DNA-guided CRISPR–Cas12a effectors for programmable RNA recognition and cleavage
CRISPR–Cas effectors typically rely on RNA guides to recognize target sequences. In Cas12a, the protospacer adjacent motif on DNA engages conserved protein residues, triggering target binding and nuclease activation. Here we reprogram Cas12a into a DNA-guided, RNA-targeting effector. Exploiting protospacer-adjacent motif-dependent interaction, we engineer synthetic CRISPR DNA that engages Cas12a to form a functional deoxyribonucleoprotein complex, while repurposing solely RNA as the programmable target. Structural, biophysical and biochemical analyses reveal the molecular basis of this DNA-guided, RNA-targeting configuration and support an activation pathway distinct from that of canonical RNA-guided systems. DNA-guided Cas12a enables direct RNA detection and efficient intracellular RNA knockdown, establishing a modular activation architecture for CRISPR–Cas12a and expanding the design space for programmable RNA manipulation.
Elastomeric sponge-supramolecular gel patch: A multifaceted skin adhesive based on non-catechol interactions for sweaty and dynamic environment
Existing wet adhesive hydrogels utilize catechol moieties or pure covalent bonding to achieve high adhesion strength but often lack operational stability and ease of detachment, limiting practical use. Additionally, these systems can suffer from dehydration or swelling, and surface incompatibilities with elastomers, leading to sensor failures in dynamic scenarios. To tackle these issues, this study introduces an innovative biocompatible adhesive patch composed of an Ecoflex sponge (ES) infiltrated with a supramolecular gel (SMG), referred to as ES-SMG. The sponge provides the structural framework, while the supramolecular deep eutectic solvent-based gel imparts non-catechol adhesion on wet skin. This design promotes effective interfacial water removal and transport while achieving repeatable, rapid (<1 min) and robust wet adhesion of 52 kPa on skin predominantly via multiple dynamic interactions. The patch demonstrates exceptional antibacterial property, mechanical resilience, featuring stretchability of 160% and 30-fold lower swelling than commercial gels. Furthermore, the patch exhibits less than a 2% decline in adhesive strength after 15 days without special storage conditions. Consequently, it effectively captures clean and stable biophysical signals from the human body in sweaty and dynamic conditions. This advanced adhesive solution can significantly enhance the performance and reliability of wearable bioelectronics for therapeutics and diagnostics.
Structure-enhanced deep learning accelerates aptamer selection for small molecule families like steroids
The efficient discovery of high-affinity small-molecule aptamers via the Systematic Evolution of Ligands by EXponential enrichment (SELEX) is often constrained by challenges in navigating vast sequence spaces and rationally designing initial libraries. In this study, we introduce Deep Learning-assisted SELEX (DL-SELEX), a novel two-step framework that employs variational autoencoders (VAEs) to accelerate and refine small-molecule aptamer selection. This approach is the first to integrate deep learning to design initial aptamer libraries, marking a significant advancement in SELEX workflows. DL-SELEX leverages shared structural features within molecular families (e.g. steroids) to guide aptamer design: AptaVAE, the first VAE enriched with transfer learning from foundation models, generates tailored initial pools, whereas AptaClux, a second VAE, identifies high-performance candidates from SELEX-derived next-generation sequencing (NGS) data by capturing consensus structural features. The application of DL-SELEX to hydrocortisone (CS) and testosterone (TES) yielded aptamers with up to 450-fold higher affinity than previously reported aptamers and reduced SELEX iterations by up to 80%. Critically, these results demonstrate that structural commonalities can be used to train deep learning models to design aptamers for structurally similar targets. DL-SELEX provides an effective, generalizable strategy to streamline aptamer discovery and enables de novo design of high-affinity aptamers for challenging small molecules.
PATENT: DETECTION OF ANALYTES BY ENZYME-MEDIATED STRAND DISPLACEMENT REACTIONS
The subject invention pertains to composition and methods of using said composition as an in vitro biosensor of small molecules in biological and/or environmental samples using enzyme-assisted nucleic acid reactions. The methods and compositions can be used to sense and/or transduce the signal of a sensing event mediated by allosteric proteins, endonucleases and nucleic acid reactions. This invention allows the rapid development and setup of one-pot assays to provide results in minutes. The methods and compositions may be used to generate an electrochemical, fluorescent, colorimetric, and/or luminescent output and the methods can be performed in different modalities, including a solution- based or paper-based assay.
