Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

Harnessing DNA computing and nanopore decoding for practical applications: from informatics to microRNA-targeting diagnostics

DNA computing represents a subfield of molecular computing with the potential to become a significant area of next-generation computation due to the high programmability inherent in the sequence-dependent molecular behaviour of DNA. Recent studies in DNA computing have extended from mathematical informatics to biomedical applications, with a particular focus on diagnostics that exploit the biocompatibility of DNA molecules. The output of DNA computing devices is encoded in nucleic acid molecules, which must then be decoded into human-recognizable signals for practical applications. Nanopore technology, which utilizes an electrical and label-free decoding approach, provides a unique platform to bridge DNA and electronic computing for practical use. In this tutorial review, we summarise the fundamental knowledge, technologies, and methodologies of DNA computing (logic gates, circuits, neural networks, and non-DNA input circuity). We then focus on nanopore-based decoding, and highlight recent advances in medical diagnostics targeting microRNAs as biomarkers. Finally, we conclude with the potential and challenges for the practical implementation of these techniques. We hope that this tutorial will provide a comprehensive insight and enable the general reader to grasp the fundamental principles and diverse applications of DNA computing and nanopore decoding, and will inspire a wide range of scientists to explore and push the boundaries of these technologies.

MXene-based aptasensors: a perspective on recent advances

Recent advancements in science and technology have significantly enhanced public health by integrating novel materials and early diagnostic methods. A key focus is on MXenes, a class of materials known for their distinctive morphology and exceptional stability in diverse environments. MXenes possess notable structural engineering capabilities, enabling their design and synthesis into various forms tailored for specific applications. Their surface can be functionalized with different groups to enable chemical binding and physical attachment to various molecules, while variations in layer thickness and elemental composition influence their electrical conductivity and stability. This perspective article examines recent structural innovations in MXenes, particularly their application in biosensors. We highlight the role of aptamer surface decorations, which offer specific and selective binding for detecting a broad spectrum of analytes, thus underscoring MXenes' potential in advancing diagnostic technologies and improving public health.

Hydrogen Sulfide-Triggered Artificial DNAzyme Switches for Precise Manipulation of Cellular Functions

The development of synthetic molecular tools responsive to biological cues is crucial for advancing targeted cellular regulation. A significant challenge is the regulation of cellular processes in response to gaseous signaling molecules such as hydrogen sulfide (H2S). To address this, we present the design of Gas signaling molecule-Responsive Artificial DNAzyme-based Switches (GRAS) to manipulate cellular functions via H2S-sensitive synthetic DNAzymes. By incorporating stimuli-responsive moieties to the phosphorothioate backbone, DNAzymes are strategically designed with H2S-responsive azide groups at cofactor binding locations within the catalytic core region. These modifications enable their activation through H2S-reducing decaging, thereby initiating substrate cleavage activity. Our approach allows for the flexible customization of various DNAzymes to regulate distinct cellular processes in diverse scenarios. Intracellularly, the enzymatic activity of GRAS promotes H2S-induced cleavage of specific mRNA sequences, enabling targeted gene silencing and inducing apoptosis in cancer cells. Moreover, integrating GRAS with dynamic DNA assembly allows for grafting these functional switches onto cell surface receptors, facilitating H2S-triggered receptor dimerization. This extracellular activation transmits signals intracellularly to regulate cellular behaviors such as migration and proliferation. Collectively, synthetic switches are capable of rewiring cellular functions in response to gaseous cues, offering a promising avenue for advanced targeted cellular engineering.

Optimized periphery-core interface increases fitness of the Bacillus subtilis glmS ribozyme

Like other functional RNAs, ribozymes encode a conserved catalytic center supported by peripheral domains that vary among ribozyme sub-families. To understand how core-periphery interactions contribute to ribozyme fitness, we compared the cleavage kinetics of all single base substitutions at 152 sites across the Bacillus subtilis glmS ribozyme by high-throughput sequencing (k-seq). The in vitro activity map mirrored phylogenetic sequence conservation in glmS ribozymes, indicating that biological fitness reports all biochemically important positions. The k-seq results and folding assays showed that most deleterious mutations lower activity by impairing ribozyme self-assembly. All-atom molecular dynamics simulations of the complete ribozyme revealed how individual mutations in the core or the IL4 peripheral loop introduce a non-native tertiary interface that rewires the catalytic center, eliminating activity. We conclude that the need to avoid non-native helix packing powerfully constrains the evolution of tertiary structure motifs in RNA.

A quantitative framework for structural interpretation of DMS reactivity

Dimethyl sulfate (DMS) chemical mapping is widely used for probing RNA structure, with low reactivity interpreted as Watson-Crick (WC) base pairs and high reactivity as unpaired nucleotides. Despite its widespread use, a quantitative understanding of how DMS reactivity relates to specific RNA 3D structural features remains incomplete. To address this gap, we systematically analyzed DMS reactivity patterns with a massive library of 7,500 RNA constructs containing two-way junctions with known 3D structures. Our results reveal that DMS reactivity exists on a continuous spectrum rather than discrete high and low bins. Approximately 10% overlap in reactivity between WC and non-WC nucleotides demonstrates that simple thresholds cannot accurately determine base-pairing status. In flanking WC pairs, DMS reactivity correlates with base stacking strength and junction dynamics. For non-WC nucleotides, increased hydrogen bonding and decreased solvent accessibility led to WC-like DMS protection. Most significantly, we discover that DMS reactivity in non-canonical pairs strongly correlates with atomic distances and base pair geometry, enabling discrimination between different 3D conformations. These quantitative relationships establish novel metrics for evaluating RNA structural models and provide a new framework for incorporating DMS reactivity patterns into structure prediction algorithms.

A strategy for detecting CSFV using DNAzyme-HCR cascade amplification

The Hybridization Chain Reaction (HCR) is an isothermal amplification technique widely used for sensing nucleic acids and small molecules. Despite its effectiveness, conventional linear HCR exhibits relatively slow kinetics and insufficient sensitivity. To address this challenge, we have innovatively combined HCR with DNAzyme technology to enhance nucleic acid detection. In this novel approach, the presence of a target molecule triggers the formation of DNAzyme, leading to the cleavage of substrate S, the initiation of HCR, and the production of DNA nanowires and labeled DNAzyme. The newly generated DNAzyme continuously cleaves substrate S, promoting sequential HCR amplification and significantly enhancing the fluorescence signal. This system offers a simple, sensitive, selective, and versatile method for nucleic acid detection, with a detection limit as low as 5 pM. When tested on classical swine fever virus (CSFV) samples, the system demonstrated detection accuracy comparable to RT-qPCR and exhibited superior repeatability.

