Furthermore, this probe was successfully applied to the sensing of Al³⁺ in living cells and zebrafish.

Properties and Applications of Graphene and Its Derivatives in Biosensors for Cancer Detection: A Comprehensive Review

Cancer is one of the deadliest diseases worldwide, and there is a critical need for diagnostic platforms for applications in early cancer detection. The diagnosis of cancer can be made by identifying abnormal cell characteristics such as functional changes, a number of vital proteins in the body, abnormal genetic mutations and structural changes, and so on. Identifying biomarker candidates such as DNA, RNA, mRNA, aptamers, metabolomic biomolecules, enzymes, and proteins is one of the most important challenges. In order to eliminate such challenges, emerging biomarkers can be identified by designing a suitable biosensor. One of the most powerful technologies in development is biosensor technology based on nanostructures. Recently, graphene and its derivatives have been used for diverse diagnostic and therapeutic approaches. Graphene-based biosensors have exhibited significant performance with excellent sensitivity, selectivity, stability, and a wide detection range. In this review, the principle of technology, advances, and challenges in graphene-based biosensors such as field-effect transistors (FET), fluorescence sensors, SPR biosensors, and electrochemical biosensors to detect different cancer cells is systematically discussed. Additionally, we provide an outlook on the properties, applications, and challenges of graphene and its derivatives, such as Graphene Oxide (GO), Reduced Graphene Oxide (RGO), and Graphene Quantum Dots (GQDs), in early cancer detection by nanobiosensors.

Chemical-Biology-derived in vivo Sensors: Past, Present, and Future

To understand the complex biochemistry and biophysics of biological systems, one needs to be able to monitor local concentrations of molecules, physical properties of macromolecular assemblies and activation status of signaling pathways, in real time, within single cells, and at high spatio-temporal resolution. Here we look at the tools that have been / are being / need to be provided by chemical biology to address these challenges. In particular, we highlight the utility of molecular probes that help to better measure mechanical forces and flux through key signalling pathways. Chemical biology can be used to both build biosensors to visualize, but also actuators to perturb biological processes. An emergent theme is the possibility to multiplex measurements of multiple cellular processes. Advances in microscopy automation now allow us to acquire datasets for 1000's of cells. This produces high dimensional datasets that require computer vision approaches that automate image analysis. The high dimensionality of these datasets are often not immediately accessible to human intuition, and, similarly to 'omics technologies, require statistical approaches for their exploitation. The field of biosensor imaging is therefore experiencing a multidisciplinary transition that will enable it to realize its full potential as a tool to provide a deeper appreciation of cell physiology.

A Rationally and Computationally Designed Fluorescent Biosensor for d-Serine

Solute-binding proteins (SBPs) have evolved to balance the demands of ligand affinity, thermostability, and conformational change to accomplish diverse functions in small molecule transport, sensing, and chemotaxis. Although the ligand-induced conformational changes that occur in SBPs make them useful components in biosensors, they are challenging targets for protein engineering and design. Here, we have engineered a d-alanine-specific SBP into a fluorescence biosensor with specificity for the signaling molecule d-serine (D-serFS). This was achieved through binding site and remote mutations that improved affinity (K_D = 6.7 ± 0.5 μM), specificity (40-fold increase vs glycine), thermostability (T_m = 79 °C), and dynamic range (∼14%). This sensor allowed measurement of physiologically relevant changes in d-serine concentration using two-photon excitation fluorescence microscopy in rat brain hippocampal slices. This work illustrates the functional trade-offs between protein dynamics, ligand affinity, and thermostability and how these must be balanced to achieve desirable activities in the engineering of complex, dynamic proteins.

