Programmable Live-Cell CRISPR Imaging with Toehold-Switch-Mediated Strand Displacement

Controllable detection threshold achieved through the toehold switch system in a mercury ion whole-cell biosensor

Due to the toxicity of mercury and its harmful effects on human health, it is essential to establish a low-cost, highly sensitive and highly specific monitoring method with a wide detection range, ideally with a simple visual readout. In this study, a whole-cell biosensor with adjustable detection limits was developed for the detection of mercury ions in water samples, allowing controllable threshold detection with an expanded detection range. Gene circuits were constructed by combining the toehold switch system with lactose operon, mercury-ion-specific operon, and inducible red fluorescent protein gene. Using MATLAB for design and selection, a total of eleven dual-input single-output sensing logic circuits were obtained based on the basic logic of gene circuit construction. Then, biosensor DTS-3 was selected based on its fluorescence response at different isopropyl β-D-Thiogalactoside (IPTG) concentrations, exhibiting the controllable detection threshold. At 5-20 μM IPTG, DTS-3 can achieve variable threshold detection in the range of 0.005-0.0075, 0.06-0.08, 1-2, and 4-6 μM mercury ion concentrations, respectively. Specificity experiments demonstrated that DTS-3 exhibits good specificity, not showing fluorescence response changes compared with other metal ions. Furthermore spiked sample experiments demonstrated its good resistance to interference, allowing it to distinguish mercury ion concentrations as low as 7.5 nM by the naked eye and 5 nM using a microplate reader. This study confirms the feasibility and performance of biosensor with controllable detection threshold, providing a new detection method and new ideas for expanding the detection range of biosensors while ensuring rapid and convenient measurements without compromising sensitivity.

Logical regulation of endogenous gene expression using programmable, multi-input processing CRISPR guide RNAs

The CRISPR-Cas system provides a versatile RNA-guided approach for a broad range of applications. Thanks to advances in RNA synthetic biology, the engineering of guide RNAs (gRNAs) has enabled the conditional control of the CRISPR-Cas system. However, achieving precise regulation of the CRISPR-Cas system for efficient modulation of internal metabolic processes remains challenging. In this work, we developed a robust dCas9 regulator with engineered conditional gRNAs to enable tight control of endogenous genes. Our conditional gRNAs in Escherichia coli can control gene expression upon specific interaction with trigger RNAs with a dynamic range as high as 130-fold, evaluating up to a three-input logic A OR (B AND C). The conditional gRNA-mediated targeting of endogenous metabolic genes, lacZ, malT and poxB, caused differential regulation of growth in Escherichia coli via metabolic flux control. Further, conditional gRNAs could regulate essential cytoskeleton genes, ftsZ and mreB, to control cell filamentation and division. Finally, three types of two-input logic gates could be applied for the conditional control of ftsZ regulation, resulting in morphological changes. The successful operation and application of conditional gRNAs based on programmable RNA interactions suggests that our system could be compatible with other Cas-effectors and implemented in other host organisms.

PAM-Engineered Toehold Switches as Input-Responsive Activators of CRISPR-Cas12a for Sensing Applications

The RNA-programmed CRISPR effector protein Cas12a has emerged as a powerful tool for gene editing and molecular diagnostics. However, additional bio-engineering strategies are required to achieve control over Cas12a activity. Here, we show that Toehold Switch DNA hairpins, presenting a rationally designed locked protospacer adjacent motif (PAM) in the loop, can be used to control Cas12a in response to molecular inputs. Reconfiguring the Toehold Switch DNA from a hairpin to a duplex conformation through a strand displacement reaction provides an effective means to modulate the accessibility of the PAM, thereby controlling the binding and cleavage activities of Cas12a. Through this approach, we showcase the potential to trigger downstream Cas12a activity by leveraging proximity-based strand displacement reactions in response to target binding. By utilizing the trans-cleavage activity of Cas12a as a signal transduction method, we demonstrate the versatility of our approach for sensing applications. Our system enables rapid, one-pot detection of IgG antibodies and small molecules with high sensitivity and specificity even within complex matrices. Besides the bioanalytical applications, the switchable PAM-engineered Toehold Switches serve as programmable tools capable of regulating Cas12a-based targeting and DNA processing in response to molecular inputs and hold promise for a wide array of biotechnological applications.

CRISPR/Cas systems combined with DNA nanostructures for biomedical applications

DNA nanostructures are easy to design and construct, have good biocompatibility, and show great potential in biosensing and drug delivery. Numerous distinctive and versatile DNA nanostructures have been developed and explored for biomedical applications. In addition to DNA nanostructures that are completely assembled from DNA, composite DNA nanostructures obtained by combining DNA with other organic or inorganic materials are also widely used in related research. The CRISPR/Cas system has attracted great attention as a powerful gene editing technology and is also widely used in biomedical diagnosis. Many researchers are committed to exploring new possibilities by combining DNA nanostructures with CRISPR/Cas systems. These explorations provide support for the development of new detection methods and cargo delivery pathways, provide inspiration for improving relevant gene editing platforms, and further expand the application scope of DNA nanostructures and CRISPR/Cas systems. This paper mainly reviews the design principles and biomedical applications of CRISPR/Cas combined with DNA nanostructures based on the types of DNA nanostructures. Finally, the application status, challenges and development prospects of CRISPR/Cas combined with DNA nanostructures in detection and delivery are summarized. It is expected that this review will enable researchers to better understand the current state of the field and provide insights into the application of CRISPR/Cas systems and the development of DNA nanostructures.

