Kristofor Robert Payer

Toward attogram mass measurements in solution with suspended nanochannel resonators.

Using suspended nanochannel resonators (SNRs), we demonstrate measurements of mass in solution with a resolution of 27 ag in a 1 kHz bandwidth, which represents a 100-fold improvement over existing suspended microchannel resonators and, to our knowledge, is the most precise mass measurement in liquid today. The SNR consists of a cantilever that is 50 microm long, 10 microm wide, and 1.3 microm thick, with an embedded nanochannel that is 2 microm wide and 700 nm tall. The SNR has a resonance frequency near 630 kHz and exhibits a quality factor of approximately 8000 when dry and when filled with water. In addition, we introduce a new method that uses centrifugal force caused by vibration of the cantilever to trap particles at the free end. This approach eliminates the intrinsic position dependent error of the SNR and also improves the mass resolution by increasing the averaging time for each particle.

Weighing nanoparticles in solution at the attogram scale

Significance Naturally occurring and engineered nanoparticles (e.g., exosomes, viruses, protein aggregates, and self-assembled nanostructures) have size- and concentration-dependent functionality, yet existing characterization methods in solution are limited for diameters below ∼50 nm. In this study, we developed a nanomechanical resonator that can directly measure the mass of individual nanoparticles down to 10 nm with single-attogram (10−18 g) precision, enabling access to previously difficult-to-characterize natural and synthetic nanoparticles. Physical characterization of nanoparticles is required for a wide range of applications. Nanomechanical resonators can quantify the mass of individual particles with detection limits down to a single atom in vacuum. However, applications are limited because performance is severely degraded in solution. Suspended micro- and nanochannel resonators have opened up the possibility of achieving vacuum-level precision for samples in the aqueous environment and a noise equivalent mass resolution of 27 attograms in 1-kHz bandwidth was previously achieved by Lee et al. [(2010) Nano Lett 10(7):2537–2542]. Here, we report on a series of advancements that have improved the resolution by more than 30-fold, to 0.85 attograms in the same bandwidth, approaching the thermomechanical noise limit and enabling precise quantification of particles down to 10 nm with a throughput of more than 18,000 particles per hour. We demonstrate the potential of this capability by comparing the mass distributions of exosomes produced by different cell types and by characterizing the yield of self-assembled DNA nanoparticle structures.

A microfluidic platform enabling single-cell RNA-seq of multigenerational lineages

We introduce a microfluidic platform that enables off-chip single-cell RNA-seq after multi-generational lineage tracking under controlled culture conditions. We use this platform to generate whole-transcriptome profiles of primary, activated murine CD8+ T-cell and lymphocytic leukemia cell line lineages. Here we report that both cell types have greater intra- than inter-lineage transcriptional similarity. For CD8+ T-cells, genes with functional annotation relating to lymphocyte differentiation and function—including Granzyme B—are enriched among the genes that demonstrate greater intra-lineage expression level similarity. Analysis of gene expression covariance with matched measurements of time since division reveals cell type-specific transcriptional signatures that correspond with cell cycle progression. We believe that the ability to directly measure the effects of lineage and cell cycle-dependent transcriptional profiles of single cells will be broadly useful to fields where heterogeneous populations of cells display distinct clonal trajectories, including immunology, cancer, and developmental biology.

Integrated microelectronic device for label-free nucleic acid amplification and detection

We present an integrated microelectronic device for amplification and label-free detection of nucleic acids. Amplification by polymerase chain reaction (PCR) is achieved with on-chip metal resistive heaters, temperature sensors, and microfluidic valves. We demonstrate a rapid thermocycling with rates of up to 50 degrees C s(-1) and a PCR product yield equivalent to that of a bench-top system. Amplicons within the PCR product are detected by their intrinsic charge with a silicon field-effect sensor. Similar to existing optical approaches with intercalators such as SYBR Green, our sensing approach can directly detect standard double-stranded PCR product, while in contrast, our sensor does not require labeling reagents. By combining amplification and detection on the same device, we show that the presence or absence of a particular DNA sequence can be determined by converting the analog surface potential output of the field-effect sensor to a simple digital true/false readout.

Monitoring of heparin and its low-molecular-weight analogs by silicon field effect.

Heparin is a highly sulfated glycosaminoglycan that is used as an important clinical anticoagulant. Monitoring and control of the heparin level in a patients blood during and after surgery is essential, but current clinical methods are limited to indirect and off-line assays. We have developed a silicon field-effect sensor for direct detection of heparin by its intrinsic negative charge. The sensor consists of a simple microfabricated electrolyte-insulator-silicon structure encapsulated within microfluidic channels. As heparin-specific surface probes the clinical heparin antagonist protamine or the physiological partner antithrombin III were used. The dose–response curves in 10% PBS revealed a detection limit of 0.001 units/ml, which is orders of magnitude lower than clinically relevant concentrations. We also detected heparin-based drugs such as the low-molecular-weight heparin enoxaparin (Lovenox) and the synthetic pentasaccharide heparin analog fondaparinux (Arixtra), which cannot be monitored by the existing near-patient clinical methods. We demonstrated the specificity of the antithrombin III functionalized sensor for the physiologically active pentasaccharide sequence. As a validation, we showed correlation of our measurements to those from a colorimetric assay for heparin-mediated anti-Xa activity. These results demonstrate that silicon field-effect sensors could be used in the clinic for routine monitoring and maintenance of therapeutic levels of heparin and heparin-based drugs and in the laboratory for quantitation of total amount and specific epitopes of heparin and other glycosaminoglycans.

Fabrication and Characterization of an Integrated Microsystem for Protein Preconcentration and Sensing

We report on a fabrication and packaging process for a microsystem consisting of a mass-based protein detector and a fully integrated preconcentrator. Preconcentration of protein is achieved by means of a nanofluidic concentrator (NC), which takes advantage of fast nonlinear electroosmotic flow near a nanochannel-microchannel junction to concentrate charged molecules inside a volume of fluid on the order of 1 pL. Detection of preconcentrated protein samples is accomplished by passing them through a suspended microchannel resonator (SMR), which is a hollow resonant cantilever serially connected to the NC on the same device. The transit of a preconcentrated sample produces a transient shift in the cantilevers resonance frequency that is proportional to the density of the sample and, hence, the concentration of protein contained in it. A device containing both NC and SMR structures was produced using a novel fabrication process which simultaneously satisfies the separate packaging requirements of the two structures. The initial testing of this prototype device has demonstrated that the integrated SMR can accurately measure the concentration of a bovine serum albumin solution, that was preconcentrated using the integrated NC. Future improvements in the fabrication process will allow site-specific surface modification of the device and compatibility with separation methods, which will create opportunities for its application to immunoassays and universal detection.

Weighing nanoparticles and viruses using suspended nanochannel resonators

We have batch fabricated suspended nanochannel resonators (SNRs) to improve the mass resolution of suspended microchannel resonators (SMRs). The SNR consists of a cantilever that is 50 µm long, 10 µm wide, and 1.3 µm thick, with an embedded nanochannel that is 2 µm wide and 700 nm tall. The SNR has a resonance frequency near 640 kHz and exhibits the maximum quality factor of approximately 16,000 when dry and when filled with water. Using the SNRs, we demonstrated mass measurements of various nanoparticles down to 20 nm in diameter and viruses in solution with a resolution of 27 ag in a 1 kHz bandwidth, which represents a 100-fold improvement over existing SMRs and, to our knowledge, is the most precise mass measurement in liquid today.