A close-looped DNAzyme walker with an available catalytic domain for electrochemiluminescent detection of acetamiprid

Traditional DNA walkers face enormous challenges due to limited biostability and reaction kinetics. Herein, we designed a self-driven close-looped DNAzyme walker (cl-DW) with high structural biostability and catalytic activity that enabled rapid electrochemiluminescence (ECL) detection of pesticide residue acetamiprid. Specifically, cl-DW exhibited increasing ability to resist nuclease degradation with a 570-fold longer half-degradation time than that of the single-stranded DNAzyme walker (ss-DW) due to the protected DNA terminal. Furthermore, cl-DW achieved high catalytic activity with a 4.3-fold faster reaction kinetic than that of ss-DW due to the circularized nanostructure of an available catalytic domain. Consequently, we utilized cl-DW as a signal amplifier and tin-based sulfide (SnS2) nanoflowers as ECL emitters to construct an ECL aptasensor, which realized the sensitive detection of acetamiprid with a limit of detection of 0.85 nM. This work provides a reliable approach to exploring DNA walkers with high catalytic activity and better biostability for molecular monitoring.

Enhanced Detection of Vibrio harveyi Using a Dual-Composite DNAzyme-Based Biosensor

Vibrio harveyi is a serious bacterial pathogen which can infect a wide range of marine organisms, such as marine fish, invertebrates, and shrimp, in aquaculture, causing severe losses. In addition, V. harveyi can be transmitted through food and water, infecting humans and posing a serious threat to public safety. Therefore, rapid and accurate detection of this pathogen is key for the prevention and control of related diseases. In this study, nine rounds of in vitro screening were conducted with Systematic Evolution of Ligands by Exponential Enrichment (SELEX) technology using unmodified DNA libraries, targeting the crude extracellular matrix (CEM) of V. harveyi. Two DNAzymes, named DVh1 and DVh3, with high activity and specificity were obtained. Furthermore, a fluorescent biosensor with dual DNAzymes was constructed which exhibited improved detection efficiency. The sensor showed a good fluorescence response to multiple aquatic products (i.e., fish, shrimp, and shellfish) infected with V. harveyi, with a detection limit below 11 CFU/mL. The fluorescence signal was observed within 30 min of reaction after target addition. This simple, inexpensive, highly effective, and easy to operate DNAzymes biosensor can be used for field detection of V. harveyi.

DNA Catalysis: Design, Function, and Optimization

Catalytic DNA has gained significant attention in recent decades as a highly efficient and tunable catalyst, thanks to its flexible structures, exceptional specificity, and ease of optimization. Despite being composed of just four monomers, DNA's complex conformational intricacies enable a wide range of nuanced functions, including scaffolding, electrocatalysis, enantioselectivity, and mechano-electro spin coupling. DNA catalysts, ranging from traditional DNAzymes to innovative DNAzyme hybrids, highlight the remarkable potential of DNA in catalysis. Recent advancements in spectroscopic techniques have deepened our mechanistic understanding of catalytic DNA, paving the way for rational structural optimization. This review will summarize the latest studies on the performance and optimization of traditional DNAzymes and provide an in-depth analysis of DNAzyme hybrid catalysts and their unique and promising properties.

Insights into the cotranscriptional and translational control mechanisms of the Escherichia coli tbpA thiamin pyrophosphate riboswitch

Riboswitches regulate gene expression by modulating their structure upon metabolite binding. These RNA orchestrate several layers of regulation to achieve genetic control. Although Escherichia coli riboswitches modulate translation initiation, several cases have been reported where riboswitches also modulate mRNA levels. Here, we characterize the regulation mechanisms of the thiamin pyrophosphate (TPP) tbpA riboswitch in E. coli. Our results indicate that the tbpA riboswitch modulates both levels of translation and transcription and that TPP sensing is achieved more efficiently cotranscriptionally than post-transcriptionally. The preference for cotranscriptional binding is also observed when monitoring the TPP-dependent inhibition of translation initiation. Using single-molecule approaches, we observe that the aptamer domain freely fluctuates between two main structures involved in TPP recognition. Our results suggest that translation initiation is controlled through the ligand-dependent stabilization of the riboswitch structure. This study demonstrates that riboswitch cotranscriptional sensing is the primary determinant in controlling translation and mRNA levels.

Self-Adaptive Activation of DNAzyme Nanoassembly for Synergistically Combined Gene Therapy

DNAzyme represents a promising gene silencing toolbox yet is obstructed by the poor substrate accessibility in specific cells. Herein, a compact DNA nanoassembly, incorporating multimeric therapeutic DNAzyme, was prepared for selective delivery of gene-silencing DNAzyme with requisite cofactors and auxiliary chemo-drugs. By virtue of the sequence-conservative duplex-specific nuclease, the endogenous miRNA catalyzes the successive and site-specific cleavage of DNA nanoassembly substrate (nominated as the localized RNA walking machine) and thus ensures the liberation/activation of therapeutic agents with high accuracy and efficacy. The miR-10b-stimulated DNAzyme was designed to downregulate the TWIST transcription factor, an upstream promotor of miR-10b, thus acquiring the self-sufficient downregulation of TWIST/miR-10b signaling nodes (self-adaptive negative feedback loop) for abrogating tumor metastasis and chemo-resistance issues.

Therapeutic applications of RNA nanostructures

RNA-based therapeutics have gained wide public interest in recent years. RNA is a versatile molecule that exists in many forms including mRNA, siRNA, miRNA, ribozymes, and other non-coding RNAs and is primarily applied for gene therapy. RNA is also used as a modular building block to construct RNA nanostructures. The programmable nature of RNA nanostructures enables the generation of simple, modulable, and multi-functional RNA-based therapeutics. Although the therapeutic application of RNA may be limited due to its structural instability, advances in RNA nanotechnology have improved the stability of RNA nanostructures for greater application. Various strategies have been developed to enhance the stability of RNA nanostructures enabling their application in vivo. In this review, we examine the therapeutic applications of RNA nanostructures. Non-immunogenic RNA nanostructures can be rationally designed with functional RNA molecules to modulate gene expression for gene therapy. On the other hand, nucleic acids can be sensed by cellular receptors to elicit an innate immune response, for which certain DNA and RNA motifs can function as adjuvants. Taking advantage of this adjuvant potential, RNA nanostructures can be used for immunotherapy and be designed for cancer vaccines. Thus, we examine the therapeutic application of immunogenic RNA nanostructures for cancer immunotherapy. RNA nanostructures represent promising platforms to design new nanodrugs, gene therapeutics, immunotherapeutic adjuvants, and cancer vaccines. Ongoing research in the field of RNA nanotechnology will continue to empower the development of RNA nanostructure-based therapeutics with high efficacy and limited toxicity.

