A DNA Logic Circuit Equipped with a Biological Amplifier Loaded into Biomimetic ZIF-8 Nanoparticles Enables Accurate Identification of Specific Cancers In Vivo

DNA logic nanomachine for the accurate identification of multiple microRNAs in tumor cells

The use of dynamic DNA logic circuits for disease diagnosis at the molecular level plays a considerable role in biomedical fields. Nevertheless, how to create programmable nanomachines based on molecular logical gates to accurately identify multiple biomarkers from tumor cells remains a pivotal challenge. Herein, we developed a DNA-based nanomachine for analyzing and imaging multiple microRNAs (miRNAs) in cancerous cells with a logical AND operation. The triangular prism design of DNA nanomachine improved its performance in living cell research with high stability and served as a modularized framework for toehold-mediated strand displacement reactions and catalytic hairpin assembly circuits. The results suggested that the nanomachine could efficiently enter cells with great biocompatibility and rapidly recognize the correct biomolecules with high sensitivity. The well-designed DNA-logic gate nanomachine enabled accurate diagnosis on multiple miRNA patterns in different cell lines and differentiation of aberrant expression in target cells, which provided a novel possibility for intelligent disease diagnosis using smart nanomachines at the molecular level.

Isotope Dilution DNA Logic Circuits for Multiple Output and Absolute Quantification

DNA logic circuits have gained great success in the past, thanks to their distinct performance regarding the scalability and correctness of computation. However, there are still two challenges often considered for DNA logic circuit-based computation. First, the mainstream optical probes are often subject to spectral overlapping interference for complex multitask analysis and outputs. Second, absolute quantification results traceable to the primary international system of units are mission impossible, especially for interlaboratory comparisons and quality assurances. Herein, we constructed DNA logic circuits encoded with lanthanide isotopes and decoded by elemental mass spectrometry. The 155Gd-enriched isotope and 145Nd-enriched isotope were incorporated in the DNA logic circuits for the isotope dilution-based absolute quantification of microRNAs. The proposed isotopic DNA logic circuits greatly enhance the multiplexity and computation accuracy, which poses a great potential for cancer biomarker-related diagnosis.

Mitoxantrone-Encapsulated ZIF-8 Enhances Chemo-Immunotherapy via Amplified Immunogenic Cell Death

Chemo-immunotherapy, combining systemic chemotherapeutic drugs and immune checkpoint blockers, is a promising paradigm in cancer treatment. However, challenges such as limited induction of immune responses and systemic immune toxicity have hindered its clinical applications. Here, a zeolite imidazolate framework-8 (ZIF-8) that encapsulates mitoxantrone (MIT), an immune cell death (ICD)-inducing chemotherapeutic agent (MIT@ZIF-8), is synthesized using a one-pot aqueous-phase process. ZIF-8 serves as a dual-functional nanomaterial for chemo-immunotherapy: a carrier to enhance tumor uptake of MIT for improved chemotherapy efficacy, and a pyroptosis inducer to amplify MIT-induced ICD for augmented anti-tumor immune responses. As a result, in vivo administration of MIT@ZIF-8 markedly inhibits tumor growth in both immunologically "hot" colon cancer and immunologically "cold" prostate cancer. Moreover, MIT@ZIF-8 treatment increases the abundance of cytotoxic CD8+ T cells and reduces the amount of immunosuppressive regulatory T cells in tumors, thereby enhancing anti-tumor immunity and sensitizing prostate cancer to anti-CTLA-4 immunotherapy. In summary, MIT@ZIF-8 offers a highly translational approach for chemo-immunotherapy.

DNA Tetrahedron-enhanced single-particle counting integrated with cascaded CRISPR Program for ultrasensitive dual RNAs logic sensing