Plug-and-Play Module for Reversible and Continuous Control of DNA Strand Displacement Kinetics

Regulatory modules for controlling the kinetics of toehold-mediated strand displacement (TMSD) play critical roles in designing dynamic and dissipative DNA chemical reaction networks (CRNs) but are hardwired into sequence designs. Herein, we introduce antitoehold (At), a plug-and-play module for reversible and continuous tuning of TMSD kinetics by temporarily occupying the toehold domain via a metastable duplex and base stacking. We demonstrate that kinetic control can be readily activated or deactivated in real time for any TMSD by simply adding At or anti-At. Continuous tuning of TMSD kinetics can also be achieved by altering the concentration of At. Moreover, the simple addition of At could readily reprogram existing TMSDs into a pulse-generation DNA CRN with continuous tunability. Our At approach also offers a new way for engineering continuously tunable DNA hybridization probes, which may find practical uses for discriminating clinically important mutations. Because of the simplicity, we anticipate that At will find wide applications for engineering DNA CRNs with diverse dynamic and dissipative behaviors, and DNA hybridization probes with tunable affinity and selectivity.

Photoactivatable Engineering of CRISPR/Cas9-Inducible DNAzyme Probe for In Situ Imaging of Nuclear Zinc Ions

DNAzyme-based fluorescent probes for imaging metal ions in living cells have received much attention recently. However, employing in situ metal ions imaging within subcellular organelles, such as nucleus, remains a significant challenge. We developed a three-stranded DNAzyme probe (TSDP) that contained a 20-base-pair (20-bp) recognition site of a CRISPR/Cas9, which blocks the DNAzyme activity. When Cas9, with its specialized nuclear localization function, forms an active complex with sgRNA within the cell nucleus, it cleaves the TSDP at the recognition site, resulting in the in situ formation of catalytic DNAzyme structure. With this design, the CRISPR/Cas9-inducible imaging of nuclear Zn2+ is demonstrated in living cells. Moreover, the superiority of CRISPR-DNAzyme for spatiotemporal control imaging was demonstrated by integrating it with photoactivation strategy and Boolean logic gate for dynamic monitoring nuclear Zn2+ in both HeLa cells and mice. Collectively, this conceptual design expands the DNAzyme toolbox for visualizing nuclear metal ions and thus provides new analytical methods for nuclear metal-associated biology.

DNAzyme-Based Dissipative DNA Strand Displacement for Constructing Temporal Logic Gates

Toehold-mediated DNA strand displacement is the foundation of dynamic DNA nanotechnology, encompassing a wide range of tools with diverse functions, dynamics, and thermodynamic properties. However, a majority of these tools are limited to unidirectional reactions driven by thermodynamics. In response to the growing field of dissipative DNA nanotechnology, we present an approach: DNAzyme-based dissipative DNA strand displacement (D-DSD), which combines the principles of dynamic DNA nanotechnology and dissipative DNA nanotechnology. D-DSD introduces circular and dissipative characteristics, distinguishing it from the unidirectional reactions observed in conventional strand displacement. We investigated the reaction mechanism of D-DSD and devised temporal control elements. By substituting temporal components, we designed two distinct temporal AND gates using fewer than 10 strands, eliminating the need for complex network designs. In contrast to previous temporal logic gates, our temporal storage is not through dynamics control or cross-inhibition but through autoregressive storage, a more modular and scalable approach to memory storage. D-DSD preserves the fundamental structure of toehold-mediated strand displacement, while offering enhanced simplicity and versatility.

Functionalized DNA nanoplatform for multi-target simultaneous imaging: Establish the atlas of cancer cell species

Detection and imaging of cell membrane receptor proteins have gained widespread interest in recent years. However, recognition based on a single biomarker can induce false positive feedback, including off-target phenomenon caused by the absence of tumor-specific antigens. In addition, nucleic acid probes often cause nonspecific and undesired cell internalization during cell imaging. In this work, we constructed a logic gate DNA nano-platform (LGDP) for single-molecule imaging of cell membrane proteins to synergistically diagnose cancer cells. The traffic light-like color response of LGDP facilitates the precise discrimination among different cell lines. Combined with single molecule technology, the target proteins were qualitatively and quantitatively analyzed synergistically. Logic-gated recognition integrated in aptamer-functionalized molecular machines will prompt fast cells analysis, laying the foundation of cancer early diagnosis and treatment.