Apollon: a deoxyribozyme that generates a yellow product

Colorimetric assays in which the color of a solution changes in the presence of an input provide a simple and inexpensive way to monitor experimental readouts. In this study we used in vitro selection to identify a self-phosphorylating kinase deoxyribozyme that produces a colorimetric signal by converting the colorless substrate pNPP into the yellow product pNP. The minimized catalytic core, sequence requirements, secondary structure, and buffer requirements of this deoxyribozyme, which we named Apollon, were characterized using a variety of techniques including reselection experiments, high-throughput sequencing, comparative analysis, biochemical activity assays, and NMR. A bimolecular version of Apollon catalyzed multiple turnover phosphorylation and amplified the colorimetric signal. Engineered versions of Apollon could detect oligonucleotides with specific sequences as well as several different types of nucleases in homogenous assays that can be performed in a single tube without the need for washes or purifications. We anticipate that Apollon will be particularly useful to reduce costs in high-throughput screens and for applications in which specialized equipment is not available.

Aurora: a fluorescent deoxyribozyme for high-throughput screening

Fluorescence facilitates the detection, visualization, and tracking of molecules with high sensitivity and specificity. A functional DNA molecule that generates a robust fluorescent signal would offer significant advantages for many applications compared to intrinsically fluorescent proteins, which are expensive and labor intensive to synthesize, and fluorescent RNA aptamers, which are unstable under most conditions. Here, we describe a novel deoxyriboyzme that rapidly and efficiently generates a stable fluorescent product using a readily available coumarin substrate. An engineered version can detect picomolar concentrations of ribonucleases in a simple homogenous assay, and was used to rapidly identify novel inhibitors of the SARS-CoV-2 ribonuclease Nsp15 in a high-throughput screen. Our work adds an important new component to the toolkit of functional DNA parts, and also demonstrates how catalytic DNA motifs can be used to solve real-world problems.

In vitro selection of N 1-methyladenosine-sensitive RNA-cleaving deoxyribozymes with 105-fold selectivity over unmethylated RNA

RNA-cleaving DNAzymes (RCDs) are catalytically active DNA molecules that cleave a wide range of RNA targets with extremely high sequence-selectivity, but none is able to faithfully discriminate methylated from unmethylated RNA (typically <30-fold). We report the first efforts to isolate RCDs from a random-sequence DNA pool by in vitro selection that cleave RNA/DNA chimera containing N 1-methyladenosine (m1A), one of the most prevalent RNA modifications that plays important regulatory roles in gene expression and human cancers. A cis-acting deoxyribozyme, RCD1-S2m1A, exhibits an observed rate constant (k obs) of 5.3 × 10-2 min-1, resulting in up to 105-fold faster cleavage of the m1A-modified versus unmethylated RNA. Furthermore, a trans-acting fluorogenic deoxyribozyme was constructed by labeling a fluorophore and a quencher at the 5' and 3' ends of the chimeric substrate, respectively. It permits the synchronization of RNA-cleaving with real-time fluorescence signaling, thus allowing the selective monitoring of ALKBH3-mediated demethylation and inhibitor screening in living cells.

Self-Powered Engineering of Cell Membrane Receptors to On-Demand Regulate Cellular Behaviors

On-demand engineering of cell membrane receptors to nongenetically intervene in cellular behaviors is still a challenge. Herein, a membraneless enzyme biofuel cell-based self-powered biosensor (EBFC-SPB) was developed for autonomously and precisely releasing Zn2+ to initiate DNAzyme-based reprogramming of cell membrane receptors, which further mediates signal transduction to regulate cellular behaviors. The critical component of EBFC-SPB is a hydrogel film on a biocathode which is prepared using a Fe3+-cross-linked alginate hydrogel film loaded with Zn2+ ions. In the working mode in the presence of glucose/O2, the hydrogel is decomposed due to the reduction of Fe3+ to Fe2+, accompanied by rapid release of Zn2+ to specifically activate a Zn2+-responsive DNAzyme nanodevice on the cell surface, leading to the dimerization of homologous or nonhomologous receptors to promote or inhibit cell proliferation and migration. This EBFC-SPB platform provides a powerful "sensing-actuating-treating" tool for chemically regulating cellular behaviors, which holds great promise in precision biomedicine.

Chemical Synthesis of Modified RNA

Ribonucleic acids (RNAs) play a vital role in living organisms. Many of their cellular functions depend critically on chemical modification. Methods to modify RNA in a controlled manner-both in vitro and in vivo-are thus essential to evaluate and understand RNA biology at the molecular and mechanistic levels. The diversity of modifications, combined with the size and uniformity of RNA (made up of only 4 nucleotides) makes its site-specific modification a challenging task that needs to be addressed by complementary approaches. One such approach is solid-phase RNA synthesis. We discuss recent developments in this field, starting with new protection concepts in the ongoing effort to overcome current size limitations. We continue with selected modifications that have posed significant challenges for their incorporation into RNA. These include deazapurine bases required for atomic mutagenesis to elucidate mechanistic aspects of catalytic RNAs, and RNA containing xanthosine, N4-acetylcytidine, 5-hydroxymethylcytidine, 3-methylcytidine, 2'-OCF3, and 2'-N3 ribose modifications. We also discuss the all-chemical synthesis of 5'-capped mRNAs and the enzymatic ligation of chemically synthesized oligoribonucleotides to obtain long RNA with multiple distinct modifications, such as those needed for single-molecule FRET studies. Finally, we highlight promising developments in RNA-catalyzed RNA modification using cofactors that transfer bioorthogonal functionalities.

