Convergence of nanotechnology and CRISPR-based diagnostics

Nature Nanotechnology | Volume 20 | October 2025 | 1365–1373 1365 nature nanotechnology https://doi.org/10.1038/s41565-025-02018-8Perspective Convergence of nanotechnology and CRISPR-based diagnostics Midori Johnston1, Schan Dissanayake-Perera2,3, James J. Collins 4,5,6, Molly M. Stevens2,3 & Can Dincer 1,7 In addition to its broad application in genome engineering and therapeutics, clustered regularly interspaced short palindromic repeats (CRISPR) technology provides field-deployable methods for the highly sensitive and selective detection of nucleic acids. From a diagnostic perspective, CRISPR-based assays hold clear clinical potential for identifying a range of both infectious and non-communicable diseases. In this Perspective we evaluate recent nanotechnologies and nanomaterials that have been engineered to interface with CRISPR systems on a nanoscale level to realize the full potential of this versatile diagnostic tool. We assess biomolecules such as enzymes and oligonucleotides, some of the more commonly used synthetic nanoparticles and detection platforms that integrate nanotechnologies in new and innovative ways. We discuss current trends and look ahead to future challenges and opportunities, including non-nucleic acid target detection, pre-amplification-free detection of nucleic acids, the development of wearable devices and integration with artificial intelligence workflows. In diagnostics, CRISPR–Cas systems consist of three functional components: the interchangeable CRISPR RNA (crRNA), the CRISPR-associated protein (Cas) and a reporter nucleic acid (Fig. 1d). The programmability and robust isothermal nuclease activity, as well as single-nucleotide specificity, have greatly accelerated the progress made within the field of CRISPR-based diagnostics (CRISPR-Dx). Companies such as Sherlock Biosciences and Mammoth Biosciences have successfully commercialized CRISPR-Dx. However, post-pandemic shifts in commercial viability 1 , growing interest in artificial intelligence (AI) and longer regulatory periods for in vitro diagnostics2 have made it harder for smaller ventures to bring their diagnostic products to market. In parallel to this rise in molecular diagnostics, the evolution of nanotechnology—and specifically the deployment of new nanomaterials in biosensing applications—has created a promising research area that has the potential to further augment CRISPR-Dx (Fig. 1a–c) and accelerate its integration into existing healthcare systems and deployment at the point of care3–5. Here we highlight recent advancements in biomolecular systems and synthetic nanoparticles (NPs) that address some of the main challenges currently faced by CRISPR-Dx and explore emerging technologies that may benefit the field. The convergence of nano (that is, the overlapping fields of nanomaterials and nanotechnology) and CRISPR-Dx, presents an exciting niche of research that has the potential to help establish CRISPR as a viable clinical tool in the future. Over the past few years, nanomate - rials have been applied to address the challenge of signal enhance - ment in CRISPR-Dx using novel catalytic, colorimetric and fluorescent Received: 10 June 2024 Accepted: 6 August 2025 Published online: 2 October 2025 Check for updates 1IMTEK–Department of Microsystems Engineering, University of Freiburg, Freiburg, Germany. 2Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, UK. 3Department of Physiology, Anatomy and Genetics, Department of Engineering Science, Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK. 4Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA. 5Institute of Medical Engineering & Science and Department of Biological Engineering, MIT, Cambridge, MA, USA. 6Broad Institute of MIT and Harvard, Cambridge, MA, USA. 7Institute of Biomedical Engineering–MIBE, Department of Electrical Engineering, TUM School of Computation, Information and Technology, Technical University of Munich, Munich, Germany. e-mail: [email protected]; [email protected] Nature Nanotechnology | Volume 20 | October 2025 | 1365–1373 1366 Perspective https://doi.org/10.1038/s41565-025-02018-8 Sample preparation Sample preparation for CRISPR detection is perhaps the most challenging part of the workflow due to the variability of available samples, but it is a common issue for most molecular diagnostic techniques. Conventional methods employ various chemical, physical and hybrid properties. We believe that this is just the tip of the iceberg in terms of the impact that nanotechnology can have on the field of CRISPR-Dx, and we anticipate