CRISPR-Cas-based technology, emerging as a leading platform for molecular assays, has been extensively researched and applied in bioanalysis. However, achieving simultaneous and highly sensitive detection of multiple nucleic acid targets remains a significant challenge for most current CRISPR-Cas systems. Herein, a CRISPR Cas12a based calibratable single particle counting-mediated biosensor was constructed for dual RNAs logic and ultra-sensitive detection in one tube based on DNA Tetrahedron (DTN)-interface supported fluorescent particle probes coupled with a novel synergistic cascaded strategy between CRISPR Cas13a system and strand displacement amplification (SDA). As expected, our platform enables dual RNA molecules intelligent detection using only one crRNA of Cas13a, achieving a sensitivity enhancement of three orders of magnitude assisted with multiple signal amplification and accurate fluorescence particle counting with DTN mediated nano-biointerface enhancement, compared to traditional bulk Cas13a assays. Moreover, the effectiveness and universality of our strategy are experimentally investigated and demonstrated through the detection of mRNAs (cervical cancer swab clinical samples and cultured cancer cells) and bacterial 16s rRNAs. This work not only proposes a highly promising avenue for designing CRISPR-based multiplex detection systems that excel in ultra-sensitivity, specificity, and clinical molecular diagnostics, but also provide new insights into the potential applications of nanotechnology in molecular diagnostics, functional surface engineering, and interface-mediated bioreactions.

A Biomimetic Mineralization Strategy for the Long-Term Preservation of Exosomes Through Non-Destructive Encapsulation Within Zeolite Imidazolate Frameworks-8

Exosomes, which are extracellular vesicles derived from endosomes, play a crucial role in mediating intercellular communication and are widely used in medical diagnostics and drug delivery. Conventional cryopreservation strategies can damage the integrity of exosomes, hindering their further application in the biomedical field. Here, a novel approach is developed for exosome storage, shell of intact exosomes holding (SHIELD), which packages exosomes in zeolite imidazolate frameworks-8 (ZIF-8) as a protective shell. ZIF-8 shell can be quickly removed, and meanwhile, the inherent morphology and biological function of exosomes can be preserved, thereby mitigating potential biocompatible risks associated with ZIF-8. Notably, the SHIELD-protected exosomes maintained their intact morphology and cellular uptake capacity, and 76% of the original protein content can be kept even after being stored for one month. Overall, the development of SHIELD overcomes the challenges of traditional techniques of exosome preservation and further broadens the biomedical applications of ZIF-8 and exosomes.

Programmable Split DNAzyme Modulators via Allosteric Cooperative Activation for mRNA Electrochemiluminescence Biosensing

DNAzymes, known for their programmability, stability, and cost-effectiveness, are powerful tools for signal transduction in complex biological systems. However, their application in responding to target effectors is often hindered by limited catalytic efficiency and susceptibility to unintended activation. Here we propose an allosteric cooperative activation strategy to program a split DNAzyme modulator (STATER) that enables sensitive and accurate electrochemiluminescence (ECL) biosensing of interleukin-6 (IL-6) mRNA. Our design features a STATER that leverages a DNA tetrahedron as a central scaffold, equipped with two pairs of T-shaped hairpin probes (TP) and helper hairpin probes (HP). Specifically, the TP contains two apurinic/apyrimidinic endonuclease 1 (APE1) recognition sites, an IL-6 mRNA recognition region, and a partzyme fragment, while the HP contains a corresponding paired partzyme fragment. Unlike conventional DNAzyme modulators that rely on single effector activation, the STATER integrates an allosteric cooperative activation mechanism, which ensures that all preblocked components are synergistically activated and assembled within a confined space, facilitating rapid and specific reconstruction of the DNAzyme's catalytic active domain. Furthermore, upon cooperative recognition by APE1 and IL-6 mRNA, two inactive partzymes undergo an allosteric assembly via a toehold exchange displacement reaction, switching on the cleavage reactivity of STATER. This mechanism enables the establishment of an activation threshold for IL-6 mRNA, thereby minimizing nonspecific activation in complex scenarios. Our studies demonstrate that the STATER exhibits outstanding sensitivity and selectivity for IL-6 mRNA detection using the supramolecular gold nanoclusters network-based ECL platform. The biosensor provides a linear detection span from 1 × 10-13 to 1 × 10-7 M, with a limit of detection as low as 3.26 × 10-14 M, highlighting STATER's potential for detecting various analytes in complex biological systems.