Aptasensor-encapsulating semi-permeable proteinosomes for direct target detection in non-treated biofluids

Detecting biomarkers in biofluids directly without sample treatments makes molecular diagnostics faster and more efficient. Aptasensors, the nucleic acid-based molecular biosensors, can detect a wide range of target molecules, but their susceptibility to degradation and aggregation by nucleases and charged proteins, respectively, limits their direct use in clinical samples. In this work, we demonstrate that when aptasensors are encapsulated in proteinosomes, the protein-based liposome mimics, clinically important small molecules can be sensitively and selectively detected in non-treated specimens, such as 100 % unpurified serum. As serum albumin is used to form the membrane, the nanomeshed proteinosomes become semi-permeable and antifouling, which enables exclusive admission of small molecules while blocking unwanted large proteins. Consequently, the enclosed aptasensors can maintain close-to-optimal performance for target binding, and nucleolytic degradation and electrostatic aggregation are effectively suppressed. Three different structure-switching aptamers specific for estradiol, dopamine, and cocaine, respectively, are demonstrated to fully conserve their high affinities and specificities inside the microcapsules. The shielding effect of proteinosomes is indeed exceptional; the enclosed DNA aptasensors remain completely intact over 18 h in serum and even in an extremely concentrated DNase solution (1 mg/ml, ∼300,000× the serum level). Moreover, the proteinosome-mediated compartmentalization enables independent operation of multiple aptasensors in the same mixture. Hence, simultaneous real-time sensing of two different targets is demonstrated with different operation modes, 'recording' target appearance and 'reporting' target concentration changes. This work is the first demonstration of small-molecule-specific aptasensors operating with optimal performance in serum environments and will find promising applications in molecular diagnostics.

Cleaving DNA with DNA: Cooperative Tuning of Structure and Reactivity Driven by Copper Ions

A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.

Atomic Mutagenesis of N6-Methyladenosine Reveals Distinct Recognition Modes by Human m6A Reader and Eraser Proteins

N6-methyladenosine (m6A) is an important modified nucleoside in cellular RNA associated with multiple cellular processes and is implicated in diseases. The enzymes associated with the dynamic installation and removal of m6A are heavily investigated targets for drug research, which requires detailed knowledge of the recognition modes of m6A by proteins. Here, we use atomic mutagenesis of m6A to systematically investigate the mechanisms of the two human m6A demethylase enzymes FTO and ALKBH5 and the binding modes of YTH reader proteins YTHDF2/DC1/DC2. Atomic mutagenesis refers to atom-specific changes that are introduced by chemical synthesis, such as the replacement of nitrogen by carbon atoms. Synthetic RNA oligonucleotides containing site-specifically incorporated 1-deaza-, 3-deaza-, and 7-deaza-m6A nucleosides were prepared by solid-phase synthesis and their RNA binding and demethylation by recombinant proteins were evaluated. We found distinct differences in substrate recognition and transformation and revealed structural preferences for the enzymatic activity. The deaza m6A analogues introduced in this work will be useful probes for other proteins in m6A research.

Chemoenzymatic Installation of Site-Specific Chemical Groups on DNA Enhances the Catalytic Activity

Functional DNAs are valuable molecular tools in chemical biology and analytical chemistry but suffer from low activities due to their limited chemical functionalities. Here, we present a chemoenzymatic method for site-specific installation of diverse functional groups on DNA, and showcase the application of this method to enhance the catalytic activity of a DNA catalyst. Through chemoenzymatic introduction of distinct chemical groups, such as hydroxyl, carboxyl, and benzyl, at specific positions, we achieve significant enhancements in the catalytic activity of the RNA-cleaving deoxyribozyme 10-23. A single carboxyl modification results in a 100-fold increase, while dual modifications (carboxyl and benzyl) yield an approximately 700-fold increase in activity when an RNA cleavage reaction is catalyzed on a DNA-RNA chimeric substrate. The resulting dually modified DNA catalyst, CaBn, exhibits a kobs of 3.76 min-1 in the presence of 1 mM Mg2+ and can be employed for fluorescent imaging of intracellular magnesium ions. Molecular dynamics simulations reveal the superior capability of CaBn to recruit magnesium ions to metal-ion-binding site 2 and adopt a catalytically competent conformation. Our work provides a broadly accessible strategy for DNA functionalization with diverse chemical modifications, and CaBn offers a highly active DNA catalyst with immense potential in chemistry and biotechnology.

Hierarchical Assembly of Single-Stranded RNA

Single-stranded RNA (ssRNA) plays a major role in the flow of genetic information-most notably, in the form of messenger RNA (mRNA)-and in the regulation of biological processes. The highly dynamic nature of chains of unpaired nucleobases challenges structural characterizations of ssRNA by experiments or molecular dynamics (MD) simulations alike. Here, we use hierarchical chain growth (HCG) to construct ensembles of ssRNA chains. HCG assembles the structures of protein and nucleic acid chains from fragment libraries created by MD simulations. Applied to homo- and heteropolymeric ssRNAs of different lengths, we find that HCG produces structural ensembles that overall are in good agreement with diverse experiments, including nuclear magnetic resonance (NMR), small-angle X-ray scattering (SAXS), and single-molecule Förster resonance energy transfer (FRET). The agreement can be further improved by ensemble refinement using Bayesian inference of ensembles (BioEn). HCG can also be used to assemble RNA structures that combine base-paired and base-unpaired regions, as illustrated for the 5' untranslated region (UTR) of SARS-CoV-2 RNA.

Topological Single-stranded DNA Encoding and Programmable Assembly of Molecular Nanostructures for NIR-II Cancer Theranostics

Molecular nanotechnology promises to offer privileged access to developing NIR-II materials with precise structural and functional manipulation for transformable theranostic applications. However, the lack of an affordable, yet general, method makes this goal currently inaccessible. By virtue of the intriguing nucleic acid chemistry, here we present an artificial base-directed topological single-strand DNA encoding design that enables one-step synthesis of valence-controlled NIR-II molecular nanostructures and spatial assembly of these nanostructures to modulate their behaviors in living systems. As proof-of-concept studies, we construct ultrasmall Ag2 S quantum dots and pH-responsive, size-tunable CuS assemblies for in vivo NIR-II fluorescence imaging and deep tumor photothermal therapy. This work paves a new way for creating functionally diversified architectures and broadens the scope of DNA-encoded material engineering.