Determination of miRNA derived from exosomes of prostate cancer via toehold-aided cyclic amplification combined with HRP enzyme catalysis and magnetic nanoparticles

MicroRNAs (miRNAs) play a significant role in tumorigenesis and tumor development. Exosomal microRNA-141 (miRNA-141, miR-141) has been reported to be overexpressed in prostate cancer (PCa) and has become a potential biomarker for the diagnosis of PCa. Herein, a novel fluorescent biosensor based on toehold-aided cyclic amplification combined with horseradish peroxidase (HRP) enzyme catalysis and magnetic nanoparticles (MNPs) was designed for determination of the exosomes-derived microRNA-141 (miRNA-141, miR-141). The synergy of HRP enzyme catalysis and toehold mediated strand display reaction (TSDR) increase the sensitivity of the method, and the good separation ability of MNPs ensures the specificity of the method. Therefore, under the optimized experimental conditions, the highly sensitive and specific detection of miRNA-141 can be realized, and the detection limit is as low as 10 fM. More importantly, the biosensor successfully determinates the exosomal miR-141 in the plasma of patients with PCa.

Structure- and mechanism-guided design of single fluorescent protein-based biosensors

Intensiometric genetically encoded biosensors, based on allosteric modulation of the fluorescence of a single fluorescent protein, are powerful tools for enabling imaging of neural activities and other cellular biochemical events. The archetypical example of such biosensors is the GCaMP series of Ca²⁺ biosensors, which have been steadily improved over the past two decades and are now indispensable tools for neuroscience. However, no other biosensors have reached levels of performance, or had revolutionary impacts within specific disciplines, comparable to that of the Ca²⁺ biosensors. Of the many reasons why this has been the case, a critical one has been a general black-box view of biosensor structure and mechanism. With this Perspective, we aim to summarize what is known about biosensor structure and mechanisms and, based on this foundation, provide guidelines to accelerate the development of a broader range of biosensors with performance comparable to that of the GCaMP series.

Rational Design of a Split Flavin-Based Fluorescent Reporter

Protein-fragment complementation assays are used ubiquitously for probing protein-protein interactions. Most commonly, the reporter protein is split in two parts, which are then fused to the proteins of interest and can reassemble and provide a readout if the proteins of interest interact with each other. The currently known split fluorescent proteins either can be used only in aerobic conditions and assemble irreversibly, or require addition of exogenous chromophores, which complicates the design of experiments. In recent years, light-oxygen-voltage (LOV) domains of several photoreceptor proteins have been developed into flavin-based fluorescent proteins (FbFPs) that, under some circumstances, can outperform commonly used fluorescent proteins such as GFP. Here, we show that CagFbFP, a small thermostable FbFP based on a LOV domain-containing protein from Chloroflexus aggregans, can serve as a split fluorescent reporter. We use the available genetic and structural information to identify three loops between the conserved secondary structure elements, Aβ-Bβ, Eα-Fα, and Hβ-Iβ, that tolerate insertion of flexible poly-Gly/Ser segments and eventually splitting. We demonstrate that the designed split pairs, when fused to interacting proteins, are fluorescent in vivo in E. coli and human cells and have low background fluorescence. Our results enable probing protein-protein interactions in anaerobic conditions without using exogenous fluorophores and provide a basis for further development of LOV and PAS (Per-Arnt-Sim) domain-based fluorescent reporters and optogenetic tools.

Synthetic protein switches: Combinatorial linker engineering with iFLinkC

Linker engineering constitutes a critical, yet frequently underestimated aspect in the construction of synthetic protein switches and sensors. Notably, systematic strategies to engineer linkers by predictive means remain largely elusive to date. This is primarily due to our insufficient understanding how the biophysical properties that underlie linker functions mediate the conformational transitions in artificially engineered protein switches and sensors. The construction of synthetic protein switches and sensors therefore heavily relies on experimental trial-and-error. Yet, methods for effectively generating linker diversity at the genetic level are scarce. Addressing this technical shortcoming, iterative functional linker cloning (iFLinkC) enables the combinatorial assembly of linker elements with functional domains from sequence verified repositories that are developed and stored in-house. The assembly process is highly scalable and given its recursive nature generates linker diversity in a combinatorial and exponential fashion based on a limited number of linker elements.