that the future convergence of these fields will facilitate the development of powerful, field-deployable diagnostic devices that incorporate innovation at multiple size scales. Sample preparation Analyte detection Readout Substrate Product Chemical Phenol extraction Magnetic beads Column separation Chelating resins Target recognition Reporter cleavage Physical Hybrid Plate reader Paper-based assay Microfluidic device a d f e b c Cas proteins for CRISPR-Dx Guide Protein Target Catalytic Fluorescence Colorimetric dCas9 Cas9 Cas12 Cas13 ssDNA ssRNAssDNA/dsDNA Spectral multiplexing using tunableemission quantum nanomaterial readouts for high signal/noise ratios Detection from raw sample/ continuous monitoring (wearable device) Nano-aided sample preparation • Sample lysis • Improved separation Multi-analyte detection • Transcriptomic • Genomic • Proteomic • Metabolomic Quantitative nano-powered amplification cascade Hands-free fluid handling AI integration for spectral deconvolution, result interpretation and patient health trend analysis Decentralized and personalized medicine NanovesiclesNanotubes Enzymes Graphene Nanozymes UCNPs Er3+ Tm3+ MOFs Electrical Mechanical Optical Chemical Fig. 1 | Nanomaterials can be integrated at various points in the workflow of conventional CRISPR-Dx to improve performance and advance the technology towards decentralized medicine. a–c, The current workflow for conventional CRISPR-based nucleic acid detection starts with chemical, physical or a hybrid form of sample purification (a), followed by collateral trans-cleavage of (in most cases) a fluorescent reporter upon target recognition by the Cas effector (b) and the final optical or electrochemical readout (c). d, Cas orthologues used in CRISPR-Dx include deactivated Cas9 (dCas9) (mostly immobilized onto an electrode, causing a voltage shift upon target recognition) and Cas9, but Cas12a and Cas13a are more commonly used for their rapid, high-turnover trans-cleavage activity. dsDNA, double-stranded DNA; ssDNA, single-stranded DNA; ssRNA, single-stranded RNA. e, Various catalytically active nanomaterials and colorimetric/fluorescent nanomaterials have been reported to enhance the performance of conventional CRISPR-Dx with regard to signal generation, amplification or optical readout. MOFs, metal–organic frameworks; UCNPs, upconverting nanoparticles. f, Nanomaterials or nanotechnology can be implemented in almost every step of the CRISPR-Dx workflow, improving sample preparation, multiplexing capabilities, signal-to-noise ratios or the time to results towards decentralized and personalized medicine. Figure elements created with BioRender.com. Nature Nanotechnology | Volume 20 | October 2025 | 1365–1373 1367 Perspective https://doi.org/10.1038/s41565-025-02018-8 methods (Fig. 1a), but the uptake of nanomaterials to aid in nucleic acid release from samples has been limited. One ‘on-chip’ lysis method uses gold nanostructures to release nucleic acids via plasmonic heating 6 ; however, these types of innovation are sample-dependent. Nanomaterials may also enable more non-invasive sampling methods, as well as continuous, single-cell monitoring. New engineering approaches have enabled nucleic acid extraction via nanobiopsies 7 . Although not quite nanoscale, microneedles coated with graphene nanoflakes and functionalized with dCas9 have been explored for monitoring cell-free DNA 8 . High-surface-area nanomaterials such as carbon nanotubes functionalized with ssDNA9 have also been used for viral RNA extraction and shown increased assay sensitivity with a relatively low-cost procedure. The potential hazards and complexity involved in handling high-aspect-ratio nanomaterials may, however, limit the clinical and commercial viability of such platforms. One notable trend in many CRISPR assays is the use of magnetic beads for either nucleic acid target capture or the removal of excess signal-generating species, yet little research addresses their improvement. Many assays use commercial products such as DynaBeads (ThermoFisher) or Sera-Mag SpeedBeads (Cytiva), which are well estab - lished for enrichment applications. Developing nanoscale magnetic beads with improved separation efficiency could substantially improve future nanomaterial-based CRISPR assays, as well as in vitro diagnostics more generally. Analyte detection The versatility of CRISPR-Dx now extends beyond just classic RNA/DNA detection. By combining relatively well-characterized ‘programmable nuclease’ behaviour with additional biomolecular transduction steps and amplification, it is possible to detect a wider range of molecular