Amplification-free detection of SARS-CoV-2 with CRISPR-Cas13a and mobile phone microscopy.

The December 2019 outbreak of a novel respiratory virus, SARS-CoV-2, has become an ongoing global pandemic due in part to the challenge of identifying symptomatic, asymptomatic, and pre-symptomatic carriers of the virus. CRISPR diagnostics can augment gold-standard PCR-based testing if they can be made rapid, portable, and accurate. Here, we report the development of an amplification-free CRISPR-Cas13a assay for direct detection of SARS-CoV-2 from nasal swab RNA that can be read with a mobile phone microscope. The assay achieved ∼100 copies/µL sensitivity in under 30 min of measurement time and accurately detected pre-extracted RNA from a set of positive clinical samples in under 5 min. We combined crRNAs targeting SARS-CoV-2 RNA to improve sensitivity and specificity and directly quantified viral load using enzyme kinetics. Integrated with a reader device based on a mobile phone, this assay has the potential to enable rapid, low-cost, point-of-care screening for SARS-CoV-2.

Accelerated RNA detection using tandem CRISPR nucleases.

Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided RNA recognition that triggers cleavage and release of a fluorescent reporter molecule, but long reaction times hamper their detection sensitivity and speed. Here, we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 molecules per µl of RNA in 20 min. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA extracted from respiratory swab samples with quantitative reverse transcriptase PCR (qRT-PCR)-derived cycle threshold (Ct) values up to 33, using a compact detector. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables sensitive, direct RNA detection in a format that is amenable to point-of-care infection diagnosis as well as to a wide range of other diagnostic or research applications.

Multifunctional plasmonic film for recording near-field optical intensity.

We demonstrate the plasmonic equivalent of photographic film for recording optical intensity in the near field. The plasmonic structure is based on gold bowtie nanoantenna arrays fabricated on SiO2 pillars. We show that it can be employed for direct laser writing of image data or recording the polarization structure of optical vector beams. Scanning electron micrographs reveal a careful sculpting of the radius of curvature and height of the triangles composing the illuminated nanoantennas, as a result of plasmonic heating, that permits spatial tunability of the resonance response of the nanoantennas without sacrificing their geometric integrity. In contrast to other memory-dedicated approaches using Au nanorods embedded in a matrix medium, plasmonic film can be used in multiple application domains. To demonstrate this functionality, we utilize the structures as plasmonic optical tweezers and show sequestering of SiO2 microparticles into optically written channels formed between exposed sections of the film. The plasmonic film offers interesting possibilities for photonic applications including optofluidic channels "without walls," in situ tailorable biochemical sensing assays, and near-field particle manipulation and sorting.

Rapid detection of SARS-CoV-2 RNA in saliva via Cas13.

Rapid nucleic acid testing is central to infectious disease surveillance. Here, we report an assay for rapid COVID-19 testing and its implementation in a prototype microfluidic device. The assay, which we named DISCoVER (for diagnostics with coronavirus enzymatic reporting), involves extraction-free sample lysis via shelf-stable and low-cost reagents, multiplexed isothermal RNA amplification followed by T7 transcription, and Cas13-mediated cleavage of a quenched fluorophore. The device consists of a single-use gravity-driven microfluidic cartridge inserted into a compact instrument for automated running of the assay and readout of fluorescence within 60 min. DISCoVER can detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in saliva with a sensitivity of 40 copies µl-1, and was 94% sensitive and 100% specific when validated (against quantitative PCR) using total RNA extracted from 63 nasal-swab samples (33 SARS-CoV-2-positive, with cycle-threshold values of 13-35). The device correctly identified all tested clinical saliva samples (10 SARS-CoV-2-positive out of 13, with cycle-threshold values of 23-31). Rapid point-of-care nucleic acid testing may broaden the use of molecular diagnostics.

Rapid, point-of-care molecular diagnostics with Cas13.

