Fluctuations of DNA mobility in nanofluidic entropic traps

Parallel computing for mobilities in periodic geometries

We examine methods for calculating the effective mobilities of molecules driven through periodic geometries in the context of particle-based simulation. The standard formulation of the mobility, based on the long-time limit of the mean drift velocity, is compared to a formulation based on the mean first-passage time of molecules crossing a single period of the system geometry. The equivalence of the two definitions is derived under weaker assumptions than similar conclusions obtained previously, requiring only that the state of the system at subsequent period crossings satisfy the Markov property. Approximate theoretical analyses of the computational costs of estimating these two mobility formulations via particle simulations suggest that the definition based on first-passage times may be substantially better suited to exploiting parallel computation hardware. This claim is investigated numerically on an example system modeling the passage of nanoparticles through the slit-well device. In this case, the traditional mobility formulation is found to perform best when the Péclet number is small, whereas the mean first-passage time formulation is found to converge much more quickly when the Péclet number is moderate or large. The results suggest that, given relatively modest access to modern GPU hardware, this alternative mobility formulation may be an order of magnitude faster than the standard technique for computing effective mobilities of biomolecules through periodic geometries.

Nonlinear electrophoretic velocity of DNA in slitlike confinement

We have applied zero-time-averaged alternating electric fields to DNA molecules in a cross-shaped nanofluidic slit. We observed a net drift of DNA molecules, the magnitude of which depends on the square of the electric field amplitude. From the rate of accumulation of DNA at the center of the device, we derive an estimate for the second-order electrophoretic mobility, μ_{2}. We observe that focusing is absent at a dipole rotation frequency >20 Hz, which suggests that μ_{2} depends on the frequency of the alternating fields. The observation of a nonzero μ_{2} raises the possibility of frequency-dependent electrophoretic DNA separation by length achievable in the absence of a sieving matrix.

Micro/nanofluidic devices for DNA/RNA detection and separation

The development and research have ramped up at a greater speed than ever in the field of diseases diagnosis. Still there is struggle in developing early detection techniques which uses complex biomolecules like RNA, DNA and proteins in order to detect diseases caused by bacteria, viruses or fungi. Until now separation techniques used before detection rely on traditional techniques like electrophoresis etc. which often require centralized services. Although efforts are made in developing devices that is capable enough on carrying out separation and detection based on microfluidic (MF) and nanofluidic (NF) or lab on chip. Hence, in this chapter, we have discussed about the advancement, limitations and future steps that needs to be taken to flourish the field of NF and MF for the detection and separation of nucleic acid.

Entropic trap purification of long DNA

Long-read genomic applications, such as genome mapping in nanochannels, require long DNA that is free of small-DNA impurities. We have developed a chip-based system based on entropic trapping that can simultaneously concentrate and purify a long DNA sample under the alternating application of an applied pressure (for sample injection) and an electric field (for filtration and concentration). In contrast, short DNA tends to pass through the filter owing to its comparatively weak entropic penalty for entering the nanoslit. The single-stage prototype developed here, which operates in a continuous pulsatile manner, achieves selectivities of up to 3.5 for λ-phage DNA (48.5 kilobase pairs) compared to a 2 kilobase pair standard based on experimental data for the fraction filtered using pure samples of each species. The device is fabricated in fused silica using standard clean-room methods, making it compatible for integration with long-read genomics technologies.

Giant Acceleration of DNA Diffusion in an Array of Entropic Barriers

We investigate with experiments and computer simulations the nonequilibrium dynamics of DNA polymers crossing arrays of entropic barriers in nanofluidic devices in a pressure-driven flow. With increasing driving pressure, the effective diffusivity of DNA rises and then peaks at a value that is many times higher than the equilibrium diffusivity. This is an entropic manifestation of "giant acceleration of diffusion." The phenomenon is sensitive to the effective energy landscape; thus, it offers a unique probe of entropic barriers in a system driven away from equilibrium.

Fluctuations of DNA mobility in nanofluidic entropic traps

We studied the mobility of DNA molecules driven by an electric field through a nanofluidic device containing a periodic array of deep and shallow regions termed entropic traps. The mobility of a group of DNA molecules was measured by fluorescent video microscopy. Since the depth of a shallow region is smaller than the DNA equilibrium size, DNA molecules are trapped for a characteristic time and must compress themselves to traverse the boundary between deep and shallow regions. Consistent with previous experimental results, we observed a nonlinear relationship between the mobility and electric field strength, and that longer DNA molecules have larger mobility. In repeated measurements under seemingly identical conditions, we measured fluctuations in the mobility significantly larger than expected from statistical variation. The variation was more pronounced for lower electric field strengths where the trapping time is considerable relative to the drift time. To determine the origin of these fluctuations, we investigated the dependence of the mobility on several variables: DNA concentration, ionic strength of the solvent, fluorescent dye staining ratio, electroosmotic flow, and electric field strength. The mobility fluctuations were moderately enhanced in conditions of reduced ionic strength and electroosmotic flow.