targets at increasingly higher levels of sensitivity. Biomolecular enhancement CRISPR-triggerable amplification cascades. Beyond capturing oligonucleotides, the collateral cleavage activity of Cas effectors can be harnessed to trigger cascade reactions and increase sensitivity in more complex systems. In combination with deoxynucleotidyl transferase (TdT), LbCas12a-mediated cleavage of ssDNA reporters was used in a scaffolding step to form copper NPs in a one-pot reaction10. Another study employed Cas9 to capture and cleave short dsDNA strands, which were subsequently T7-amplified and extended by Klenow (exo-) polymerase 11 . SpyCas9 (alongside Klenow fragments and ssDNA binding protein TP32) was also used in isothermal strand displacement amplification, a technique that could potentially outperform PCR12. The collateral cleavage activity of Cas13a was also employed in a modular cascade to release HaloTag-tobacco etch virus protease and TCS-bound mCherry from an agarose matrix13. The utility of cascade reactions triggered by Cas cleavage is debatable when compared with conventional amplification strategies owing to their increased complexity and a higher risk of false positives from non-specific effector activation. Non-nucleic acid target detection. Despite evolving primarily as an RNA/DNA targeting platform, CRISPR and CRISPR-Dx can also be combined with new biomolecular entities to detect non-nucleic acids via various ‘primer release’ strategies. Although the final readout may remain nucleic acid-based, the ability to activate CRISPR orthologues using alternative analytes offers promising multiplexing potential. Most prominently, collateral trans-cleavage of activated Cas proteins has been combined with nucleic acid aptamers. As CRISPR effectors cannot directly detect non-nucleic acid targets, aptamers serve as activators, blockers, anchors or target recognition elements for analyte detection 14 . One study used a duplexed aptamer, consisting of an activator (dsDNA) and a complementary blocker (ssDNA), for adenosine detection. Upon target binding, the blocker dissociates and Cas12a is activated, cleaving a fluorescent reporter 15 . Similarly, an activator/recognizer duplex for the detection of epithelial cell adhesion molecules on circulating breast cancer cells was coupled with visualization via fluorescence resonance energy transfer (FRET)16. DNAzymes, a class of nucleic acid-based nanocatalyst (discussed later), were used in conjunction with Cas12a to detect lead ions. Following the capture of the ion, the DNAzyme releases a short ssDNA strand that activates the Cas effector, triggering reporter cleavage17. A similar method was used to detect aflatoxin B1 (AFB1), although here Cas12a cleaved a G-rich four-stranded oligonucleotide with bound haemin (G4-DNAzyme). In the absence of the analyte trigger, the G4-DNAzyme catalyses 3,3′,5,5′-tetramethylbenzidine (TMB) oxidation, leading to a colorimetric output18. Another approach uses protease-activated or cleavable peptides coupled to nanocarriers to release synthetic DNA barcodes in a disease-specific manner. Cas12 is then used to capture these barcodes and, in the process, cleave a ssDNA reporter, producing a fluorescent signal19,20. Physical enhancement by nanoconfinement In addition to biomolecular methods for enhancing analyte detection, several nanoengineering strategies have emerged to address key limitations of CRISPR-Dx. Nucleic acid-pre-amplification is a substantial challenge in CRISPR-Dx that influences the assay complexity, sensitivity, cost and time to results. Although isothermal methods (such as recombinase polymerase amplification and loop-mediated isothermal amplification) bypass thermocyclers, recent studies have explored bioinspired confinement effects (Fig. 2a) to locally increase reagent concentrations and improve detection kinetics. The Combinatorial Array Reactions for Multiplexed Evaluation of Nucleic acids (CARMEN) platform implements on-device fusion of CRISPR reagent vesicles to multiplex assays for the clinical detection of SARS-CoV-2 and other respiratory viruses (Fig. 2b) 21 . Its latest version includes microfluidic mixing to reduce the time to results and improve accessibility. Similarly, an ultralocalized Cas13a-powered assay with picolitre-sized droplets achieved single-molecule miRNA detection in a one-step, isothermal reaction22. Assay sensitivity was improved more than 10,000-fold, moving towards digital, single-molecule quantification. While such confinement approaches present promising platforms for multiplexing and signal enhancement, the droplet sizes used are