Exogenously and Endogenously Sequential Regulation of DNA Nanodevices Enables Organelle-Specific Signal Amplification in Subcellular ATP Profiling

Adenosine triphosphate (ATP), the primary energy currency in cells, is dynamically regulated across different subcellular compartments. The ATP interplay between mitochondria and endoplasmic reticulum (ER) underscores their coordinated roles in various biochemical processes, highlighting the necessity for precise profiling of subcellular ATP dynamics. Here we present an exogenously and endogenously dual-regulated DNA nanodevice for spatiotemporally selective, subcellular-compartment specific signal amplification in ATP sensing. The system allows for exogenous NIR light-controlled spatiotemporal localization and activation of the aptamer sensor in mitochondria or ER, while a specific endogenous enzyme in the organelles further drives signal amplification via the consumption of molecular beacon fuels, resulting in significantly enhanced sensitivity and spatial precision for the subcellular ATP profiling in the organelle of interest. Furthermore, we demonstrate the application of this system for robust monitoring of ATP fluctuations in mitochondria and ER following drug interventions. This advancement provides a powerful tool for improving our understanding of cellular energetics at the subcellular level and holds potential for the development of targeted therapeutics.

Dynamic Nanostructure-Based DNA Logic Gates for Cancer Diagnosis and Therapy

DNA logic gates with dynamic nanostructures have made a profound impact on cancer diagnosis and treatment. Through programming the dynamic structure changes of DNA nanodevices, precise molecular recognition with signal amplification and smart therapeutic strategies have been reported. This enhances the specificity and sensitivity of cancer theranostics, and improves diagnosis precision and treatment outcomes. This review explores the basic components of dynamic DNA nanostructures and corresponding DNA logic gates, as well as their applications for cancer diagnosis and therapies. The dynamic DNA nanostructures would contribute to cancer early detection and personalized treatment.

Spatioselective Imaging of Noncoding RNAs in Mitochondria via an Organelle-Specific DNA Assembly Strategy

Precise imaging of noncoding RNAs (ncRNAs) in specific organelles allows decoding of their functions at subcellular level but lacks advanced tools. Here we present a DNA-based nanobiotechnology for spatially selective imaging of ncRNA (e.g., microRNA (miRNA)) in mitochondria via an organelle-specific DNA assembly strategy. The target miRNA-initiated assembly of DNA hairpins is inhibited by the block of toehold-mediated strand displacement reaction but can be exclusively activated by a mitochondria-encoded ribosomal RNA (rRNA) for hybridization chain reaction, enabling spatial control over miRNA imaging. We demonstrate that the conditionally controlled DNA assembly technology allows for minimization of nonspecific activation and thus improves the spatial precision of miRNA detection. In addition, the strategy is adaptable to visualizing other ncRNAs such as long noncoding RNAs in mitochondria, highlighting the universality of the approach. Overall, this work provides a useful tool for spatially selective imaging of ncRNAs and investigating the functions of organelle-located RNA.

Recent advances in zeolitic imidazolate frameworks as drug delivery systems for cancer therapy

Biological nanotechnologies based on functional nanoplatforms have synergistically catalyzed the emergence of cancer therapies. As a subtype of metal-organic frameworks (MOFs), zeolitic imidazolate frameworks (ZIFs) have exploded in popularity in the field of biomaterials as excellent protective materials with the advantages of conformational flexibility, thermal and chemical stability, and functional controllability. With these superior properties, the applications of ZIF-based materials in combination with various therapies for cancer treatment have grown rapidly in recent years, showing remarkable achievements and great potential. This review elucidates the recent advancements in the use of ZIFs as drug delivery agents for cancer therapy. The structures, synthesis methods, properties, and various modifiers of ZIFs used in oncotherapy are presented. Recent advances in the application of ZIF-based nanoparticles as single or combination tumor treatments are reviewed. Furthermore, the future prospects, potential limitations, and challenges of the application of ZIF-based nanomaterials in cancer treatment are discussed. We except to fully explore the potential of ZIF-based materials to present a clear outline for their application as an effective cancer treatment to help them achieve early clinical application.

