Modelling DNA extension and fragmentation in contractive microfluidic devices: a Brownian dynamics and computational fluid dynamics approach

Fragmenting DNA into short pieces is an essential manipulation in many biological studies, ranging from genome sequencing to molecular diagnosis. Among various DNA fragmentation methods, microfluidic hydrodynamic DNA fragmentation has huge advantages especially in terms of handling small-volume samples and being integrated into automatic and all-in-one DNA analysis equipment. Despite the fast progress in experimental studies and applications, a systematic understanding of how DNA molecules are distributed, stretched and fragmented in a confined microfluidic field is still lacking. In this work, we investigate the extension and fragmentation of DNA in a typical contractive microfluidic field, which consists of a shear flow-dominated area and an elongational flow-dominated area, using the Brownian dynamics-computational fluid dynamics method. Our results show that the shear flow at the straight part of the microfluidic channel and the elongational flow at the contractive bottleneck together determine the performance of DNA fragmentation. The average fragment size of DNA decreases with the increase of the strain rate of the elongational flow, and the upstream shear flow can significantly precondition the conformation of DNA to produce shorter and more uniform fragments. A systematic study of the dynamics of DNA fragmentation shows that DNA tends to break at the mid-point when the strain rate of elongational flow is small, and the breakage point largely deviates from the midpoint as the strain rate increases. Our simulation of the thorough DNA fragmentation process in a realistic microfluidic field agrees well with experimental results. We expect that our study can shed new light on the development of future microfluidic devices for DNA fragmentation and integrated DNA analysis devices.

Magnetic nanochain integrated microfluidic biochips

Microfluidic biochips hold great potential for liquid analysis in biomedical research and clinical diagnosis. However, the lack of integrated on-chip liquid mixing, bioseparation and signal transduction presents a major challenge in achieving rapid, ultrasensitive bioanalysis in simple microfluidic configurations. Here we report magnetic nanochain integrated microfluidic chip built upon the synergistic functions of the nanochains as nanoscale stir bars for rapid liquid mixing and as capturing agents for specific bioseparation. The use of magnetic nanochains enables a simple planar design of the microchip consisting of flat channels free of common built-in components, such as liquid mixers and surface-anchored sensing elements. The microfluidic assay, using surface-enhanced Raman scattering nanoprobes for signal transduction, allows for streamlined parallel analysis of multiple specimens with greatly improved assay kinetics and delivers ultrasensitive identification and quantification of a panel of cancer protein biomarkers and bacterial species in 1 μl of body fluids within 8 min.

Microfluidic platforms are an attractive setup for performing clinical tests but integrated liquid mixing and bioseparation is difficult at small scales. Here Xiong et al. propose magnetic nanochains which can stir the solution and capture agents and thus enable liquid analysis in a short amount of time.

Sensitive Detection of MMP9 Enzymatic Activities in Single Cell-Encapsulated Microdroplets as an Assay of Cancer Cell Invasiveness

Matrix metalloproteinases (MMPs) are typically up-regulated in cancer cells, and play a critical role in assisting metastasis by the breakdown of the extracellular matrix. Here we report an effective strategy for cell invasiveness assay by integrating MMP9 functional activity analysis with single cell-encapsulated microdroplets. A flow focusing capillary microfluidic device has been assembled using "off-the-shelf" fluidic components for high-throughput generation of microdroplets. Tumor cells, MMP9 specific peptides, and other cofactors can be loaded into the device and encapsulated into individual droplets as dynamic microreactors for proteolytic cleavage of the substrate. This design allows for rapid and robust detection of MMP9 enzymatic activities by fluorescent signals in a few minutes. It represents the first demonstration of quantifying MMP9 enzymatic activities at the single cell level with a high throughput performance. This new technique promises functional evaluation of cancer cell invasiveness for important diagnostic or prognostic applications.

Eliminating Size-Associated Diffusion Constraints for Rapid On-Surface Bioassays with Nanoparticle Probes

Nanoparticle probes enable implementation of advanced on-surface assay formats, but impose often underappreciated size-associated constraints, in particular on assay kinetics and sensitivity. The present study highlights substantially slower diffusion-limited assay kinetics due to the rapid development of a nanoprobe depletion layer next to the surface, which static incubation and mixing of bulk solution employed in conventional assay setups often fail to disrupt. In contrast, cyclic solution draining and replenishing yields reaction-limited assay kinetics irrespective of the probe size. Using common surface bioassays, enzyme-linked immunosorbent assays and immunofluorescence, this study shows that this conceptually distinct approach effectively "erases" size-dependent diffusion constraints, providing a straightforward route to rapid on-surface bioassays employing bulky probes and procedures involving multiple labeling cycles, such as multicycle single-cell molecular profiling. For proof-of-concept, the study demonstrates that the assay time can be shortened from hours to minutes with the same probe concentration and, at a typical incubation time, comparable target labeling can be achieved with up to eight times lower nanoprobe concentration. The findings are expected to enable realization of novel assay formats and stimulate development of rapid on-surface bioassays with nanoparticle probes.

Rapid hybridization of nucleic acids using isotachophoresis

We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants.

Rapid microarray processing using a disposable hybridization chamber with an integrated micropump

We present a disposable microarray hybridization chamber with an integrated micropump to speed up diffusion based reaction kinetics by generating convective flow. The time-to-result for the hybridization reaction was reduced from 60 min (standard protocol) down to 15 min for a commercially available microarray. The integrated displacement micropump is pneumatically actuated. It includes two active microvalves and is designed for low-cost, high volume manufacturing. The setup is made out of two microstructured polymer parts realized in polycarbonate (PC) separated by a 25 μm thermoplastic elastomer (TPE) membrane. Pump rate can be controlled between 0.3 μl s(-1) and 5.7 μl s(-1) at actuation frequencies between 0.2 Hz and 8.0 Hz, respectively.

Deciding whether to go with the flow: evaluating the merits of flow reactors for synthesis

The fine chemicals and pharmaceutical industries are transforming how their products are manufactured, where economically favorable, from traditional batchwise processes to continuous flow. This evolution is impacting synthetic chemistry on all scales-from the laboratory to full production. This Review discusses the relative merits of batch and micro flow reactors for performing synthetic chemistry in the laboratory.