CRISPR/Cas systems for in situ imaging of intracellular nucleic acids: Concepts and applications

Accurate and precise localization of intracellular nucleic acids is crucial for regulating genetic information transcription and diagnosing diseases. Although intracellular nucleic acid imaging methods are available for various cell types, their widespread utilization is impeded by the intricate nature of the process and its exorbitant cost. Recently, numerous intracellular nucleic acid labeling techniques based on clustered regularly interspaced short palindromic repeats (CRISPR) have been established due to their modularity, flexibility, and specificity. In this work, we present various CRISPR methods that are currently employed for visualizing intracellular genomic sequences and RNA, based on their detection principles and application scenarios. Furthermore, we discuss the advantages and drawbacks of the existing CRISPR imaging methods, as well as future research directions. We anticipate that with continued refinement, more advanced CRISPR-based imaging techniques can be developed to better elucidate the localization and dynamics of intracellular nucleic acids, thereby providing a powerful tool for molecular biology research and clinical molecular pathology diagnosis.

Unmodificated stepless regulation of CRISPR/Cas12a multi-performance

As CRISPR technology is promoted to more fine-divided molecular biology applications, its inherent performance finds it increasingly difficult to cope with diverse needs in these different fields, and how to more accurately control the performance has become a key issue to develop CRISPR technology to a new stage. Herein, we propose a CRISPR/Cas12a regulation strategy based on the powerful programmability of nucleic acid nanotechnology. Unlike previous difficult and rigid regulation of core components Cas nuclease and crRNA, only a simple switch of different external RNA accessories is required to change the reaction kinetics or thermodynamics, thereby finely and almost steplessly regulating multi-performance of CRISPR/Cas12a including activity, speed, specificity, compatibility, programmability and sensitivity. In particular, the significantly improved specificity is expected to mark advance the accuracy of molecular detection and the safety of gene editing. In addition, this strategy was applied to regulate the delayed activation of Cas12a, overcoming the compatibility problem of the one-pot assay without any physical separation or external stimulation, and demonstrating great potential for fine-grained control of CRISPR. This simple but powerful CRISPR regulation strategy without any component modification has pioneering flexibility and versatility, and will unlock the potential for deeper applications of CRISPR technology in many finely divided fields.

Cascade dynamic assembly/disassembly of DNA nanoframework enabling the controlled delivery of CRISPR-Cas9 system

CRISPR-Cas9 has been explored as a therapeutic agent for down-regulating target genes; the controlled delivery of Cas9 ribonucleoprotein (RNP) is essential for therapeutic efficacy and remains a challenge. Here, we report cascade dynamic assembly/disassembly of DNA nanoframework (NF) that enables the controlled delivery of Cas9 RNP. NF was prepared with acrylamide-modified DNA that initiated cascade hybridization chain reaction (HCR). Through an HCR, single-guide RNA was incorporated to NF; simultaneously, the internal space of NF was expanded, facilitating the loading of Cas9 protein. NF was designed with hydrophilic acylamino and hydrophobic isopropyl, allowing dynamic swelling and aggregation. The responsive release of Cas9 RNP was realized by introducing disulfide bond-containing N,N-bis(acryloyl)cystamine that was specifically in response to glutathione of cancer cells, triggering the complete disassembly of NF. In vitro and in vivo investigations demonstrated the high gene editing efficiency in cancer cells, the hypotoxicity in normal cells, and notable antitumor efficacy in a breast cancer mouse model.

Regulating the trans-Cleavage Activity of CRISPR/Cas12a by Using an Elongation-Caged Single-Stranded DNA Activator and the Biosensing Applications

The CRISPR/Cas12a system exhibits extraordinary capability in the field of biosensing and molecular diagnosis due to its trans-cleavage ability. However, it is still desirable for precise control and programmable regulation of Cas12a trans-cleavage activity to promote the in-depth studies and application expansion of Cas12a-based sensing platforms. In this work, we have developed a new and robust CRISPR/Cas12a regulation mechanism by endowing the activator with the function of caging crRNA ingeniously. Specifically, we constructed an integrated elongation-caged activator (EL-activator) by extending the ssDNA activator on the 3'-end. We found that appending only about 8 nt that is complementary to the crRNA repeat region is enough to cage the crRNA spacer/repeat region, thus effectively inhibiting Cas12a trans-cleavage activity. The inner inhibition mechanism was further uncovered after a thorough investigation, demonstrating that the EL-activator works by impeding the conformation of crRNA required for Cas12a recognition and destroying its affinity with Cas12a. By further switching on the elongated moiety on the EL-activator using target biomarkers, the blocked trans-cleavage activity of Cas12a can be rapidly recovered. Finally, a versatile sensing platform was established based on the EL-activator regulation mechanism, expanding the conventional Cas12a system that only directly recognizes DNA to the direct detection of enzymes and RNA biomarkers. This work has enriched the CRISPR/Cas12a regulation toolbox and expanded its sensing applications.