CRISPR/Cas12a-Powered Electrochemical Platform for Dual-miRNA Detection via an AND Logic Circuit

The CRISPR/Cas technology shows great potential in molecular detection and diagnostics. However, it is still challenging to detect multiple targets simultaneously using the CRISPR-Cas system. Herein, we ingeniously leverage the synergistic effect of two short single-stranded DNA activators to construct a CRISPR/Cas12a-driven electrochemical sensing platform based on an AND logic circuit ("AND" LC-CRISPR) for the simultaneous detection of dual miRNAs. Specifically, the exponential amplification reaction products triggered by the dual-specific miRNAs are designed as binary inputs to bind with Cas12a/crRNA, forming an AND logic circuit and activating the trans-cleavage ability of the CRISPR-Cas12a system. Subsequently, the hairpin probe biogate on the surface of the functionalized electrochemical signal probe (MB@HP-Fe-MOF) is cleaved by activated Cas12a, leading to the release of the encapsulated electroactive signal molecule methylene blue, thereby generating a strong electrochemical signal. As a result, this "AND" LC-CRISPR sensing platform, requiring only a single crRNA assembled with Cas12a, achieves simultaneous detection of miRNA-155 and miRNA-21 at concentrations as low as 3.2 fM. Moreover, the platform allows easy adjustment of the AND logic circuit inputs according to different detection targets, allowing it to be easily expanded for the analysis and diagnosis of other multibiomarkers. This approach demonstrates promising potential for future applications in intelligent diagnostic medicine.

Spatially Preorganized Hybridization Chain Reaction for the Prompt Diagnosis of Inflammation

Biological systems utilize precise spatial organization to facilitate and regulate information transmission within signaling networks. Inspired by this, artificial scaffolds that enable delicate spatial arrangements are desirable to increase the local concentration of reactants, expedite specific interactions, and minimize undesired interference. In this study, we presented an integrated biosensing nanodevice, termed TRI-HCR, in which hybridization chain reaction (HCR) probes were precisely organized on a triangular DNA origami nanostructure (TRI) with finely-tuned distance, quantity, and pattern. Compared to traditional HCR in the free form, this nanodevice demonstrated increased reaction rate and signal level. We further employed the optimized TRI-HCR for in vivo imaging of a nucleic acid biomarker of inflammatory diseases. In both acute gouty arthritis (AGA) and sepsis-associated acute kidney injury (SA-AKI) model mice, TRI-HCR was capable of diagnosing inflammation in the early stages, significantly earlier than histological examination. We anticipate that this precise spatial preorganization strategy for HCR holds promise for broader applications in early disease detection and monitoring.

Empowering DNA-Based Information Processing: Computation and Data Storage

Information processing is a critical topic in the digital age, as silicon-based circuits face unprecedented challenges such as data explosion, immense energy consumption, and approaching physical limits. Deoxyribonucleic acid (DNA), naturally selected as a carrier for storing and using genetic information, possesses unique advantages for information processing, which has given rise to the emerging fields of DNA computing and DNA data storage. To meet the growing practical demands, a wide variety of materials and interfaces have been introduced into DNA information processing technologies, leading to significant advancements. This review summarizes the advances in materials and interfaces that facilitate DNA computation and DNA data storage. We begin with a brief overview of the fundamental functions and principles of DNA computation and DNA data storage. Subsequently, we delve into DNA computing systems based on various materials and interfaces, including microbeads, nanomaterials, DNA nanostructures, hydrophilic-hydrophobic compartmentalization, hydrogels, metal-organic frameworks, and microfluidics. We also explore DNA data storage systems, encompassing encapsulation materials, microfluidics techniques, DNA nanostructures, and living cells. Finally, we discuss the current bottlenecks and obstacles in the fields and provide insights into potential future developments.

Integration of STING activation and COX-2 inhibition via steric-hindrance effect tuned nanoreactors for cancer chemoimmunotherapy

Integrating immunotherapy with nanomaterials-based chemotherapy presents a promising avenue for amplifying antitumor outcomes. Nevertheless, the suppressive tumor immune microenvironment (TIME) and the upregulation of cyclooxygenase-2 (COX-2) induced by chemotherapy can hinder the efficacy of the chemoimmunotherapy. This study presents a TIME-reshaping strategy by developing a steric-hindrance effect tuned zinc-based metal-organic framework (MOF), designated as CZFNPs. This nanoreactor is engineered by in situ loading of the COX-2 inhibitor, C-phycocyanin (CPC), into the framework building blocks, while simultaneously weakening the stability of the MOF. Consequently, CZFNPs achieve rapid pH-responsive release of zinc ions (Zn2+) and CPC upon specific transport to tumor cells overexpressing folate receptors. Accordingly, Zn2+ can induce reactive oxygen species (ROS)-mediated cytotoxicity therapy while synchronize with mitochondrial DNA (mtDNA) release, which stimulates mtDNA/cGAS-STING pathway-mediated innate immunity. The CPC suppresses the chemotherapy-induced overexpression of COX-2, thus cooperatively reprogramming the suppressive TIME and boosting the antitumor immune response. In xenograft tumor models, the CZFNPs system effectively modulates STING and COX-2 expression, converting "cold" tumors into "hot" tumors, thereby resulting in ≈ 4-fold tumor regression relative to ZIF-8 treatment alone. This approach offers a potent strategy for enhancing the efficacy of combined nanomaterial-based chemotherapy and immunotherapy.