not yet strictly nanoscale. Hypothetical versions of these assays using nanodroplets to confine single enzymes could further enhance their performance. In practice, these assays are still limited by considerations such as reagent housing and device portability. Another approach to circumvent diffusion limitations uses optothermal nanotweezers to trap the AuNP-conjugated reporter, Cas effectors and crRNA while simultaneously heating to 37 °C, thereby accelerating kinetics (Fig. 2c) 23 . The principle of local confinement was used to achieve an impressive improvement over conventional CRISPR-based sensing. Although the infrastructure and overhead costs associated with the instrumentation required to carry out this type of confinement are a limiting factor, it does highlight the potential improvement that can be made by non-destructively manipulating the CRISPR components. A different local confinement strategy concentrates FAM-labelled reporters and anchored crRNA–Cas12a complexes onto 20-nm AuNPs, forming ‘CRISPR nanorobots’ with reduced distances between the enzyme and substrate (Fig. 2b). Owing to the high local concentration of reagents, this system can be used with markedly lower concentra - tions of Mg2+ cofactors, while also mitigating diffusion limitations24. Readout Colorimetric readouts The colloidal stability of AuNPs has enabled aggregation-based assays in which Cas effector activation produces a colour change (Fig. 1e). Nature Nanotechnology | Volume 20 | October 2025 | 1365–1373 1368 Perspective https://doi.org/10.1038/s41565-025-02018-8 One such system involves the trans-cleavage of DNA or RNA hybridization linkers that result in functionalized AuNPs remaining physically separated, thus retaining their characteristic red colour (as opposed to the blue colour they adopt upon hybridization and aggregation 25 ). The CRISPR/CAS-based Colorimetric nucleic Acid DEtection (CASCADE) platform takes a reverse approach: AuNPs are initially stabilized with ssRNA 26 and trans-cleavage induces a ‘crashing-out’ effect, causing a colour change and achieving attomolar sensitivity when combined with isothermal amplification. The versatility of AuNPs has facilitated the rapid development of lateral flow assays during the COVID-19 pandemic27 and for diseases that disproportionately affect developing countries28. e– Sample preparation Analyte detection Readout Micrometre Nanometre a b c Nano-approach Nano-approach Nano-approach Nano-aided cell interfacing Physical nanosorption Nanocatalysts Nano-composite fluorescence Electrochemical detection Biomolecular systems • DNA displacement/ hybridization reaction • Secondary enzymes • In situ nanoparticle formation Confinement approaches Conjugated polymer Synthetic: MOF/nanoclusters Pt GOx 6–8 nm 4–5 nm HRP Mn Ce Single atoms Organic: Dye/DNA template OECTs (2D) Nanopore (1D) NIE + DNA hydrogel (3D) Graphene MXene Droplet Optics Nanoparticle/ nanorobots Enzymes Nanozymes Photothermal localized heating effect Nanowire/needle-based single-cell sampling Increased surface area for sample capture Lower mass = faster separation High-aspect-ratio nanomaterial ssDNA anchor Surface coating/functionalization for higher, more specific yield and improved colloidal stability Capture Elution Non-nucleic acid detection using CRISPR Aptamer binding Protease cleavage RNA/DNAzyme CRISPR-mediated reporter cleavage CRISPR trigger Nanopowered cascade Substrate Pb Fig. 2 | Nano-aided mitigation strategies that address challenges in sample preparation, analyte detection and signal readout of conventional CRISPRDx. a, Sample preparation. To access genetic material in bacteria or other cells, techniques for mechanical lysis (such as nanospikes and localized heating) facilitated by gold nanoparticles (AuNPs) have been employed. The preparation of complex sample matrices can be performed using high-aspectratio materials such as single-walled carbon nanotubes, but functionalized magnetic beads are more commonly used. Nanometre-sized beads offer better performance than larger ones due to their increased surface area and lower mass. b, Analyte detection. Cas proteins are primarily used for the detection of nucleic acid targets, but can also be used to trigger secondary reactions for signal amplification or readout of more complex systems. Approaches to improve detection kinetics by increasing the local concentration of reagents include the confinement of reaction components into droplets or onto the surfaces of NPs and the use of optothermal nanotweezers. c, Readout. Whereas enzymes such as glucose oxidase (GOx) or Horseradish peroxidase (HRP) provide established methods for signal amplification as well as electrochemical/colorimetric readout in combination with CRISPR-Dx, nanozymes present a synthetic, scalable, highturnover alternative. One strategy to enhance fluorescence intensity, specifically in CRISPR-based assays, is to combine porous MOFs with dsDNA-caged fluorescein that is released by Cas12 trans-cleavage activity followed by magnetic separation and strand displacement. 