Plasmonic Metasensors Based on 2D Hybrid Atomically Thin Perovskite Nanomaterials

In this work, we have designed highly sensitive plasmonic metasensors based on atomically thin perovskite nanomaterials with a detection limit up to 10⁻¹⁰ refractive index units (RIU) for the target sample solutions. More importantly, we have improved phase singularity detection with the Goos–Hänchen (GH) effect. The GH shift is known to be closely related to optical phase signal changes; it is much more sensitive and sharp than the phase signal in the plasmonic condition, while the experimental measurement setup is much more compact than that of the commonly used interferometer scheme to exact the phase signals. Here, we have demonstrated that plasmonic sensitivity can reach a record-high value of 1.2862 × 10⁹ µm/RIU with the optimum configurations for the plasmonic metasensors. The phase singularity-induced GH shift is more than three orders of magnitude larger than those achievable in other metamaterial schemes, including Ag/TiO₂ hyperbolic multilayer metamaterials (HMMs), metal–insulator–metal (MIM) multilayer waveguides with plasmon-induced transparency (PIT), and metasurface devices with a large phase gradient. GH sensitivity has been improved by more than 10⁶ times with the atomically thin perovskite metasurfaces (1.2862 × 10⁹ µm/RIU) than those without (918.9167 µm/RIU). The atomically thin perovskite nanomaterials with high absorption rates enable precise tuning of the depth of the plasmonic resonance dip. As such, one can optimize the structure to reach near zero-reflection at the resonance angle and the associated sharp phase singularity, which leads to a strongly enhanced GH lateral shift at the sensor interface. By integrating the 2D perovskite nanolayer into a metasurface structure, a strong localized electric field enhancement can be realized and GH sensitivity was further improved to 1.5458 × 10⁹ µm/RIU. We believe that this enhanced electric field together with the significantly improved GH shift would enable single molecular or even submolecular detection for hard-to-identify chemical and biological markers, including single nucleotide mismatch in the DNA sequence, toxic heavy metal ions, and tumor necrosis factor-α (TNFα).

Genetic Biosensor Design for Natural Product Biosynthesis in Microorganisms

Low yield and low titer of natural products are common issues in natural product biosynthesis through microbial cell factories. One effective way to resolve such bottlenecks is to design genetic biosensors to monitor and regulate the biosynthesis of target natural products. In this review, we evaluate the most recent advances in the design of genetic biosensors for natural product biosynthesis in microorganisms. In particular, we examine strategies for selection of genetic parts and construction principles for the design and evaluation of genetic biosensors. We also review the latest applications of transcription factor- and riboswitch-based genetic biosensors in natural product biosynthesis. Lastly, we discuss challenges and solutions in designing genetic biosensors for the biosynthesis of natural products in microorganisms.

Revisiting and Redesigning Light-Activated Cyclic-Mononucleotide Phosphodiesterases

As diffusible second messengers, cyclic nucleoside monophosphates (cNMPs) relay and amplify molecular signals in myriad cellular pathways. The triggering of downstream physiological responses often requires defined cNMP gradients in time and space, generated through the concerted action of nucleotidyl cyclases and phosphodiesterases (PDEs). In an approach denoted optogenetics, sensory photoreceptors serve as genetically encoded, light-responsive actuators to enable the noninvasive, reversible, and spatiotemporally precise control of manifold cellular processes, including cNMP metabolism. Although nature provides efficient photoactivated nucleotidyl cyclases, light-responsive PDEs are scarce. Through modular recombination of a bacteriophytochrome photosensor and the effector of human PDE2A, we previously generated the light-activated, cNMP-specific PDE LAPD. By pursuing parallel design strategies, we here report a suite of derivative PDEs with enhanced amplitude and reversibility of photoactivation. Opposite to LAPD, far-red light completely reverts prior activation by red light in several PDEs. These improved PDEs thus complement photoactivated nucleotidyl cyclases and extend the sensitivity of optogenetics to red and far-red light. More generally, our study informs future efforts directed at designing bacteriophytochrome photoreceptors.