CoLAMP: CRISPR-based one-pot loop-mediated isothermal amplification enables at-home diagnosis of SARS-CoV-2 RNA with nearly eliminated contamination utilizing amplicons depletion strategy
Rapid point-of-care diagnostics, essential in settings such as airport on-site testing and home-based screening, displayed important implications for infectious disease control during the SARS-CoV-2 outbreak. However, the deployment of simple and sensitive assays in real-life scenarios still faces the concern of aerosol contamination. Here, we report an amplicon-depleting CRISPR-based one-pot loop-mediated isothermal amplification (CoLAMP) assay for point-of-care diagnosis of SARS-CoV-2 RNA. In this work, AapCas12b sgRNA is designed to recognize the activator sequence sited in the loop region of the LAMP product, which is crucial for exponential amplification. By destroying the aerosol-prone amplifiable products at the end of each amplification reaction, our design can significantly reduce the amplicons contamination that causes false positive results in point-of-care diagnostics. For at-home self-testing, we designed a low-cost sample-to-result device for fluorescence-based visual interpretation. As well, a commercial portable electrochemical platform was deployed as a proof-of-concept of ready-to-use point-of-care diagnostic systems. The field deployable CoLAMP assay can detect as low as 0.5 copies/μL of SARS-CoV-2 RNA in clinical nasopharyngeal swab samples within 40 min without the need for specialists for its operation. Read More >
Prediction of Aptamer–Small-Molecule Interactions Using Metastable States from Multiple Independent Molecular Dynamics Simulations
Understanding aptamer–ligand interactions is necessary to rationally design aptamer-based systems. Commonly used in silico tools have proven to be accurate to predict RNA and DNA oligonucleotide tertiary structures. However, given the complexity of nucleic acids, the most thermodynamically stable conformation is not necessarily the one with the highest affinity for a specific ligand. Because many metastable states may coexist, it remains challenging to predict binding sites through molecular docking simulations using available computational pipelines. In this study, we used independent simulations to broaden the conformational diversity sampled from DNA initial models of distinct stability and assessed the binding affinity of selected metastable representative structures. Read More >
Disposable and low-cost pen-like sensor incorporating nucleic-acid amplification based lateral-flow assay for at-home tests of communicable pathogens
Highlights: A Fast, Low-cost, Aerosol-contamination-free, and Sensitive molecular assay for at-Home tests (FLASH). The lateral flow-based FLASH enabled Covid-19 testing achieving a sensitivity as low as 0.5 copies/μL. Complete accuracy in comparison to the qPCR in samples mimicking 11% of prevalence. A simplified sample-to-result workflow of FLASH with a total assay time in 20–30 min. Pen-like devices and the miniaturized FLASH platform readily for untrained user. Read More >
Highly Stretchable and Skin Adhesive Soft Bioelectronic Patch for Long-Term Ambulatory Electrocardiography Monitoring
Wearable devices offer a revolutionary approach to ambulatory electrocardiography (ECG) for cardiovascular disease diagnosis. Herein, an adhesive, highly stretchable and conformal (ASC) patch for long-term ambulatory ECG monitoring is presented. The ASC patch is designed with a “three-bridge” structure to provide inhomogeneous strain distribution during stretching. Meanwhile, the electrical stability is achieved by stretchable liquid metal interconnects at the domain experiencing larger strain. Read More >
Organic electrochemical transistor array for monitoring barrier integrity of epithelial cells invaded by nasopharyngeal carcinoma
Organic electrochemical transistor was used to distinguish epithelial/cancer cell types based on transconductance spectrums. Results showed that the novel nasopharyngeal cancer cells NPC43 demonstrated distinct morphology and invasive properties. Our OECT array was able to spatially map cancer/epithelial cell co-culture patterns based on 100-Hz transconductance. This multi-channel OECT array could be a complementary tool to optical imaging for studying cancer cell-cell interactions. Read More >