2D materials, such as graphene and MXenes (a family of metal carbides/nitrides) or conjugated polymers, are used as substrates for immobilizing reaction components and for electrochemical readout with OECTs. Other electrochemical methods that have been used in tandem with CRISPR include nanopore sequencing (1D) and nano-impact electrochemistry (NIE), for which the reaction components are cross-linked into a DNA hydrogel (3D). OECTs, organic electrochemical transistors. Figure elements created with BioRender.com. Nature Nanotechnology | Volume 20 | October 2025 | 1365–1373 1369 Perspective https://doi.org/10.1038/s41565-025-02018-8 Catalytic readouts Enzymes. Enzymes, by virtue of being multiple-turnover biomolecules, are often used for signal generation as well as amplification in electrochemical or colorimetric readouts. HRP is often paired with tetramethylbenzidine29–31, whereas GOx is used with 3,3′-diaminobenzidine (ref. 32) or to catalyse the oxidation of glucose, generating hydrogen peroxide for downstream electrochemical detection. In this instance, multiplexed microfluidic chips have used GOx to enable pre-amplification-free detection of miRNAs in the femtomolar range 33 . HRP has also been integrated into chemiluminescence resonance energy transfer systems on AuNPs, where Cas13a cleaves an RNA linker, releasing HRP to produce a chemiluminescent optical readout after the addition of luminol34. Although enzymes are tried-and-true staples of signal generation in various methodologies, they are limited with respect to long-term stability, scalability and cost. Synthetic, high-turnover nanomolecules could present a viable alternative. Nanozymes. Nanozymes are a class of metalor metal oxide-based NP and fulfil the functions of biological enzymes while retaining the versatility and robustness of synthetic NPs35. Alongside their functional surface chemistry, these characteristics make nanozymes broadly deployable for signal generation and amplification in CRISPR-Dx, especially in non-laboratory settings. One such platform, termed CrisprZyme, uses streptavidinfunctionalized platinum core–shell NPs in combination with a Cas13a detection system. These nanozymes bind to a biotin-labelled reporter and catalyse the ‘post’ amplification of the initial immunosorbent signal, allowing clinically relevant sensitivities to be achieved in a colorimetric assay without the need for target pre-amplification 36 . More recently, a dual-mode assay using cerium dioxide (CeO2), a phosphatase-mimicking nanozyme and Cas12a was reported37. The hydrolysed nucleotide products released by Cas12a collateral cleavage are further broken down by the nanozymes, releasing phosphate and hydroxide free radicals, which oxidize TMB downstream, producing a colorimetric signal alongside the fluorescent signal produced in the initial Cas12a reaction. Synthetic nanozymes are also susceptible to batch-to-batch variability, but this that can be minimized when scaled up industrially. Challenges in reproducibility are common to all forms of enzyme-based diagnostic, not just CRISPR-Dx. While these challenges persist, there is motivation to incorporate more synthetic elements (such as nanomaterials) into assay workflows. Nanocomposite fluorescent systems Small-molecule dyes are typically used to generate fluorescence in CRISPR assays, but synthetic NP systems have been proposed to enhance brightness, improve sensitivity and overcome issues such as photobleaching and other detrimental environmental effects. In the development of CRISPR-responsive fluorescent NPs, successful efforts have often involved the combination of synthetic and organic materials. One strategy uses porous MOFs loaded with Cy5 to create highly concentrated fluorescent NPs. Following Cas12 activation, these MOFs release their cargo, producing a pre-amplification-free quantitative readout, detecting circulating tumour DNA from liquid biopsies 38 . Similarly, DNA-templated silver nanoclusters show promise in FRET-incompatible applications39. AuNPs can also be used as fluorescence quenchers and, due to the ease of surface functionalization using thiol chemistry, have been demonstrated to enhance the