Establishing artificial gene connections through RNA displacement-assembly-controlled CRISPR/Cas9 function

Construction of synthetic circuits that can reprogram genetic networks and signal pathways is a long-term goal for manipulation of biosystems. However, it is still highly challenging to build artificial genetic communications among endogenous RNA species due to their sequence independence and structural diversities. Here we report an RNA-based synthetic circuit that can establish regulatory linkages between expression of endogenous genes in both Escherichiacoli and mammalian cells. This design employs a displacement-assembly approach to modulate the activity of guide RNA for function control of CRISPR/Cas9. Our experiments demonstrate the great effectiveness of this RNA circuit for building artificial connections between expression of originally unrelated genes. Both exogenous and naturally occurring RNAs, including small/microRNAs and long mRNAs, are capable of controlling expression of another endogenous gene through this approach. Moreover, an artificial signal pathway inside mammalian cells is also successfully established to control cell apoptosis through our designed synthetic circuit. This study provides a general strategy for constructing synthetic RNA circuits, which can introduce artificial connections into the genetic networks of mammalian cells and alter the cellular phenotypes.

"Toehold Switches; a foothold for Synthetic Biology"

Toehold switches are de novo designed riboregulators that contain two RNA components interacting through linear-linear RNA interactions, regulating the gene expression. These are highly versatile, exhibit excellent orthogonality, wide dynamic range, and are highly programmable, so can be used for various applications in synthetic biology. In this review, we summarized and discussed the design characteristics and benefits of toehold switch riboregulators over conventional riboregulators. We also discussed applications and recent advancements of toehold switch riboregulators in various fields like gene editing, DNA nanotechnology, translational repression, and diagnostics (detection of microRNAs and some pathogens). Toehold switches, therefore, furnished advancement in synthetic biology applications in various fields with their prominent features.

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.

Fluorescence-Enhanced Dual-Driven "OR-AND" DNA Logic Platform for Accurate Cell Subtype Identification

Developing an endogenous stimuli-responsive and ultrasensitive DNA sensing platform that contains a logic gate biocomputation for precise cell subtype identification holds great potential for disease diagnosis and prognostic estimation. Herein, a fluorescence-enhanced "OR-AND" DNA logic platform dual-driven by intracellular apurinic/apyrimidinic endonuclease 1 (APE 1) or a DNA strand anchored on membrane protein Mucin 1 (MUC 1) for sensitive and accurate cell subtype identification was rationally designed. The recognition toehold of the traditional activated probe (TP) was restrained by introducing a blocking sequence containing an APE 1 cleavable site (AP-site) that can be either cleaved by APE 1 or replaced by Mk-apt, ensuring the "OR-AND" gated molecular imaging for cell subtype identification. It is worth noting that this "OR-AND" gated design can effectively avoid the missing logical computation caused by membrane protein heterogeneous spatial distribution as a single input. In addition, a benefit from the excellent plasmon-enhanced fluorescence (PEF) ability of Au NSTs is that the detection limit can be decreased by nearly 165 times. Based on this, not only different kinds of MCF-7, HepG2, and L02 cells, but also different breast cancer cell subtypes, including malignant MCF-7, metastatic MDA-MB-231, and nontumorigenic MCF-10A cells, can be accurately identified by the proposed "OR-AND" gated DNA logic platform, indicating the prospect of this simple and universal design in accurate cancer screening.

CasSABER for Programmable In Situ Visualization of Low and Nonrepetitive Gene Loci

Site-specific imaging of target genes using CRISPR probes is essential for understanding the molecular mechanisms of gene function and engineering tools to modulate its downstream pathways. Herein, we develop CRISPR/Cas9-mediated signal amplification by exchange reaction (CasSABER) for programmable in situ imaging of low and nonrepetitive regions of the target gene in the cell nucleus. The presynthesized primer-exchange reaction (PER) probe is able to hybridize multiple fluorophore-bearing imager strands to specifically light up dCas9/sgRNA target-bound gene loci, enabling in situ imaging of fixed cellular gene loci with high specificity and signal-to-noise ratio. In combination with a multiround branching strategy, we successfully detected nonrepetitive gene regions using a single sgRNA. As an intensity-codable and orthogonal probe system, CasSABER enables the adjustable amplification of local signals in fixed cells, resulting in the simultaneous visualization of multicopy and single-copy gene loci with similar fluorescence intensity. Owing to avoiding the complexity of controlling in situ mutistep enzymatic reactions, CasSABER shows good reliability, sensitivity, and ease of implementation, providing a rapid and cost-effective molecular toolkit for studying multigene interaction in fundamental research and gene diagnosis.

