On the Hydrodynamic Nature of DNA Acoustic Sensing

Acoustic detection of a mutation-specific Ligase Chain Reaction based on liposome amplification

Single nucleotide variants (SNVs) play a crucial role in understanding genetic diseases, cancer development, and personalized medicine. However, existing ligase-based amplification and detection techniques, such as Rolling Circle Amplification and Ligase Detection Reaction, suffer from low efficiency and difficulties in product detection. To address these limitations, we propose a novel approach that combines Ligase Chain Reaction (LCR) with acoustic detection using highly dissipative liposomes. In our study, we are using LCR combined with biotin- and cholesterol-tagged primers to produce amplicons also modified at each end with a biotin and cholesterol molecule. We then apply the LCR mix without any purification directly on a neutravidin modified QCM device Au-surface, where the produced amplicons can bind specifically through the biotin end. To improve sensitivity, we finally introduce liposomes as signal enhancers. For demonstration, we used the detection of the BRAF V600E point mutation versus the wild-type allele, achieving an impressive detection limit of 220 aM of the mutant target in the presence of the same amount of the wild type. Finally, we combined the assay with a microfluidic fluidized bed DNA extraction technology, offering the potential for semi-automated detection of SNVs in patients' crude samples. Overall, our LCR/acoustic method outperforms other LCR-based approaches and surface ligation biosensing techniques in terms of detection efficiency and time. It effectively overcomes challenges related to DNA detection, making it applicable in diverse fields, including genetic disease and pathogen detection.

Quartz crystal microbalance and atomic force microscopy to characterize mimetic systems based on supported lipids bilayer

Quartz Crystal Microbalance (QCM) with dissipation and Atomic Force Microscopy (AFM) are two characterization techniques that allow describing processes taking place at solid-liquid interfaces. Both are label-free and, when used in combination, provide kinetic, thermodynamic and structural information at the nanometer scale of events taking place at surfaces. Here we describe the basic operation principles of both techniques, addressing a non-specialized audience, and provide some examples of their use for describing biological events taking place at supported lipid bilayers (SLBs). The aim is to illustrate current strengths and limitations of the techniques and to show their potential as biophysical characterization techniques.

Acoustic Array Biochip Combined with Allele-Specific PCR for Multiple Cancer Mutation Analysis in Tissue and Liquid Biopsy

Regular screening of point mutations is of importance to cancer management and treatment selection. Although techniques like next-generation sequencing and digital polymerase chain reaction (PCR) are available, these are lacking in speed, simplicity, and cost-effectiveness. The development of alternative methods that can detect the extremely low concentrations of the target mutation in a fast and cost-effective way presents an analytical and technological challenge. Here, an approach is presented where for the first time an allele-specific PCR (AS-PCR) is combined with a newly developed high fundamental frequency quartz crystal microbalance array as biosensor for the amplification and detection, respectively, of cancer point mutations. Increased sensitivity, compared to fluorescence detection of the AS-PCR amplicons, is achieved through energy dissipation measurement of acoustically "lossy" liposomes binding to surface-anchored dsDNA targets. The method, applied to the screening of BRAF V600E and KRAS G12D mutations in spiked-in samples, was shown to be able to detect 1 mutant copy of genomic DNA in an excess of 10⁴ wild-type molecules, that is, with a mutant allele frequency (MAF) of 0.01%. Moreover, validation of tissue and plasma samples obtained from melanoma, colorectal, and lung cancer patients showed excellent agreement with Sanger sequencing and ddPCR; remarkably, the efficiency of this AS-PCR/acoustic methodology to detect mutations in real samples was demonstrated to be below 1% MAF. The combined high sensitivity and technology-readiness level of the methodology, together with the ability for multiple sample analysis (24 array biochip), cost-effectiveness, and compatibility with routine workflow, make this approach a promising tool for implementation in clinical oncology labs for tissue and liquid biopsy.

Quantitative description of the response of finite size adsorbates on a quartz crystal microbalance in liquids using analytical hydrodynamics

Despite being a fundamental tool in soft matter research and biosensing, quartz crystal microbalance (QCM) analyses of discrete macromolecules in liquids so far lack a firm theoretical basis. Quite often, acoustic signals of discrete particles are qualitatively interpreted using ad hoc frameworks based on effective electrical circuits, effective springs and trapped-solvent models with many fitting parameters. Nevertheless, due to its extreme sensitivity, the QCM technique pledges to become an accurate predictive tool. Using unsteady low Reynolds hydrodynamics we derive analytical expressions for the acoustic impedance of adsorbed discrete spheres. The present approach is successfully validated against 3D simulations and a plethora of experimental results covering more than a decade of research on proteins, viruses, liposomes, and massive nanoparticles, with sizes ranging from a few to hundreds of nanometers. The agreement without fitting parameters indicates that the acoustic response is dominated by the hydrodynamic propagation of the particle surface stress over the resonator. Understanding this leading contribution is a prerequisite for deciphering the secondary contributions arising from the relevant specific molecular and physico-chemical forces.