stability of small-molecule reporters immobilized on their surfaces 40 . AuNP-based nanobeacons with surface-bound hairpin assemblies have been used to detect miRNAs within the femtomolar range from human serum samples41. Quantum dots offer high quantum yield, photostability and multiplexable emission. An interesting example of their application in CRISPR-Dx involves the conjugation of ZnS-coated quantum dots with nucleic acid hairpins using peptide nucleic acid stems42. Quantum dots have also demonstrated their versatility in a Cas13a lateral flow assay targeting the SARS-CoV-2 S gene, in which quantum dot-containing microspheres were used to generate contrast43. More recently, streptavidin-coated quantum dots were used 16 to design a multi-step aptamer assay to measure traces of circulating tumour cells in human blood. UCNPs are another class of fluorescent nanomaterial. Their ability to ‘combine’ two or more incident photons into one higher-energy fluorescent emission is particularly useful in producing a readout with low background autofluorescence, thus improving the signal-to-noise ratios of bioassays. Many studies use broad-spectrum-absorbing NaYF 4 core–shell NPs with a variety of surface coatings such as polyacrylic acid 44 to enable the surface conjugation of a short CRISPR-responsive nucleic acid sequence. UCNPs have also been designed with dual functionality in mind; for example, combining them with magnetic NPs enables in situ sample matrix purification 45 . NaYF 4 -based UCNPs have also been applied to deliver photo-initiated in vivo biosensing platforms. Electrochemical detection Nanopores. Nanopores use nucleotide-specific electrical signatures to sequence nucleic acids passing through nanopores in an electrically insulated membrane. A key example combining nanopore sequencing with CRISPR is short tandem repeat identification, quantification, and evaluation (STRIque). This method uses Cas12 and Cas9 to enrich genetic targets by inserting identifiable overhang sequences for nanopore recognition46. STRIque ensures that only targets cleaved by the CRISPR enzymes are sequenced by downstream nanopore analysis, W e a r a b l e s / i n - v i v o m o n i t o r i n g High signal-to -noise-ratio output Lower-toxicity materials to de-risk wearables Needle-based biosensors for in vivo sensing Resettable CRISPR for continuous monitoring Safe, low-intensity excitation Low-volume automated liquid handling AI-assisted CRISPR guide design Signal deconvolution UCNPs Nanodiamonds Quantum dots Carbon meta materials Q u a n t u m s y s t e m s w i t h t u n a b l e e m i s s i o n D e v i c e e n g i n e e r i n g a n d A I i n t e g r a t i o n W e a r a b l e s / i n v i v o m o n i t o r i n g Fig. 3 | An integrated future device combining CRISPR-Dx with nanomaterials and/or nanotechnology would ideally employ quantum systems for multiplexing as well as AI for data evaluation. An integrated wearable device or monitoring application that combines emerging nanotechnologies or nanomaterials with CRISPR-Dx would need to enable the delivery of robust CRISPR assays on biocompatible or biodegradable materials. The implementation of quantum systems with tunable emission peaks would ease orthogonal multiplexing, lower the energy consumption for signal generation and offer superior performance to conventional fluorescence readouts in terms of signal-to-noise ratios. Sample volumes, as well as user intervention, would be kept to a minimum, and readout and data interpretation could be performed by AI. Figure elements created with BioRender.com. Nature Nanotechnology | Volume 20 | October 2025 | 1365–1373 1370 Perspective https://doi.org/10.1038/s41565-025-02018-8 boosting the resultant signal-to-noise ratio. Similar Cas9 enrichment techniques have also been used to sequence complex genomic features such as single-nucleotide and structural variations47 and mobile element insertions48. Overall, CRISPR—particularly Cas9—serves as a powerful tool for improving the efficiency and cost-effectiveness of nanopore-based sequencing by opening up difficult-to-reach regions of the human genome. Transistor-based systems. Many modern electrochemical sensors rely on organic electrochemical transistor or field-effect transistor technologies, which detect molecular changes across a two-dimensional (2D) conductive surface. The properties of the surface will ultimately influence sensor sensitivity, encouraging the implementation of novel nanomaterials such as conjugated polymers and 2D nanomaterials. Graphene, a well-characterized electroactive 2D material, has already inspired several