Circular DNAzyme-Switched CRISPR/Cas12a Assay for Electrochemiluminescent Response of Demethylase Activity

DNA nanostructure provides powerful tools for DNA demethylase activity detection, but its stability has been significantly challenged. By virtue of circular DNA with resistance to exonuclease degradation, herein, the circular DNAzyme duplex with artificial methylated modification was constructed to identify the target and output the DNA activators to drive the CRISPR/Cas12a, constructing an "on-off-on" electrochemiluminescence (ECL) biosensor for monitoring the activity of the O6-methylguanine-DNA methyltransferase (MGMT). Specifically, the circular DNAzyme duplex consisted of the chimeric RNA-DNA substrate ring with double activator sequences and two single-stranded DNAzymes, whose catalytic domains were premodified with the methyl groups. When the MGMT was present, the methylated DNAzymes were repaired and restored the catalytic activity to cleave the chimeric RNA-DNA substrates, followed by the output of DNA activators to initiate the CRISPR/Cas12a. Subsequently, the ECL signals of silver nanoparticle-modified SnO2 nanospheres (Ag@SnO2) were recovered by releasing the ferrocene-labeled quenching probes (Fc-DNA) from the electrode surface because of the trans-cleavage activity of CRISPR/Cas12a, thus achieving the specific and sensitive ECL detection of MGMT from 2.5 × 10-4 to 2.5 × 102 ng/mL with a low limit (9.69 × 10-5 ng/mL). This strategy affords novel ideas and insights into research on how to project stable nucleic acid probes to detect DNA demethylases beyond traditional methods.

Functional Nucleic Acid-Based Immunomodulation for T Cell-Mediated Cancer Therapy

T cell-mediated immunity plays a pivotal role in cancer immunotherapy. The anticancer actions of T cells are coordinated by a sequence of biological processes, including the capture and presentation of antigens by antigen-presenting cells (APCs), the activation of T cells by APCs, and the subsequent killing of cancer cells by activated T cells. However, cancer cells have various means to evade immune responses. Meanwhile, these vulnerabilities provide potential targets for cancer treatments. Functional nucleic acids (FNAs) make up a class of synthetic nucleic acids with specific biological functions. With their diverse functionality, good biocompatibility, and high programmability, FNAs have attracted widespread interest in cancer immunotherapy. This Review focuses on recent research progress in employing FNAs as molecular tools for T cell-mediated cancer immunotherapy, including corresponding challenges and prospects.

Multidimensional Applications and Challenges of Riboswitches in Biosensing and Biotherapy

Riboswitches have received significant attention over the last two decades for their multiple functionalities and great potential for applications in various fields. This article highlights and reviews the recent advances in biosensing and biotherapy. These fields involve a wide range of applications, such as food safety detection, environmental monitoring, metabolic engineering, live cell imaging, wearable biosensors, antibacterial drug targets, and gene therapy. The discovery, origin, and optimization of riboswitches are summarized to help readers better understand their multidimensional applications. Finally, this review discusses the multidimensional challenges and development of riboswitches in order to further expand their potential for novel applications.

Structure-guided metagenome mining to tap microbial functional diversity

Scientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadly, we encourage the scientific community to look beyond global sequence and structure alignments by considering fine-grained descriptors such as distance to ligand, active site, and tertiary interactions between amino acid residues scaling to microbiomes. Finally, we highlight structure-inspired approaches to chart new areas of microbial protein-coding sequence space.

Cell Surface Engineering Tools for Programming Living Assemblies

Breakthroughs in precision cell surface engineering tools are supporting the rapid development of programmable living assemblies with valuable features for tackling complex biological problems. Herein, the authors overview the most recent technological advances in chemically- and biologically-driven toolboxes for engineering mammalian cell surfaces and triggering their assembly into living architectures. A particular focus is given to surface engineering technologies for enabling biomimetic cell-cell social interactions and multicellular cell-sorting events. Further advancements in cell surface modification technologies may expand the currently available bioengineering toolset and unlock a new generation of personalized cell therapeutics with clinically relevant biofunctionalities. The combination of state-of-the-art cell surface modifications with advanced biofabrication technologies is envisioned to contribute toward generating living materials with increasing tissue/organ-mimetic bioactivities and therapeutic potential.

Cross-Binding of Adenosine by Aptamers Selected Using Theophylline

We recently reported that some adenosine binding aptamers can also bind caffeine and theophylline with around 20-fold lower affinities. This discovery led to the current work to examine the cross-binding of adenosine to theophylline aptamers. For the DNA aptamer for theophylline, cross-binding to adenosine was observed, and the affinity was 18 to 38-fold lower for adenosine based on assays using isothermal titration calorimetry and ThT fluorescence spectroscopy. The binding complexes were characterized using NMR spectroscopy, and both adenosine and theophylline showed an overall similar binding structure to the DNA theophylline aptamer, although small differences were also observed. In contrast, the RNA aptamer did not show binding to adenosine, although both aptamers have very similar relative selectivity for various methylxanthines including caffeine. After a negative selection, a few new aptamers with completely different primary sequences for theophylline were obtained and they did not show binding to adenosine. Thus, there are many ways for aptamers to bind theophylline and some can have cross-binding to adenosine. In biology, theophylline, caffeine, and adenosine can bind to the same protein receptors to regulate sleep, and their binding to the same DNA motifs may suggest an early role of nucleic acids in similar regulatory functions.

A SAM analogue-utilizing ribozyme for site-specific RNA alkylation in living cells

Post-transcriptional RNA modification methods are in high demand for site-specific RNA labelling and analysis of RNA functions. In vitro-selected ribozymes are attractive tools for RNA research and have the potential to overcome some of the limitations of chemoenzymatic approaches with repurposed methyltransferases. Here we report an alkyltransferase ribozyme that uses a synthetic, stabilized S-adenosylmethionine (SAM) analogue and catalyses the transfer of a propargyl group to a specific adenosine in the target RNA. Almost quantitative conversion was achieved within 1 h under a wide range of reaction conditions in vitro, including physiological magnesium ion concentrations. A genetically encoded version of the SAM analogue-utilizing ribozyme (SAMURI) was expressed in HEK293T cells, and intracellular propargylation of the target adenosine was confirmed by specific fluorescent labelling. SAMURI is a general tool for the site-specific installation of the smallest tag for azide-alkyne click chemistry, which can be further functionalized with fluorophores, affinity tags or other functional probes.

Split aptazyme-based signal amplification for AβO analysis

Aptazyme is a chimera of functional nucleic acids, which integrates recognition and amplification elements to simplify the assay process and improve sensing efficiency. However, its application may be limited by signal leakage. In this work, we innovatively integrate the AβO aptamer and an MNAzyme (multicomponent nucleic acid enzyme) for highly efficient detection of AβO. The aptamer and half of the MNAzyme are positioned at one strand, and the other half of the MNAzyme is integrated with a toehold sequence. These two sequences cannot hybridize to activate the MNAzyme until the target is added. The background signal is significantly reduced by the split format and the secondary structure of DNA probes formed in the absence of the target. The proposed aptazyme can not only achieve amplification through enzymatic catalysis but also greatly improve the efficiency of signal transduction and output. We systematically investigated the influence of different DNA probes on the detection performance, and the optimized aptazyme can detect as low as 26.5 pM targets in 1h. The stability of this method was also investigated by detection targets in real biological samples.