Genetic switches based on nucleic acid strand displacement

Toehold-mediated strand displacement (TMSD) is an isothermal switching process that enables the sequence-programmable and reversible conversion of DNA or RNA strands between single- and double-stranded conformations or other secondary structures. TMSD processes have already found widespread application in DNA nanotechnology, where they are used to drive DNA-based molecular devices or for the realization of synthetic biochemical computing circuits. Recently, researchers have started to employ TMSD also for the control of RNA-based gene regulatory processes in vivo, in particular in the context of synthetic riboregulators and conditional guide RNAs for CRISPR/Cas. Here, we provide a review over recent developments in this emerging field and discuss the opportunities and challenges for such systems in in vivo applications.

DNA strand displacement based computational systems and their applications

DNA computing has become the focus of computing research due to its excellent parallel processing capability, data storage capacity, and low energy consumption characteristics. DNA computational units can be precisely programmed through the sequence specificity and base pair principle. Then, computational units can be cascaded and integrated to form large DNA computing systems. Among them, DNA strand displacement (DSD) is the simplest but most efficient method for constructing DNA computing systems. The inputs and outputs of DSD are signal strands that can be transferred to the next unit. DSD has been used to construct logic gates, integrated circuits, artificial neural networks, etc. This review introduced the recent development of DSD-based computational systems and their applications. Some DSD-related tools and issues are also discussed.

Controlling CRISPR-Cas9 by guide RNA engineering

The clustered regularly interspaced short palindromic repeats (CRISPR) system is a product of million years of evolution by microbes to fight against invading genetic materials. Around 10 years ago, scientists started to repurpose the CRISPR as genetic tools by molecular engineering approaches. The guide RNA provides a versatile and unique platform for the innovation to improve and expand the application of CRISPR-Cas9 system. In this review, we will first introduce the basic sequence and structure of guide RNA and its role during the function of CRISPR-Cas9. We will then summarize recent progress on the development of various guide RNA engineering strategies. These strategies have been dedicated to improve the performance of CRISPR-Cas9, to achieve precise spatiotemporal control of CRISPR-Cas9, and to broaden the application of CRISPR-Cas9. Finally, we will briefly discuss the uniqueness and advantage of guide RNA-engineering based systems versus those with engineered Cas9 proteins and speculate potential future directions in guide RNA engineering. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico RNA Methods > RNA Nanotechnology Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.

Aptamer-Based Traceless Multiplexed Cell Isolation Systems

In both biomedical research and clinical cell therapy manufacturing, there is a need for cell isolation systems that recover purified cells in the absence of any selection agent. Reported traceless cell isolation methods using engineered antigen-binding fragments or aptamers have been limited to processing a single cell type at a time. There remains an unmet need for cell isolation processes that rapidly sort multiple target cell types. Here, we utilized two aptamers along with their designated complementary strands (reversal agents) to tracelessly isolate two cell types from a mixed cell population with one aptamer-labeling step and two sequential cell elution steps with reversal agents. We engineered a CD71-binding aptamer (rvCD71apt) and a reversal agent pair to be used simultaneously with our previously reported traceless purification approach using the CD8 aptamer (rvCD8apt) and its reversal agent. We verified the compatibility of the two aptamer displacement mechanisms by flow cytometry and the feasibility of incorporating rvCD71apt with a magnetic solid state. We then combined rvCD71apt with rvCD8apt to isolate activated CD4⁺ T cells and resting CD8⁺ cells by eluting these target cells into separate fractions with orthogonal strand displacements. This is the first demonstration of isolating different cell types using two aptamers and reversal agents at the same time. Potentially, different or more aptamers can be included in this traceless multiplexed isolation system for diverse applications with a shortened operation time and a lower production cost.

RNA-Responsive gRNAs for Controlling CRISPR Activity: Current Advances, Future Directions, and Potential Applications

CRISPR-Cas9 has emerged as a major genome manipulation tool. As Cas9 can cause off-target effects, several methods for controlling the expression of CRISPR systems were developed. Recent studies have shown that CRISPR activity could be controlled by sensing expression levels of endogenous transcripts. This is particularly interesting, as endogenous RNAs could harbor important information about the cell type, disease state, and environmental challenges cells are facing. Single-guide RNA (sgRNA) engineering played a major role in the development of RNA-responsive CRISPR systems. Following further optimizations, RNA-responsive sgRNAs could enable the development of novel therapeutic and research applications. This review introduces engineering strategies that could be employed to modify Streptococcus pyogenes sgRNAs with a focus on recent advances made toward the development of RNA-responsive sgRNAs. Future directions and potential applications of these technologies are also discussed.