A polymer deposition-mediated surface-charge reformation strategy: reversing the MOF biomineralization behavior

Biomineralization of a porous metal-organic framework (MOF) shell onto biomacromolecule templates is a burgeoning strategy to construct robust biocatalysts. However, it strongly relies on the interfacial interaction between MOF precursors and enzyme surface, significantly limiting the generalization of this nanotechnology. Herein, we identify polymers that are well-suited for deposition onto target biomacromolecules via supramolecular interactions and introduce a polymer deposition-mediated surface-charge reformation strategy to facilitate the biomineralization of porous MOFs, including ZIF-8, ZIF-90, and ZIF-zni onto enzymes. We investigate nine commercially available polymers to find that those with dense -SO3H and -COOH groups effectively regulate the surface-charge properties of the enzymes that are unfavorable for biomineralization. The polymer-enzyme complex thus formed retains its original bioactivity and offers significantly elevated sites to accumulate metal precursors, triggering the in-place MOF biomineralization. We demonstrate that this approach allows access to diverse MOF biocatalysts independent of the enzyme surface chemistry, which are difficult to be synthesized by previous biomineralization methods. Given the highly specific bioactivity and structural stability of the MOF biocatalysts, a chemiluminiscence sensor platform is developed for the sensitive detection of hydrogen sulfide (H2S) biomarkers, with a low limit of detection of 0.09 nM that is superior to most of the reported methods. This study provides an effective and universal strategy for MOF biomineralization using fragile enzymes as biotemplates and offers new insights into accessing multifunctional MOF hybrid biocatalysts.

Logically Activatable Nanoreporter for Multiplexed Time-Phased Imaging Assessment of Hepatic Ischemia-Reperfusion Injury and Systemic Inflammation

Hepatic ischemia-reperfusion injury (HIRI) and induced systemic inflammation is a time-dependent multistage process which poses a risk of causing direct hepatic dysfunction and multiorgan failure. Real-time in situ comprehensive visualization assessment is important and scarce for imaging-guided therapeutic interventions and timely efficacy evaluation. Here, a logically activatable nanoreporter (termed QD@IR783-TK-FITC) is developed for time-phase imaging quantification of HIRI and induced systemic inflammation. The nanoreporters could be used for in vivo ratiometric NIR-IIb fluorescence sensing of reactive oxygen species (ROS), which can depict the in situ hepatic ROS fluctuation for the early diagnosis of HIRI in the initial 3 h. Meanwhile, the ROS-specific reaction releases renal-clearable fluorophore fragments from nanoreporters for monitoring the systematic inflammation induced by HIRI via longitudinal urinalysis. In addition, a functional relationship between digitized signal outputs (NIR-IIb ratios, urinary fluorescence) with hepatic injury scores has been established, realizing precise prediction of HIRI severity and preassessment of therapeutic efficacy. Such a time-phased modular toolbox can dynamically report HIRI-induced systemic inflammation in vivo, providing an efficient approach for HIRI treatment.