Advanced Self-Powered Biofuel Cells with Capacitor and Nanogenerator for Biomarker Sensing

Self-powered biofuel cells (BFCs) have evolved for highly sensitive detection of biomarkers such as noncodon micro ribonucleic acids (miRNAs) in the presence of interfering substrates. Self-charging supercapacitive BFCs for in vivo and in vitro cellular microenvironments represent the most prevalent sensing mechanism for diagnosis. Therefore, self-powered biosensing (SPB) with a capacitor and contact separation with a triboelectric nanogenerator (TENG) offers electrochemical and colorimetric dual-mode detection via improved electrical signal intensity. In this review, we discuss three major components: stretchable self-powered BFC design, miRNA sensing, and impedance spectroscopy. A specific focus is given to 1) assembling of sensors for biomarkers, 2) electrical output signal intensification, and 3) role of supercapacitors and nanogenerators in SPBs. We outline the key features of stretchable SPBs and the sequence of miRNA sensing by SPBs. We have emphasized the need of a supercapacitor and nanogenerator for SPBs in the context of advanced assembly of the sensing unit. Finally, we outline the role of impedance spectroscopy in the detection and estimation of biomarkers. We highlight key challenges in SPBs for biomarker sensing, which needs improved sensing accuracy, integration strategies of electrochemical biosensing for in vitro and in vivo microenvironments, and the impact of miRNA sensing on cancer diagnostics. This article attempts a specific focus on the accuracy and limitations of sensing unit for miRNA biomarkers and associated tool for boosting electrical signal intensity for a potential big step further.

Riboswitches, from cognition to transformation

Riboswitches are functional RNA elements that regulate gene expression by directly detecting metabolites. Twenty years have passed since it was first discovered, researches on riboswitches are becoming increasingly standardized and refined, which could significantly promote people's cognition of RNA function as well. Here, we focus on some representative orphan riboswitches, enumerate the structural and functional transformation and artificial design of riboswitches including the coupling with ribozymes, hoping to attain a comprehensive understanding of riboswitch research.

Development of 8-17 XNAzymes that are functional in cells

DNA enzymes (DNAzymes), which cleave target RNA with high specificity, have been widely investigated as potential oligonucleotide-based therapeutics. Recently, xeno-nucleic acid (XNA)-modified DNAzymes (XNAzymes), exhibiting cleavage activity in cultured cells, have been developed. However, a versatile approach to modify XNAzymes that function in cells has not yet been established. Here, we report an X-ray crystal structure-based approach to modify 8-17 DNAzymes; this approach enables us to effectively locate suitable XNAs to modify. Our approach, combined with a modification strategy used in designing antisense oligonucleotides, rationally designed 8-17 XNAzyme ("X8-17") that achieved high potency in terms of RNA cleavage and biostability against nucleases. X8-17, modified with 2'-O-methyl RNA, locked nucleic acid and phosphorothioate, successfully induced endogenous MALAT-1 and SRB1 RNA knockdown in cells. This approach may help in developing XNAzyme-based novel therapeutic agents.

Biomedical applications of nanomaterials in the advancement of nucleic acid therapy: Mechanistic challenges, delivery strategies, and therapeutic applications

In the past few decades, substantial advancement has been made in nucleic acid (NA)-based therapies. Promising treatments include mRNA, siRNA, miRNA, and anti-sense DNA for treating various clinical disorders by modifying the expression of DNA or RNA. However, their effectiveness is limited due to their concentrated negative charge, instability, large size, and host barriers, which make widespread application difficult. The effective delivery of these medicines requires safe vectors that are efficient & selective while having non-pathogenic qualities; thus, nanomaterials have become an attractive option with promising possibilities despite some potential setbacks. Nanomaterials possess ideal characteristics, allowing them to be tuned into functional bio-entity capable of targeted delivery. In this review, current breakthroughs in the non-viral strategy of delivering NAs are discussed with the goal of overcoming challenges that would otherwise be experienced by therapeutics. It offers insight into a wide variety of existing NA-based therapeutic modalities and techniques. In addition to this, it provides a rationale for the use of non-viral vectors and a variety of nanomaterials to accomplish efficient gene therapy. Further, it discusses the potential for biomedical application of nanomaterials-based gene therapy in various conditions, such as cancer therapy, tissue engineering, neurological disorders, and infections.

Rapid Kinetics of Pistol Ribozyme: Insights into Limits to RNA Catalysis

Pistol ribozyme (Psr) is a distinct class of small endonucleolytic ribozymes, which are important experimental systems for defining fundamental principles of RNA catalysis and designing valuable tools in biotechnology. High-resolution structures of Psr, extensive structure-function studies, and computation support a mechanism involving one or more catalytic guanosine nucleobases acting as a general base and divalent metal ion-bound water acting as an acid to catalyze RNA 2'-O-transphosphorylation. Yet, for a wide range of pH and metal ion concentrations, the rate of Psr catalysis is too fast to measure manually and the reaction steps that limit catalysis are not well understood. Here, we use stopped-flow fluorescence spectroscopy to evaluate Psr temperature dependence, solvent H/D isotope effects, and divalent metal ion affinity and specificity unconstrained by limitations due to fast kinetics. The results show that Psr catalysis is characterized by small apparent activation enthalpy and entropy changes and minimal transition state H/D fractionation, suggesting that one or more pre-equilibrium steps rather than chemistry is rate limiting. Quantitative analyses of divalent ion dependence confirm that metal aquo ion pK_a correlates with higher rates of catalysis independent of differences in ion binding affinity. However, ambiguity regarding the rate-limiting step and similar correlation with related attributes such as ionic radius and hydration free energy complicate a definitive mechanistic interpretation. These new data provide a framework for further interrogation of Psr transition state stabilization and show how thermal instability, metal ion insolubility at optimal pH, and pre-equilibrium steps such as ion binding and folding limit the catalytic power of Psr suggesting potential strategies for further optimization.

Intricate 3D architecture of a DNA mimic of GFP

Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures1-3. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates4 conditional fluorophores derived from GFP. To extend previous structural studies5,6 of fluorogenic RNAs, GFP and other fluorescent proteins7 to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen8 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.