Self-Customized Multichannel Exponential Amplifications Regulate Powered Monitoring of Terminal Deoxynucleotidyl Transferase Activity

The discovery and function analysis of terminal deoxynucleotidyl transferase (TdT) add a new dimension to the understanding of leukemia mechanisms and stimulate the development of new analytical tools for leukemia diagnosis. Herein, taking advantage of the inherent property of TdT for performing DNA synthesis using only single-stranded DNA as the nucleic acid substrate, we developed a self-customized multichannel exponential amplification (SMEA) system for the fluorescent sensing of TdT activity. The SMEA design employs an intermolecular DNA interaction made of a nicking site-incorporated elongation primer (EP) and a nicking site-incorporated poly-thymine tailed molecular beacon (Poly-T-MB). The absence of TdT is unable to bridge the relationship between EP and Poly-T-MB, ensuring the SMEA has an ultralow background. The presence of TdT, however, leads to the elongation of EP to poly-adenine tailed EP (Poly-A-EP) under a dATP pool responsible for further hybridization with numerous Poly-T-MB. With the aid of polymerase and nickase to react with the hybridization product of Poly-A-EP/(Poly-T-MB)_n, it can cause bidirectional strand nicking, polymerization, and displacement in many cycles and channels. In this case, the SMEA is found to be associated with the configuration transformation and splitting of all Poly-T-MBs for a significant fluorescence enhancement. Depending on this high target signal amplification and strong background inhibition abilities, the SMEA sensing system is powerful for the qualitative and quantitative determination of TdT activity, showing that it has great promise for biomedical study and disease diagnosis.

Preparation of Distant Quaternary Carbon Stereocenters by Double Selective Ring-Opening of 1,1-Biscyclopropyl Methanol Derivatives

The diastereoselective double carbometalation reaction of cyclopropenes provides, in a single‐pot operation, two ω‐ene‐[1,1]‐bicyclopropyl ester derivatives. One regioisomer then undergoes a Pd‐catalyzed addition of aryl iodide to provide skipped dienes possessing several distant stereocenters including two congested quaternary carbon centers with excellent diastereoselectivity.

Protecting Heterochiral DNA Nanostructures against Exonuclease-Mediated Degradation

Heterochiral DNA nanotechnology employs nucleic acids of both chiralities to construct nanoscale devices for applications in the intracellular environment. Interacting directly with cellular nucleic acids can be done most easily using D-DNA of the naturally occurring right-handed chirality; however, D-DNA is more vulnerable to degradation than enantiometric left-handed L-DNA. Here we report a novel combination of D-DNA and L-DNA nucleotides in triblock heterochiral copolymers, where the L-DNA domains act as protective caps on D-DNA domains. We demonstrate that the D-DNA components of strand displacement-based molecular circuits constructed using this technique resist exonuclease-mediated degradation during extended incubations in serum-supplemented media more readily than similar devices without the L-DNA caps. We show that this protection can be applied to both double-stranded and single-stranded circuit components. Our work enhances the state of the art for robust heterochiral circuit design and could lead to practical applications such as in vivo biomedical diagnostics.

A microRNA-gated thgRNA platform for multiplexed activation of gene expression in mammalian cells

To effectively reprogram cellular regulatory networks towards desired phenotypes, it is critical to have the ability to provide precise gene regulation in a spatiotemporal manner. We have previously engineered toehold-gated guide RNA (thgRNA) to enable conditional activation of dCas9-mediated transcriptional upregulation in mammalian cells using synthetic RNA triggers. Here, we demonstrate that microRNA (miR)-gated thgRNAs can be transcribed by type II RNA polymerase to allow multiplexed transcriptional activation using both mRNA and miR. Activation is achieved only by proper miR-mediated processing of the flanking 5' cap and 3' poly A tail and hairpin unblocking by mRNA via strand displacement. This new AND-gate design is exploited to elicit conditional protein degradation based on induced expression of a specific ubiquibody. This new strategy may find many new applications in an RNA-responsive manner.

A Proton-Activatable DNA-Based Nanosystem Enables Co-Delivery of CRISPR/Cas9 and DNAzyme for Combined Gene Therapy

CRISPR/Cas9 is emerging as a platform for gene therapeutics, and the treatment efficiency is expected to be enhanced by combination with other therapeutic agents. Herein, we report a proton-activatable DNA-based nanosystem that enables co-delivery of Cas9/sgRNA and DNAzyme for the combined gene therapy of cancer. Ultra-long ssDNA chains, which contained the recognition sequences of sgRNA in Cas9/sgRNA, DNAzyme sequence and HhaI enzyme cleavage site, were synthesized as the scaffold of the nanosystem. The DNAzyme cofactor Mn²⁺ was used to compress DNA chains to form nanoparticles and acid-degradable polymer-coated HhaI enzymes were assembled on the surface of nanoparticles. In response to protons in lysosome, the polymer coating was decomposed and HhaI enzyme was consequently exposed to recognize and cut off the cleavage sites, thus triggering the release of Cas9/sgRNA and DNAzyme to regulate gene expressions to achieve a high therapeutic efficacy of breast cancer.