Rapid nucleic acid testing is a critical component of a robust infrastructure for increased disease surveillance. Here, we report a microfluidic platform for point-of-care, CRISPR-based molecular diagnostics. We first developed a nucleic acid test which pairs distinct mechanisms of DNA and RNA amplification optimized for high sensitivity and rapid kinetics, linked to Cas13 detection for specificity. We combined this workflow with an extraction-free sample lysis protocol using shelf-stable reagents that are widely available at low cost, and a multiplexed human gene control for calling negative test results. As a proof-of-concept, we demonstrate sensitivity down to 40 copies/µL of SARS-CoV-2 in unextracted saliva within 35 minutes, and validated the test on total RNA extracted from patient nasal swabs with a range of qPCR Ct values from 13-35. To enable sample-to-answer testing, we integrated this diagnostic reaction with a single-use, gravity-driven microfluidic cartridge followed by real-time fluorescent detection in a compact companion instrument. We envision this approach for Diagnostics with Coronavirus Enzymatic Reporting (DISCoVER) will incentivize frequent, fast, and easy testing.

Accelerated RNA detection using tandem CRISPR nucleases.

Direct, amplification-free detection of RNA has the potential to transform molecular diagnostics by enabling simple on-site analysis of human or environmental samples. CRISPR-Cas nucleases offer programmable RNA-guided recognition of RNA that triggers cleavage and release of a fluorescent reporter molecule1,2, but long reaction times hamper sensitivity and speed when applied to point-of-care testing. Here we show that unrelated CRISPR nucleases can be deployed in tandem to provide both direct RNA sensing and rapid signal generation, thus enabling robust detection of ~30 RNA copies/microliter in 20 minutes. Combining RNA-guided Cas13 and Csm6 with a chemically stabilized activator creates a one-step assay that detected SARS-CoV-2 RNA from nasopharyngeal samples with PCR-derived Ct values up to 29 in microfluidic chips, using a compact imaging system. This Fast Integrated Nuclease Detection In Tandem (FIND-IT) approach enables direct RNA detection in a format amenable to point-of-care infection diagnosis, as well as to a wide range of other diagnostic or research applications.

Highly sensitive and label-free digital detection of whole cell E. coli with Interferometric Reflectance Imaging.

Bacterial infectious diseases are a major threat to human health. Timely and sensitive pathogenic bacteria detection is crucial in bacterial contaminations identification and preventing the spread of infectious diseases. Due to limitations of conventional bacteria detection techniques there have been concerted research efforts towards developing new biosensors. Biosensors offering label-free, whole bacteria detection are highly desirable over those relying on label-based or pathogenic molecular components detection. The major advantage is eliminating the additional time and cost required for labeling or extracting the desired bacterial components. Here, we demonstrate rapid, sensitive and label-free Escherichia coli (E. coli) detection utilizing interferometric reflectance imaging enhancement allowing visualizing individual pathogens captured on the surface. Enabled by our ability to count individual bacteria on a large sensor surface, we demonstrate an extrapolated limit of detection of 2.2 CFU/ml from experimental data in buffer solution with no sample preparation. To the best of our knowledge, this level of sensitivity for whole E. coli detection is unprecedented in label-free biosensing. The specificity of our biosensor is validated by comparing the response to target bacteria E. coli and non-target bacteria S. aureus, K. pneumonia and P. aeruginosa. The biosensor's performance in tap water proves that its detection capability is unaffected by the sample complexity. Furthermore, our sensor platform provides high optical magnification imaging and thus validation of recorded detection events as the target bacteria based on morphological characterization. Therefore, our sensitive and label-free detection method offers new perspectives for direct bacterial detection in real matrices and clinical samples.

Dynamic susceptibility evidence of surface spin freezing in ultrafine NiFe2O4 nanoparticles.

We investigated the dynamic behavior of ultrafine NiFe2O4 nanoparticles (average size D = 3.5 nm) that exhibit anomalous low temperature magnetic properties such as low saturation magnetization and high-field irreversibility in both M(H) and ZFC-FC processes. Besides the expected blocking of the superspin, observed at T1 approximately 45 K, the system undergoes a magnetic transition at T2 approximately 6 K. For the latter, frequency- and temperature-resolved dynamic susceptibility data reveal characteristics that are unambiguously related to collective spin freezing: the relative variation (per frequency decade) of the in-phase susceptibility peak temperature is approximately 0.025, critical dynamics analysis yields an exponent znu = 9.6 and a zero-field freezing temperature T(F) = 5.8 K, and, in a magnetic field, T(F)(H) is excellently described by the de Almeida-Thouless line delta T(F) = 1 - T(F)(H)/T(F) alpha H(2/3). Moreover, out-of-phase susceptibility versus temperature datasets collected at different frequencies collapse on a universal dynamic scaling curve. All these observations indicate the existence of a spin-glass-like surface layer that surrounds the superparamagnetic core and undergoes a transition to a frozen state upon cooling below 5.8 K.