CRISPR-Dx assays. For instance, graphene-based photoelectrochemical systems and quantum dots, in combination with immobilized Cas, have enabled the label-free detection of miRNAs49. In these detection systems, target recognition by Cas13a50, Cas12a51 or Cas952 facilitates a readout via voltage shifts, enhanced by the high electrical conductivity of graphene. Beyond graphene, 2D materials such as MXenes, chemically stable metal carbides, have also recently entered the CRISPR-Dx field. Cas12a has been paired with MXenes to detect endotoxins, bacteria53, AFB1 18 and nucleic acids 54 . MXenes offer complete metal atomic layers alongside large hydroxyl-terminated surfaces for ssRNA/ssDNA immobilization and visible light absorption that quench fluorescence. These properties, especially their ability to strongly bind ssDNA, make MXenes very promising for applications in CRISPR-Dx. Nano-impact electrochemistry. Approaching electrochemistry from a different angle, and introducing another dimension, a recent study reported the use of nano-impact electrochemistry in combination with a CRISPR-responsive DNA hydrogel (embedded within AgNPs), strand displacement amplification and catalytic hairpin assembly55. Upon target recognition, Cas12a cleaves the DNA within the 3D nanostructure and thus causes a phase shift from a gel to a solid matrix, with the released AgNPs oxidizing at the electrode. The development of new CRISPR-responsive, nanostructured 3D materials could have numerous applications, not just in CRISPR-Dx but also in therapeutics and beyond. Outlook An oft-cited advantage of CRISPR-Dx is the theoretical suitability of the platform for point-of-care applications. However, several challenges must be addressed before it can become a gold standard for diagnostics. While many strategies are emerging to resolve these issues, particularly those leveraging nanomaterials and nanotechnology (Fig. 3), additional Table 1 | Overview of recent studies combining CRISPR-Dx with nanomaterials Nano component Effector Targets Function Readout Time to results Sensitivity Reference Sample preparation Carbon nanotubes N/A SARS-CoV-2 RNA RNA capture RT-qPCR ~30 min 6.4 copies per µl 10 Analyte detection ssDNA Cas9 DNA Scaffold Optical 1.5 h 2.5 aM 13 DNA duplex Cas12a Adenosine Target detection/ Cas activation Optical 7 min 15.67 nM 16 DNAzyme Cas12a Lead ions Capture Optical N/A 0.48 nM 18 Microfluidics Cas12a Cas13a Viral RNA Scale-up Optical <5 h 500 copies per μl 22 Optothermal nanotweezers Cas12a Viral ssDNA Manipulation Optical 2 min 25 aM 24 CRISPR nanorobots Cas12a miRNA Confinement Optical N/A N/A 25 Readout AuNPs Cas12a Cas13a dsDNA viral DNA miRNA Colorimetry Optical 1 h 200 genome copies per l 26 AuNPs Cas12a miRNA viral RNA Substrate Optical <40 min 10 fM 28 HRP-oligonucleotides on microbeads Cas13a and Cas12a SARS-CoV-2 RNA and ATP Colorimetry Optical < 1 h 10 fM 32 GOx Cas13a SARS-CoV-2 RNA Glucose to H2O2 conversion Electrochemical 30 min 2,000 copies per µl 34 Platinum-shell AuNPs Cas13a Non-coding RNA Colorimetry Optical 4.5 h 4.72 pM 37 DNA-templated Ag nanoclusters Cas12a cDNA Reporter Optical 1 h 1.19 pM 40 Quantum dots Cas12a Cas13a RNA: Yersinia pestis DNA: synthetic target Reporter Optical 1 h DNA: 40 pM RNA: 100 pM 43 MUCNP Cas13a miRNA Upconversion Optical N/A 83.2 fM 46 gFET dCas9 Genomic DNA Electrode Electronic 3.5 h 6.3 fM 53 AgNPs Cas12a miRNA Substrate Electrochemical 3.5 h 4.21 aM 56 The focus here is on nanomaterials and their respective functions within the systems, Cas orthologues, targeted analytes and readout strategies, as well as specific features. cDNA, circular DNA; MUCNP, magnetic-upconversion nanoparticle; gFET, graphene field effect transistor; HRP-oligonucleotide, horseradish peroxidase oligonucleotide; RT-qPCR, reverse transcription quantitative polymerase chain reaction. Nature Nanotechnology | Volume 20 | October 2025 | 1365–1373 1371 Perspective https://doi.org/10.1038/s41565-025-02018-8 innovation is still needed to bridge the gaps between CRISPR-Dx, nanotechnology and established clinical workflows. Newly developed optically active nanomaterials, such as UCNPs and quantum dots, offer emission tunability and enhanced signal-to-noise ratios for in vitro diagnostics. These materials could synergize well with CRISPR-Dx, especially in the design of orthogonally multiplexed assays (Fig. 1f). However, their dependence on bulky optical instrumentation limits their suitability to be deployed in lower-resource settings such as field clinics. Devices such as the handheld FluorPen FP 11 or benchtop Quidel Sofia 2 Fluorescence Immunoassay