Deciphering the Design Rules of Toehold-Gated sgRNA for Conditional Activation of Gene Expression and Protein Degradation in Mammalian Cells

A new class of toehold-gated gRNAs (thgRNAs) has been created to provide conditional gene regulation via RNA-mediated activation. However, the detailed design principles remain elusive. Here, we presented an investigation into the design rules for conditional gRNAs by systematically varying the toehold, stem, and flexible loop regions of thgRNA for optimal gene activation in HeLa cells. We determined that nonspecific interactions between the toehold region and the flexible loop are the main driver for the background leak observed in the OFF state. By trimming the toehold length from 15 to 5 nt, the improved thgNT-F design led to a 38-fold increase in the activated ON state with no observable background leak. The same design rule was successfully adapted to target two different regions on the mCherry mRNA with the same impressive fold change. Using the thgRNA to direct conditional protein degradation, we showed up to 8-fold knockdown of a reporter protein through activating expression of a bifunctional ubiquibody GS2-IpaH9.8. This new strategy may find many new applications for cell culture control or cell therapy by removing unwanted proteins in an RNA-responsive manner.

Biosupramolecular networks: Taking inspiration from nature to create powerful synthetic platforms

Nature is predicated on the ability to process large number of parallel signals to produce specific downstream outputs. Biosupramolecular networks are beginning to allow such processing power in synthetic systems, particularly through harnessing the recognition power of biomolecules. Such systems can be summarised through the reductionist view of containing inputs, circuitry motifs and functional outputs, with each of these elements able to be readily combined in a modular approach. Through the inherent 'plug and play' nature of these systems the field continues to rapidly expand, providing a wealth of new smart diagnostic and therapeutic systems.

Nucleic acid-based molecular computation heads towards cellular applications

Nucleic acids, with the advantages of programmability and biocompatibility, have been widely used to design different kinds of novel biocomputing devices. Recently, nucleic acid-based molecular computing has shown promise in making the leap from the test tube to the cell. Such molecular computing can perform logic analysis within the confines of the cellular milieu with programmable modulation of biological functions at the molecular level. In this review, we summarize the development of nucleic acid-based biocomputing devices that are rationally designed and chemically synthesized, highlighting the ability of nucleic acid-based molecular computing to achieve cellular applications in sensing, imaging, biomedicine, and bioengineering. Then we discuss the future challenges and opportunities for cellular and in vivo applications. We expect this review to inspire innovative work on constructing nucleic acid-based biocomputing to achieve the goal of precisely rewiring, even reconstructing cellular signal networks in a prescribed way.

Signal amplification and output of CRISPR/Cas-based biosensing systems: A review

CRISPR (clustered regularly interspaced short palindromic repeats)/Cas (CRISPR-associated) proteins are powerful gene-editing tools because of their ability to accurately recognize and manipulate nucleic acids. Besides gene-editing function, they also show great promise in biosensing applications due to the superiority of easy design and precise targeting. To improve the performance of CRISPR/Cas-based biosensing systems, various nucleic acid-based signal amplification techniques are elaborately incorporated. The incorporation of these amplification techniques not only greatly increases the detection sensitivity and specificity, but also extends the detectable target range, as well as makes the use of various signal output modes possible. Therefore, summarizing the use of signal amplification techniques in sensing systems and elucidating their roles in improving sensing performance are very necessary for the development of more superior CRISPR/Cas-based biosensors for various applications. In this review, CRISPR/Cas-based biosensors are summarized from two aspects: the incorporation of signal amplification techniques in three kinds of CRISPR/Cas-based biosensing systems (Cas9, Cas12 and Cas13-based ones) and the signal output modes used by these biosensors. The challenges and prospects for the future development of CRISPR/Cas-based biosensors are also discussed.

Advancing sensing technology with CRISPR: From the detection of nucleic acids to a broad range of analytes - A review

The CRISPR/Cas technology, derived from an adaptive immune system in bacteria, has been awarded the Nobel Prize in Chemistry in 2020 for its success in gene editing. Increasing reports reveal that CRISPR/Cas technology has a wide scope of applications and it could be incorporated into biosensors for detecting critical analytes. CRISPR-powered biosensors have attracted significant research interest due to their advantages including high accuracy, good specificity, rapid response, and superior integrity. Now the CRISPR technology is not only admirable in nucleic acid monitoring, but also promising for other kinds of biomarkers' detection, including metal ions, small molecules, peptides, and proteins. Therefore, it is of great worth to explore the prospect, and summarize the strategies in applying CRISPR technology for the recognition of a broad range of targets. In this review, we summarized the strategies of CRISPR biosensing for non-nucleic-acid analytes, the latest development of nucleic acid detection, and proposed the challenges and outlook of CRISPR-powered biosensors.

Engineered RNA biosensors enable ultrasensitive SARS-CoV-2 detection in a simple color and luminescence assay

This work reports engineered toehold RNA–based biosensors for COVID-19 diagnostics, with a simple color or luminescence readout that makes it easily deployable in both well-equipped labs as well as low resource settings.