The First-in-Human Whole-Body Dynamic Pharmacokinetics Study of Aptamer

Serving as targeting ligands, aptamers have shown promise in precision medicine. However, the lack of knowledge of the biosafety and metabolism patterns in the human body largely impeded aptamers' clinical translation. To bridge this gap, here we report the first-in-human pharmacokinetics study of protein tyrosine kinase 7 targeted SGC8 aptamer via in vivo PET tracking of gallium-68 (⁶⁸Ga) radiolabeled aptamers. The specificity and binding affinity of a radiolabeled aptamer, named ⁶⁸Ga[Ga]-NOTA-SGC8, were maintained as proven in vitro. Further preclinical biosafety and biodistribution evaluation confirmed that aptamers have no biotoxicity, potential mutation risks, or genotoxicity at high dosage (40 mg/kg). Based on this result, a first-in-human clinical trial was approved and carried out to evaluate the circulation and metabolism profiles, as well as biosafety, of the radiolabeled SGC8 aptamer in the human body. Taking advantage of the cutting-edge total-body PET, the aptamers' distribution pattern in the human body was acquired in a dynamic fashion. This study revealed that radiolabeled aptamers are harmless to normal organs and most of them are accumulated in the kidney and cleared from the bladder via urine, which agrees with preclinical studies. Meanwhile, a physiologically based pharmacokinetic model of aptamer was developed, which could potentially predict therapeutic responses and plan personalized treatment strategies. This research studied the biosafety and dynamic pharmacokinetics of aptamers in the human body for the first time, as well as demonstrated the capability of novel molecular imaging fashion in drug development.

Integrating Water Purification with Electrochemical Aptamer Sensing for Detecting SARS-CoV-2 in Wastewater

Wastewater analysis of pathogens, particularly SARS-CoV-2, is instrumental in tracking and monitoring infectious diseases in a population. This method can be used to generate early warnings regarding the onset of an infectious disease and predict the associated infection trends. Currently, wastewater analysis of SARS-CoV-2 is almost exclusively performed using polymerase chain reaction for the amplification-based detection of viral RNA at centralized laboratories. Despite the development of several biosensing technologies offering point-of-care solutions for analyzing SARS-CoV-2 in clinical samples, these remain elusive for wastewater analysis due to the low levels of the virus and the interference caused by the wastewater matrix. Herein, we integrate an aptamer-based electrochemical chip with a filtration, purification, and extraction (FPE) system for developing an alternate in-field solution for wastewater analysis. The sensing chip employs a dimeric aptamer, which is universally applicable to the wild-type, alpha, delta, and omicron variants of SARS-CoV-2. We demonstrate that the aptamer is stable in the wastewater matrix (diluted to 50%) and its binding affinity is not significantly impacted. The sensing chip demonstrates a limit of detection of 1000 copies/L (1 copy/mL), enabled by the amplification provided by the FPE system. This allows the integrated system to detect trace amounts of the virus in native wastewater and categorize the amount of contamination into trace (<10 copies/mL), medium (10-1000 copies/mL), or high (>1000 copies/mL) levels, providing a viable wastewater analysis solution for in-field use.

Programmable DNA Interstrand Crosslinking by Alkene-Alkyne [2 + 2] Photocycloaddition

Covalent crosslinking of DNA strands provides a useful tool for medical, biochemical, and DNA nanotechnology applications. Here we present a light-induced interstrand DNA crosslinking reaction using the modified nucleoside 5-phenylethynyl-2'-deoxyuridine (^PhedU). The crosslinking ability of ^PhedU was programmed by base pairing and by metal ion interaction at the Watson-Crick base pairing site. Rotation to intrahelical positions was favored by hydrophobic stacking and enabled an unexpected photochemical alkene-alkyne [2 + 2] cycloaddition within the DNA duplex, resulting in efficient formation of a ^PhedU dimer after short irradiation times of a few seconds. A ^PhedU-dimer-containing DNA was shown to efficiently bind a helicase complex, but the covalent crosslink completely prevented DNA unwinding, suggesting possible applications in biochemistry or structural biology.

Reflections on the Origin and Early Evolution of the Genetic Code

Examination of the genetic code (GeCo) reveals that amino acids coded by (A/U) codons display a large functional spectrum and bind RNA whereas, except for Arg, those coded by (G/C) codons do not. From a stereochemical viewpoint, the clear preference for (A/U)-rich codons to be located at the GeCo half blocks suggests they were specifically determined. Conversely, the overall lower affinity of cognate amino acids for their (G/C)-rich anticodons points to their late arrival to the GeCo. It is proposed that i) initially the code was composed of the eight (A/U) codons; ii) these codons were duplicated when G/C nucleotides were added to their wobble positions, and three new codons with G/C in their first position were incorporated; and iii) a combination of A/U and G/C nucleotides progressively generated the remaining codons.

Homogeneous, Simple, and Direct Analysis of Exosomal PD-L1 via Aptamer-Bivalent-Cholesterol-Anchor Assembly of DNAzyme (ABCzyme) for Tumor Immunotherapy

Breakthroughs in immune checkpoint inhibitor (ICI) therapy have revolutionized clinical tumor therapy. Immunohistochemistry (IHC) analysis of PD-L1 in tumor tissue has been used to predict the response to tumor immunotherapy, but the results are not reproducible, and IHC is invasive and cannot be used to monitor the dynamic changes in PD-L1 expression during treatment. Monitoring the expression level of the PD-L1 protein on exosomes (exosomal PD-L1) is promising for both tumor diagnosis and tumor immunotherapy. Here, we established an aptamer-bivalent-cholesterol-anchor assembly of DNAzyme (ABCzyme) analytical strategy that can directly detect exosomal PD-L1 with a minimum lower limit of detection of 5.21 pg/mL. In this way, we found that the levels of exosomal PD-L1 are significantly elevated in the peripheral blood of patients with progressive disease. The precise analysis of exosomal PD-L1 by the proposed ABCzyme strategy provides a potentially convenient method for the dynamic monitoring of tumor progression in patients who receive immunotherapy and proves to be a potential and effective liquid biopsy method for tumor immunotherapy.