Hybrid Sensor Device for Simultaneous Surface Plasmon Resonance and Surface Acoustic Wave Measurements

Surface plasmon resonance (SPR) and Love wave (LW) surface acoustic wave (SAW) sensors have been established as reliable biosensing technologies for label-free, real-time monitoring of biomolecular interactions. This work reports the development of a combined SPR/LW-SAW platform to facilitate simultaneous optical and acoustic measurements for the investigation of biomolecules binding on a single surface. The system’s output provides recordings of two acoustic parameters, phase and amplitude of a Love wave, synchronized with SPR readings. We present the design and manufacturing of a novel experimental set-up employing, in addition to the SPR/LW-SAW device, a 3D-printed plastic holder combined with a PDMS microfluidic cell so that the platform can be used in a flow-through mode. The system was evaluated in a systematic study of the optical and acoustic responses for different surface perturbations, i.e., rigid mass loading (Au deposition), pure viscous loading (glycerol and sucrose solutions) and protein adsorption (BSA). Our results provide the theoretical and experimental basis for future application of the combined system to other biochemical and biophysical studies.

Acoustic Methodology for Selecting Highly Dissipative Probes for Ultrasensitive DNA Detection

The objective of this work is to present a methodology for the selection of nanoparticles such as liposomes to be used as acoustic probes for the detection of very low concentrations of DNA. Liposomes, applied in the past as mass amplifiers and detected through frequency measurement, are employed in the current work as probes for energy-dissipation enhancement. Because the dissipation signal is related to the structure of the sensed nanoentity, a systematic investigation of the geometrical features of the liposome/DNA complex was carried out. We introduce the parameter of dissipation capacity by which several sizes of liposome and DNA structures were compared with respect to their ability to dissipate acoustic energy at the level of a single molecule/particle. Optimized 200 nm liposomes anchored to a dsDNA chain led to an improvement of the limit of detection (LoD) by 3 orders of magnitude when compared to direct DNA detection, with the new LoD being 1.2 fmol (or 26 fg/μL or 2 pM). Dissipation monitoring was also shown to be 8 times more sensitive than the corresponding frequency response. The high versatility of this new methodology is demonstrated in the detection of genetic biomarkers down to 1-2 target copies in real samples such as blood. This study offers new prospects in acoustic detection with potential use in real-world diagnostics.

Branched hybridization chain reaction-using highly dimensional DNA nanostructures for label-free, reagent-less, multiplexed molecular diagnostics

The specific and multiplexed detection of DNA underpins many analytical methods, including the detection of microorganisms that are important in the medical, veterinary, and environmental sciences. To achieve such measurements generally requires enzyme-mediated amplification of the low concentrations of the target nucleic acid sequences present, together with the precise control of temperature, as well as the use of enzyme-compatible reagents. This inevitably leads to compromises between analytical performance and the complexity of the assay. The hybridization chain reaction (HCR) provides an attractive alternative, as a route to enzyme-free DNA amplification. To date, the linear nucleic acid products, produced during amplification, have not enabled the development of efficient multiplexing strategies, nor the use of label-free analysis. Here, we show that by designing new DNA nanoconstructs, we are able, for the first time, to increase the molecular dimensionality of HCR products, creating highly branched amplification products, which can be readily detected on label-free sensors. To show that this new, branching HCR system offers a route for enzyme-free, label-free DNA detection, we demonstrate the multiplexed detection of a target sequence (as the initiator) in whole blood. In the future, this technology will enable rapid point-of-care multiplexed clinical analysis or in-the-field environmental monitoring.

3D-printed Point-of-Care Platform for Genetic Testing of Infectious Diseases Directly in Human Samples Using Acoustic Sensors and a Smartphone

The objective of this work is to develop a methodology and associated platform for nucleic acid detection at the point-of-care (POC) that is sensitive, user-friendly, affordable, rapid, and robust. The heart of this system is an acoustic wave sensor, based on a Surface Acoustic Wave (SAW) or Quartz Crystal Microbalance (QCM) device, which is employed for the label-free detection of isothermally amplified target DNA. Nucleic acids amplification and detection is demonstrated inside three crude human samples, i.e., whole blood, saliva, and nasal swab, spiked in with 10-100 Salmonella cells. To qualify for POC applications, a portable platform was developed based on 3D printing, integrating inside a single box: (i) simple fluidics based on plastic tubing and a mini peristaltic pump, (ii) a heating plate combined with disposable reaction tubes for isothermal amplification; (iii) a mini antenna analyzer operated through a tablet; and (iv) an acoustic wave device housing unit. The simplicity of the method combined with smartphone operation and detection, rapid sample-to-answer analysis time (30 min), and high performance (detection limit 4 × 10³ CFU/ml) in three of the most important human samples in diagnostics suggest that the methodology could become a tool of choice for nucleic acid detection at the POC. In addition, the low cost of the platform and assay holds promise for its adoption in resource limited areas. The acoustic detection method is shown to give similar results with a standard colorimetric assay carried out in saliva and nasal swab but can also be used to detect nucleic acids inside whole blood, where a colorimetric assay failed to perform.

A model derived from hydrodynamic simulations for extracting the size of spherical particles from the quartz crystal microbalance

A model derived from hydrodynamic simulations is presented for extracting the size of adsorbed nanoparticles in QCM-D measurements, and is applicable to both low and high surface coverage regimes.

Sample-to-answer acoustic detection of DNA in complex samples

The present study demonstrates the sensitive and label-free acoustic detection of dsDNA amplicons produced from whole Salmonella Thyphimurium cells without employing any DNA extraction and/or purification step, in the presence of the lysed bacterial cells and in a hybridization-free assay.