A Self-Cascade Oxygen-Generating Nanomedicine for Multimodal Tumor Therapy

Natural and artificial enzyme oxygen-generating systems for photodynamic therapy (PDT) are developed for tumor treatment, yet they have fallen short of the desired efficacy. Moreover, both the enzymes and photosensitizers usually need carriers for efficient delivery to tumor sites. Here, a self-cascade-enhanced multimodal tumor therapy is developed by ingeniously integrating self-cascade-enhanced PDT with Zn2+-overloading therapy. Manganese-porphyrin (TCPP-Mn) is chosen both as the photosensitizer and catalase (CAT) mimic, which can be encapsulated within glucose oxidase (GOx). Acid-responsive zeolitic imidazolate framework-8 (ZIF-8) is applied as the carrier for TCPP-Mn@GOx (T@G), attaining TCPP-Mn@GOx@ZIF-8 (T@G@Z). T@G@Z demonstrates robust anti-tumor ability as follows: upon the structural degradation of ZIF-8, GOx can mediate the oxidation of glucose and generate hydrogen peroxide (H2O2); TCPP-Mn can catalyze H2O2 into O2 for self-cascade-enhanced PDT; meanwhile, the released Zn2+ can enhance oxidative stress and induce mitochondrial dysfunction by destroying mitochondrial membrane potential; furthermore, immunotherapy can be activated to resist primary tumor and tumor metastasis. The self-cascade-enhanced T@G@Z exhibited its potential application for further tumor management.

FRAME: flap endonuclease 1-engineered PAM module for precise and sensitive modulation of CRISPR/Cas12a trans-cleavage activity

CRISPR/Cas12a system, renowned for its precise recognition and efficient nucleic acid cleavage capabilities, has demonstrated remarkable performance in molecular diagnostics and biosensing. However, the reported Cas12a activity regulation methods often involved intricate CRISPR RNA (crRNA) structural adjustments or costly chemical modifications, which limited their applications. Here, we demonstrated a unique enzyme activity engineering strategy using flap endonuclease 1 (FEN1) to regulate the accessibility of the protospacer adjacent motif (PAM) module in the double-stranded DNA activator (FRAME). By identifying the three-base overlapping structure between the target inputs and substrate, FEN1 selectively cleaved and released the 5'-flap containing the 'TTTN' sequence, which triggered the secondary cleavage of FEN1 while forming a nicked PAM, ultimately achieving the sensitive switching of Cas12a's activity. The FRAME strategy exemplified the 'two birds with one stone' principle, as it not only precisely programmed Cas12a's activity but also simultaneously triggered isothermal cyclic amplification. Moreover, the FRAME strategy was applied to construct a sensing platform for detecting myeloperoxidase and miR-155, which demonstrated high sensitivity and specificity. Importantly, it proved its versatility in detecting multiple targets using a single crRNA without redesign. Collectively, the FRAME strategy opens up a novel avenue for modulating Cas12a's activity, promising immense potential in the realm of medical diagnostics.

GlycoSS: A DNA Glycosignal Sieve for Deciphering Spatially Resolved EpCAM-Specific Glycoforms

Malignant transformation of cancer is often accompanied by aberrant glycopatterns. Epithelial-mesenchymal transition (EMT) is a crucial biological process in cancer migration and invasion, accelerating cancer deterioration. High-precision analysis of protein-glycan spatial profiling in the EMT process is essential for elucidating glycosylation functions and cancer progression. However, the diversity of glycans in composition and conformation complicates their spatial analysis. Here, we develop a DNA glycosignal sieve (GlycoSS) visualization platform for screening glycoform expression with a protein spatial dimension. GlycoSS utilizes protein-anchored DNA nanoscanners of distinct lengths to control glycosignal readout, enabling protein-glycan distance modulations, and simultaneously orthogonally amplify glycoform output through signal amplification by an exchange reaction. Using GlycoSS, we screened EpCAM-specific hypoglycosylated glycoform signals in different breast cancer cell subtypes, especially characterizing the spatial distribution of glycans on the MCF-7 cell surface. Considering that the EpCAM-specific N-glycan dysregulation in EMT is pivotal, GlycoSS revealed dynamic glycan fluctuations during IGF-1-induced EMT, revealing that the N-glycans were positively associated with tumor malignancy and metastasis. GlycoSS is anticipated to accelerate the identification of aberrant N-glycosylation in tumor progression, advancing systemic glycobiology insights. Notably, GlycoSS is capable of analyzing diverse glycoprotein profiles, offering additional dimensions into the role of glycoprotein nanoenvironments in regulating membrane protein function.