Sensitive Small Molecule Aptasensing based on Hybridization Chain Reaction and CRISPR/Cas12a Using a Portable 3D-Printed Visualizer

Next-generation biosensing tools based on CRISPR/Cas have revolutionized the molecular detection. A number of CRISPR/Cas-based biosensors have been reported for the detection of nucleic acid targets. The establishment of efficient methods for non-nucleic acid target detection would further broaden the scope of this technique, but up to now, the concerning research is limited. In the current study, we reported a versatile biosensing platform for non-nucleic acid small-molecule detection called SMART-Cas12a (small-molecule aptamer regulated test using CRISPR/Cas12a). Simply, hybridization chain reaction cascade signal amplification was first trigged by functional nucleic acid (aptamer) through target binding. Then, the CRISPR/Cas system was integrated to recognize the amplified products followed by activation of the trans-cleavage. As such, the target can be ingeniously converted to nucleic acid signals and then fluorescent signals that can be readily visualized and analyzed by a customized 3D-printed visualizer with the help of a home-made App-enabled smartphone. Adenosine triphosphate was selected as a model target, and under the optimized conditions, we achieved fine analytical performance with a linear range from 0.1 to 750 μM and a detection limit of 1.0 nM. The satisfactory selectivity and recoveries that we have obtained further demonstrated this method to be suitable for a complex sample environment. The sample-to-answer time was less than 100 min. Our work not only expanded the reach of the CRISPR-Cas system in biosensing but also provided a prototype method that can be generalized for detecting a wider range of analytes with desirable adaptability, sensitivity, specificity, and on-site capability.

programmably engineered FRET-nanoflare for ratiometric live-cell ATP imaging with anti-interference capability

Herein, we present a poly-adenine (polyA)-mediated programmably engineered FRET-nanoflare for ratiometric intracellular ATP imaging with anti-interference capability. The programmable polyA attachment is advantageous in enhancing the signal response for ATP. Moreover, the FRET-based nanoflare is capable of avoiding false-positive signals due to probe degradation in a complex environment, which has great potential for clinical diagnosis.

Electrochemical DNAzyme-based biosensors for disease diagnosis

DNAzyme-based electrochemical biosensors provide exceptional analytical sensitivity and high target recognition specificity for disease diagnosis. This review provides a critical perspective on the fundamental and applied impact of incorporating DNAzymes in the field of electrochemical biosensing. Specifically, we highlight recent advances in creating DNAzyme-based electrochemical biosensors for diagnosing infectious diseases, cancer and regulatory diseases. We also develop an understanding of challenges around translating the research in the field of DNAzyme-based electrochemical biosensors from labs to clinics, followed by a discussion on different strategies that can be applied to enhance the performance of the currently existing technologies to create truly point-of-care electrochemical DNAzyme biosensors.

FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride

Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid (RNA)-based biosensor specific for fluoride is introduced. The molecule consists of two RNA aptamer modules, a fluoride-specific sensor derived from the crcB riboswitch which changes its structure upon interaction with the target ion, and the light-up RNA Mango-III that emits fluorescence when complexed with a fluorogen. The two modules are connected by an optimized communication module identified by ultrahigh-throughput screening, which results in extremely high fluorescence of FluorMango in the presence of fluoride, and background fluorescence in its absence. The value and efficiency of this biosensor by direct monitoring of defluorinase activity in living bacterial cells is illustrated, and the use of this new tool in future screening campaigns aiming at discovering new defluorinase activities is discussed.

Conformational-switch biosensors as novel tools to support continuous, real-time molecular monitoring in lab-on-a-chip devices

Recent years have seen continued expansion of the functionality of lab on a chip (LOC) devices. Indeed LOCs now provide scientists and developers with useful and versatile platforms across a myriad of chemical and biological applications. The field still fails, however, to integrate an often important element of bench-top analytics: real-time molecular measurements that can be used to "guide" a chemical response. Here we describe the analytical techniques that could provide LOCs with such real-time molecular monitoring capabilities. It appears to us that, among the approaches that are general (i.e., that are independent of the reactive or optical properties of their targets), sensing strategies relying on binding-induced conformational change of bioreceptors are most likely to succeed in such applications.

Synthetic biology-based bioreactor and its application in biochemical analysis

In the past few years, synthetic biologists have established some biological elements and bioreactors composed of nucleotides under the guidance of engineering methods. Following the concept of engineering, the common bioreactor components in recent years are introduced and compared. At present, biosensors based on synthetic biology have been applied to water pollution monitoring, disease diagnosis, epidemiological monitoring, biochemical analysis and other detection fields. In this paper, the biosensor components based on synthetic bioreactors and reporters are reviewed. In addition, the applications of biosensors based on cell system and cell-free system in the detection of heavy metal ions, nucleic acid, antibiotics and other substances are presented. Finally, the bottlenecks faced by biosensors and the direction of optimization are also discussed.

Biosensors based on functional nucleic acids and isothermal amplification techniques

In the past few years, with the in-depth research of functional nucleic acids and isothermal amplification techniques, their applications in the field of biosensing have attracted great interest. Since functional nucleic acids have excellent flexibility and convenience in their structural design, they have significant advantages as recognition elements in biosensing. At the same time, isothermal amplification techniques have higher amplification efficiency, so the combination of functional nucleic acids and isothermal amplification techniques can greatly promote the widespread application of biosensors. For the purpose of further improving the performance of biosensors, this review introduces several widely used functional nucleic acids and isothermal amplification techniques, as well as their classification, basic principles, application characteristics, and summarizes their important applications in the field of biosensing. We hope to provide some references for the design and construction of new tactics to enhance the detection sensitivity and detection range of biosensing.

Gold Nanoparticles Synthesized Using Various Reducing Agents and the Effect of Aging for DNA Sensing

Gold nanoparticles (AuNPs) are one of the most commonly used reagents in colloidal science and biosensor technology. In this work, we first compared AuNPs prepared using four different reducing agents including citrate, glucose, ascorbate, and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES). At the same absorbance at the surface plasmon peak of 520-530 nm, citrate-AuNPs and glucose-AuNPs adsorbed more DNA and achieved higher affinity to the adsorbed DNA. In addition, citrate-AuNPs had better sensitivity than glucose-AuNPs for label-free DNA detection. Then, using citrate-AuNPs, the effect of aging was studied by incubation of the AuNPs at 22 °C (room temperature) and at 4 °C for up to 6 months. During aging, the colloidal stability and DNA adsorption efficiency gradually decreased. In addition, the DNA sensing sensitivity using a label-free method also dropped around 4-fold after 6 months. Heating at boiling temperature of the aged citrate-AuNPs could not rejuvenate the sensing performance. This study shows that while citrate-AuNPs are initially better than the other three AuNPs in their colloid properties and sensing properties, this edge in performance might gradually decrease due to constantly changing surface properties caused from the aging effect.