Analyzer show promise, but further miniaturization and automation—particularly with respect to nanofluidic handling—are critical for real-world CRISPR-Dx applications. More transparency and discussions between device manufacturers and wet-laboratory researchers would be beneficial for the field, ensuring that research is performed with applications in mind. Paper-based lateral flow CRISPR readouts, while portable, often compromise on sensitivity, thus leaving room for improvement in terms of reaction kinetics. Advanced fluid-handling techniques such as optothermal tweezers could improve kinetics by addressing diffusion limitations. As these technologies become more affordable, they may enter clinical use, reducing the performance gap between CRISPR-Dx and PCR. Wearable diagnostics integrating nanomaterials are also gaining interest 56 . The integration of CRISPR tools into face masks 57 is a creative approach to non-invasive wearables; however, these are currently restricted to a single measurement. As the field of nanoscience advances, we predict an increase in research on non-toxic nanomaterials, as biocompatibility will increasingly become a priority 58 , and we anticipate that a strategy to implement continuous monitoring using a form of resettable CRISPR would be a worthwhile application to pursue, inspired by recent developments in active-reset protein sensors 59 . The need to consider multiple factors, such as sample type, environment, resource availability and affordability, depending on the application means that there is no single solution to design the ideal assay (Table 1). For CRISPR-Dx to fulfil the niche of at-home or low-resource testing, we imagine that a fully integrated device (including sample purification and a strategy to enhance sensitivity) would need to have minimal requirements for user intervention, potentially even offer on-device fluid manipulation and produce an optical signal that is readable by the naked eye. Integrating novel biomolecular transduction steps into the assay workflow would not only extend the range of detectable analytes, but also enable alternative readout strategies. Where these limiting factors do not apply (that is, in laboratorybased settings), sensitivity does not need to be sacrificed for ease of handling. In such settings a digital readout (for instance, electrochemical) could be integrated into AI workflows to facilitate assay fine-tuning (for example, by improving selectivity and sensitivity of in silico designed CRISPR guides) and the interpretation of the results, particularly where orthogonal multiplexing has been implemented in complex devices60,61. CRISPR-Dx and in vitro nanomaterials have evolved in parallel over the past decade and are now converging, enabling new signal amplification and readout mechanisms that have the potential to reduce the time to results, improve sensitivity and integrate sample preparation into a new generation of assays62. 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Acknowledgements M.J. and C.D. would like to thank the Bundesministerium für Bildung und Forschung (BMBF, Federal Ministry of Education and Research) and the European Union’s Horizon Europe’s research and innovation programme for partially funding this work under grant numbers 13GW0493 (MERGE) and 101079473 (OrChESTRA). M.M.S. was supported by the Department of Science, Innovation and Technology (DSIT) and the Royal Academy of Engineering under the Chair in Emerging Technologies programme (CiET2021\94) and the Oxford-Berlin research partnership. J.J.C. was supported by a grant from Good Ventures. Competing interests J.J.C. was a co-founder and board member of Sherlock Biosciences, which was focused on developing CRISPR-based diagnostics and recently acquired by Orasure. M.M.S. has invested in, consults for (or was on scientific advisory boards or boards of directors) and conducts sponsored research funded by companies related to the biomaterials field; and has filed patent applications related to nanocatalysts for biosensing. M.M.S. and S.D-P. have filed a patent application (patent no. US20250092459 - US only) on nanozyme-catalysed detection. M.J. and C.D. declare no competing interests. Additional information Correspondence should be addressed to Molly M. Stevens or Can Dincer. Peer review information Nature Nanotechnology thanks Fei Deng and Devleena Samanta for their contribution to the peer review of this work. Reprints and permissions information is available at www.nature.com/reprints. Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. 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