Towards do-it-yourself planar optical components using plasmon-assisted etching.

In recent years, the push to foster increased technological innovation and basic scientific and engineering interest from the broadest sectors of society has helped to accelerate the development of do-it-yourself (DIY) components, particularly those related to low-cost microcontroller boards. The attraction with DIY kits is the simplification of the intervening steps going from basic design to fabrication, albeit typically at the expense of quality. We present herein plasmon-assisted etching as an approach to extend the DIY theme to optics, specifically the table-top fabrication of planar optical components. By operating in the design space between metasurfaces and traditional flat optical components, we employ arrays of Au pillar-supported bowtie nanoantennas as a template structure. To demonstrate, we fabricate a Fresnel zone plate, diffraction grating and holographic mode converter--all using the same template. Applications to nanotweezers and fabricating heterogeneous nanoantennas are also shown.

Plasmon-assisted audio recording.

We present the first demonstration of the recording of optically encoded audio onto a plasmonic nanostructure. Analogous to the "optical sound" approach used in the early twentieth century to store sound on photographic film, we show that arrays of gold, pillar-supported bowtie nanoantennas could be used in a similar fashion to store sound information that is transferred via an amplitude modulated optical signal to the near field of an optical microscope. Retrieval of the audio information is achieved using standard imaging optics. We demonstrate that the sound information can be stored either as time-varying waveforms or in the frequency domain as the corresponding amplitude and phase spectra. A "plasmonic musical keyboard" comprising of 8 basic musical notes is constructed and used to play a short song. For comparison, we employ the correlation coefficient, which reveals that original and retrieved sound files are similar with maximum and minimum values of 0.995 and 0.342, respectively. We also show that the pBNAs could be used for basic signal processing by ablating unwanted frequency components on the nanostructure thereby enabling physical notch filtering of these components. Our work introduces a new application domain for plasmonic nanoantennas and experimentally verifies their potential for information processing.

Reconfigurable nanoantennas using electron-beam manipulation.

Plasmonic nanoantennas have been of increasing interest due to their ability to confine and enhance electric fields in deep sub-wavelength volumes, leading to large near-field optical forces and high refractive index sensitivity. Recently, to enhance the response for sensor applications, metal nanoantennas have been fabricated on pillars. An overlooked consequence of this elevated geometry is the introduction of the mechanical properties, for example, stiffness, as a tunable degree of freedom. Here we demonstrate pillar-bowtie nanoantenna arrays, fabricated on optically transparent SiO2, as a candidate system that couples intrinsic mechanical and electromagnetic degrees of freedom via gradient forces. We show that using a standard scanning electron microscope, individual nanoantenna gap sizes can be controllably tuned down to 5 nm, a factor of ~4 × smaller than what is currently achievable using conventional electron-beam lithography. This approach opens new avenues for fabricating reconfigurable nanoantennas that can inform exciting photonic applications.

Understanding and controlling plasmon-induced convection.

The heat generation and fluid convection induced by plasmonic nanostructures is attractive for optofluidic applications. However, previously published theoretical studies predict only nanometre per second fluid velocities that are inadequate for microscale mass transport. Here we show both theoretically and experimentally that an array of plasmonic nanoantennas coupled to an optically absorptive indium-tin-oxide (ITO) substrate can generate >micrometre per second fluid convection. Crucially, the ITO distributes thermal energy created by the nanoantennas generating an order of magnitude increase in convection velocities compared with nanoantennas on a SiO2 base layer. In addition, the plasmonic array alters absorption in the ITO, causing a deviation from Beer-Lambert absorption that results in an optimum ITO thickness for a given system. This work elucidates the role of convection in plasmonic optical trapping and particle assembly, and opens up new avenues for controlling fluid and mass transport on the micro- and nanoscale.