Just-in-Time Generation of Nanolabels via In Situ Biomineralization of ZIF-8 Enabling Ultrasensitive MicroRNA Detection on Unmodified Electrodes

Nanolabels can enhance the detection performance of electrochemical biosensing methods, yet their practical application is hindered by complex preparation, batch-to-batch variability, and poor long-term storage stability. Herein, we present a novel electrochemical method for miRNA detection based on the just-in-time generation of zeolitic imidazolate framework-8 (ZIF-8) nanolabels initiated by nucleic acids. In this design, the target miRNA-21 is captured with magnetic beads and polyadenylated by Escherichia coli Poly(A) polymerase (EPP), producing miRNA-21 molecules with poly(A) tails (miR-21-poly(A)). These molecules are then adsorbed onto a bare gold electrode (AuE) surface via adenine-gold affinity interactions, serving as nucleation sites for the rapid in situ formation of ZIF-8 nanoparticles. The ZIF-8 nanoparticles function as signal labels, impeding electron transfer at the electrode interfaces and thereby generating a notable electrochemical signal. The developed method demonstrated exceptional sensitivity, with a detection limit (LOD) as low as 2.3 aM and a linear detection range from 10 aM to 1000 fM. The practical application of the developed method was validated by using it to evaluate miRNA-21 expression levels in various biological samples, including cell lines, tumor tissues, and clinical blood samples from non-small cell lung cancer (NSCLC) patients. This approach simplifies the detection process by eliminating the need for presynthesized nanomaterials and premodified electrodes. Its simplicity and high sensitivity make this method a promising tool for point-of-care testing and a wide range of biomedical research applications.

Advancements in DNA computing: exploring DNA logic systems and their biomedical applications

DNA computing is regarded as one of the most promising candidates for the next generation of molecular computers, utilizing DNA to execute Boolean logic operations. In recent decades, DNA computing has garnered widespread attention due to its powerful programmable and parallel computing capabilities, demonstrating significant potential in intelligent biological analysis. This review summarizes the latest advancements in DNA logic systems and their biomedical applications. Firstly, it introduces recent DNA logic systems based on various materials such as functional DNA sequences, nanomaterials, and three-dimensional DNA nanostructures. The material innovations driving DNA computing have been summarized, highlighting novel molecular reactions and analytical performance metrics like efficiency, sensitivity, and selectivity. Subsequently, it outlines the biomedical applications of DNA computing-based multi-biomarker analysis in cellular imaging, clinical diagnosis, and disease treatment. Additionally, it discusses the existing challenges and future research directions for the development of DNA computing.

An electrochemical biosensor equipped with a logic circuit as a smart automaton for two-miRNA pattern detection

Detecting multiple targets in complex cellular and biological environments yields more reliable results than single-label assays. Here, we introduced an electrochemical biosensor equipped with computing functions, acting as a smart automaton to enable computing-based detection. By defining the logic combinations of miR-21 and miR-122 as detection patterns, we proposed the corresponding AND and OR detection automata. In both logic gate modes, miR-21 and miR-122 could be replaced with single-stranded FO or FA, modified with Fc, binding to the S chain on the electrode surface. This process led to a significant decrease in the square wave voltammetry (SWV) of Fc on the same sensing platform, as numerous ferrocene (Fc)-tagged DNA fragments escaped from the electrode surface. Experimental results indicated that both automata efficiently and sensitively detected the presence of the two targets. This strategy highlighted how a small amount of target could generate a large current signal decrease in the logic automata, significantly reducing the detection limit for monitoring low-abundance targets. Moreover, the short-stranded DNA components of the detection automata exhibited a simple composition and easy programmability of probe sequences, offering an innovative detection mode. This simplified the complex process of detection, data collection, computation, and evaluation. The direct detection result ("0" or "1") was exported according to the embedded computation code. This approach could be expanded into a detection system for identifying other sets of biomarkers, enhancing its potential for clinical applications.