The continued resurgence of the COVID-19 pandemic with multiple variants underlines the need for diagnostics that are adaptable to the virus. We have developed toehold RNA–based sensors across the SARS-CoV-2 genome for direct and ultrasensitive detection of the virus and its prominent variants. Here, isothermal amplification of a fragment of SARS-CoV-2 RNA coupled with activation of our biosensors leads to a conformational switch in the sensor. This leads to translation of a reporter protein, for example, LacZ or nano-lantern that is easily detected using color/luminescence. By optimizing RNA amplification and biosensor design, we have generated a highly sensitive diagnostic assay that is capable of detecting as low as 100 copies of viral RNA with development of bright color. This is easily visualized by the human eye and quantifiable using spectrophotometry. Finally, this PHAsed NASBA-Translation Optical Method (PHANTOM) using our engineered RNA biosensors efficiently detects viral RNA in patient samples. This work presents a powerful and universally accessible strategy for detecting COVID-19 and variants. This strategy is adaptable to further viral evolution and brings RNA bioengineering center-stage.

Visualizing Live Chromatin Dynamics through CRISPR-Based Imaging Techniques

The three-dimensional organization of chromatin and its time-dependent changes greatly affect virtually every cellular function, especially DNA replication, genome maintenance, transcription regulation, and cell differentiation. Sequencing-based techniques such as ChIP-seq, ATAC-seq, and Hi-C provide abundant information on how genomic elements are coupled with regulatory proteins and functionally organized into hierarchical domains through their interactions. However, visualizing the time-dependent changes of such organization in individual cells remains challenging. Recent developments of CRISPR systems for site-specific fluorescent labeling of genomic loci have provided promising strategies for visualizing chromatin dynamics in live cells. However, there are several limiting factors, including background signals, off-target binding of CRISPR, and rapid photobleaching of the fluorophores, requiring a large number of target-bound CRISPR complexes to reliably distinguish the target-specific foci from the background. Various modifications have been engineered into the CRISPR system to enhance the signal-to-background ratio and signal longevity to detect target foci more reliably and efficiently, and to reduce the required target size. In this review, we comprehensively compare the performances of recently developed CRISPR designs for improved visualization of genomic loci in terms of the reliability of target detection, the ability to detect small repeat loci, and the allowed time of live tracking. Longer observation of genomic loci allows the detailed identification of the dynamic characteristics of chromatin. The diffusion properties of chromatin found in recent studies are reviewed, which provide suggestions for the underlying biological processes.

A Cascade Signal Amplification Based on Dynamic DNA Nanodevices and CRISPR/Cas12a Trans-cleavage for Highly Sensitive MicroRNA Sensing

The variations of microRNA (miRNA) expression can be valuable biomarkers in disease diagnosis and prognosis. However, current miRNA detection techniques mainly rely on reverse transcription and template replication, which suffer from slowness, contamination risk, and sample loss. To address these limitations, here we introduce a cascade toehold-mediated strand displacement reaction (CTSDR) and CRISPR/Cas12a trans-cleavage for highly sensitive fluorescent miRNA sensing, namely CTSDR-Cas12a. In this work, the target miRNA hybridizes with the terminal toehold site of a rationally designed probe and subsequently initiates dynamic CTSDR, leading to enzyme-free target recycling and the production of multiple programmable DNA duplexes. The obtained DNA duplex acts as an activator to trigger Cas12a trans-cleavage, generating significantly amplified fluorescence readout for highly sensitive detection of the miRNA target. Under the optimal conditions, the developed sensing method can detect target miRNA down to 70.28 fM with a wide linear range from 100 fM to 100 pM. In particular, by designing a set of probes and crRNAs, we demonstrate its broad applicability for the detection of six kinds of miRNAs with high sequence specificity. Furthermore, the method can be satisfactorily applied to monitor miR-21 in total RNA extracted from cells and clinical serum samples. Considering the high sensitivity, specificity, universality, and ease of handling, this strategy provides a great potential platform for the detection of miRNA biomarkers in molecular diagnostic practice.

Engineering a Second-Order DNA Logic-Gated Nanorobot to Sense and Release on Live Cell Membranes for Multiplexed Diagnosis and Synergistic Therapy

Tumor biomarker-based theranostics have achieved broad interest and success in recent years. However, single biomarker-based recognition can cause false-positive feedback, including the on-target off-tumor phenomenon, in the absence of tumor-specific antigen. Multibiomarker-based recognition molecules often elicit nonspecific and undesired internalization when they bind to "bystander" cells. We report a universal DNA tetrahedral scaffold (DTS) that anchors on the cell membrane to load multiple aptamers and therapeutics for precise and effective theranostics. This DNA logic-gated nanorobot (DLGN) not only facilitates precise discrimination among five cell lines, but also triggers synergistic killing of effector aptamer-tethered synergistic drugs (EASDs) to target cancer cells. Logic-gated recognition integrated into aptamer-functionalized molecular machines will prompt fast tumor profiling, in situ capture and isolation, and safe delivery of precise medicine.