A DNA Molecular Logic Circuit for Precise Tumor Identification

Tumor-associated antigens (TAAs) are not exclusively expressed in cancer cells, inevitably causing the "on target, off tumor" effect of molecular recognition tools. To achieve precise recognition of cancer cells, by using protein tyrosine kinase 7 (PTK7) as a model TAA, a DNA molecular logic circuit Aisgc8 was rationally developed by arranging H+-binding i-motif, ATP-binding aptamer, and PTK7-targeting aptamer Sgc8c in a DNA sequence. Aisgc8 output the conformation of Sgc8c to recognize PTK7 on cells in a simulated tumor microenvironment characterized by weak acidity and abundant ATP, but not in a simulated physiological environment. Through in vitro and in vivo results, Aisgc8 demonstrated its ability to precisely recognize cancer cells and, as a result, displayed excellent performance in tumor imaging. Thus, our studies produced a simple and efficient strategy to construct DNA logic circuits, opening new possibilities to develop convenient and intelligent precision diagnostics by using DNA logic circuits.

Aptamer-Based DNA Allosteric Switch for Regulation of Protein Activity

Allostery is a fundamental way to regulate the function of biomolecules playing crucial roles in cell metabolism and proliferation and is deemed the second secret of life. Given the limited understanding of the structure of natural allosteric molecules, the development of artificial allosteric molecules brings a huge opportunity to transform the allosteric mechanism into practical applications. In this study, the concept of bionics is introduced into the design of artificial allosteric molecules and an allosteric DNA switch with an activity site and an allosteric site based on two aptamers for selective inhibition of thrombin activity. Compared with the single aptamer, the allosteric switch possesses a significantly enhanced inhibition ability, which can be precisely regulated by converting the switch states. Moreover, the dynamic allosteric switch is further subjected to the control of the DNA threshold circuit for realizing automatic concentration determination and activity inhibition of thrombin. These compelling results confirm that this allosteric switch equipped with self-sensing and information-processing modules puts a new slant on the research of allosteric mechanisms and further application of allosteric tactics in chemical and biomedical fields.

Self-Assembled DNA Nanospheres Driven by Carbon Dots for MicroRNAs Imaging in Tumor via Logic Circuit

DNA nanostructures with diverse biological functions have made significant advancements in biomedical applications. However, a universal strategy for the efficient production of DNA nanostructures is still lacking. In this work, a facile and mild method is presented for self-assembling polyethylenimine-modified carbon dots (PEI-CDs) and DNA into nanospheres called CANs at room temperature. This makes CANs universally applicable to multiple biological applications involving various types of DNA. Due to the ultra-small size and strong cationic charge of PEI-CDs, CANs exhibit a dense structure with high loading capacity for encapsulated DNA while providing excellent stability by protecting DNA from enzymatic hydrolysis. Additionally, Mg2+ is incorporated into CANs to form Mg@CANs which enriches the performance of CANs and enables subsequent biological imaging applications by providing exogenous Mg2+. Especially, a DNAzyme logic gate system that contains AND and OR Mg@CANs is constructed and successfully delivered to tumor cells in vitro and in vivo. They can be specifically activated by endogenic human apurinic/apyrimidinic endonuclease 1 and recognize the expression levels of miRNA-21 and miRNA-155 at tumor sites by logic biocomputing. A versatile pattern for delivery of diverse DNA and flexible logic circuits for multiple miRNAs imaging are developed.

DNA Robots for CRISPR/Cas12a Activity Management and Universal Platforms for Biosensing

The CRISPR/Cas12a system is a revolutionary genome editing technique that is widely employed in biosensing and molecular diagnostics. However, there are few reports on precisely managing the trans-cleavage activity of Cas12a by simple modification since the traditional methods to manage Cas12a often require difficult and rigorous regulation of core components. Hence, we developed a novel CRISPR/Cas12a regulatory mechanism, named DNA Robots for Enzyme Activity Management (DREAM), by introducing two simple DNA robots, apurinic/apyrimidinic site (AP site) or nick on target activator. First, we revealed the mechanism of how the DREAM strategy precisely regulated Cas12a through different binding affinities. Second, the DREAM strategy was found to improve the selectivity of Cas12a for identifying base mismatch. Third, a modular biosensor for base excision repair enzymes based on the DREAM strategy was developed by utilizing diversified generation ways of DNA robots, and a multi-signal output platform such as fluorescence, colorimetry, and visual lateral flow strip was constructed. Furthermore, we extended logic sensing circuits to overcome the barrier that Cas12a could not detect simultaneously in a single tube. Overall, the DREAM strategy not only provided new prospects for programmable Cas12a biosensing systems but also enabled portable, specific, and humanized detection with great potential for molecular diagnostics.