Measurements of diffusion coefficients in 1-D micro- and nanochannels using shear-driven flows

Integration of porous layers in ordered pillar arrays for liquid chromatography

The present paper describes a method for the production of partly porous micro-pillars in columns suitable for use in liquid chromatography. These layers increase the available surface at least two orders of magnitude without destroying the huge benefits of the ordered nature of the system. A process flow was developed that enabled us to create a 550 nm thick porous layer on the pillar array in a sealed channel configuration, withstanding pressures up to at least 70 bar. Measuring band broadening under non-retained conditions, only a modest increase in plate height was observed in the porous pillar array as compared to that in a non-porous pillar array. The homogeneity of the layers was demonstrated using an optical microscope and SEM pictures and by monitoring peak velocities at constant pressures. The internal porosity was determined using particles with a diameter larger than the mesopores in combination with a dye that could penetrate into the pores.

Experimental investigation of the band broadening originating from the top and bottom walls in micromachined nonporous pillar array columns

We report on the experimental investigation of the effect of the top and bottom wall plates in micromachined nonporous pillar array columns. It has been found that their presence yields an additional c-term type of band broadening that can make up a significant fraction of the total band broadening (at least if considering nonporous pillars and a nonretained tracer). Their presence also induces a clear (downward) shift of the optimal velocity. These observations are, however in excellent quantitative agreement with the theoretical expectations obtained from a computational fluid dynamics study. The presently obtained experimental results, hence, demonstrate that the employed high aspect ratio Bosch etching process can be used to fabricate micromachined pillar arrays that are sufficiently refined to achieve the theoretical performance limit.

Fourier analysis to measure diffusion coefficients and resolve mixtures on a continuous electrophoresis chip

We report a method to measure diffusion coefficients of fluorescent solutes in the 10(2)-10(6) Da molecular mass range in a glass-PDMS chip. Upon applying a permanent electric field, the solute is introduced through a narrow channel into a wide analysis chamber where it migrates along the injection axis and diffuses in two dimensions. The diffusion coefficient is extracted after 1D Fourier transform of the resulting stationary concentration pattern. Analysis is straightforward, requiring no numerical integration or velocity field simulation. The diffusion coefficients measured for fluorescein, rhodamine green-labeled oligonucleotides, and YOYO-1-stained dsDNA fragments agree with the literature values and with our own fluorescence correlation spectroscopy measurements. As shown for 151 and 1257 base pair dsDNA mixtures, the present method allows us to rely on diffusion to quantitatively characterize the nature and the composition of binary mixtures. In particular, we implement a DNA hybridization assay to illustrate the efficiency of the proposed protocol for library screening.

Continuous-flow single-molecule CE with high detection efficiency

This paper describes the use of two-beam line-confocal detection geometry for measuring the total mobility of individual molecules undergoing continuous-flow CE separation. High-sensitivity single-molecule confocal detection is usually performed with a diffraction limited focal spot (approximately 500 nm in diameter), which necessitates the use of nanometer-sized channels to ensure all molecules flow through the detection volume. To allow for the use of larger channels that are a few micrometers in width, we employed cylindrical optics to define a rectangular illumination area that is diffraction-limited (approximately 500 nm) in width, but a few micrometers in length to match the width of the microchannel. We present detailed studies that compare the performance of this line-confocal detection geometry with the more widely used point-confocal geometry. Overall, we found line-confocal detection to provide the highest combination of signal-to-background ratio and spatial detection efficiency when used with micrometer-sized channels. For example, in a 2 microm wide channel we achieved a 94% overall detection efficiency for single Alexa488 dye molecules when a 2 microm x 0.5 microm illumination area was used, but only 34% detection efficiency with a 0.5 microm-diameter detection spot. To carry out continuous-flow CE, we used two-beam fluorescent cross-correlation spectroscopy where the transit time of each molecule is determined by cross-correlating the fluorescence registered by two spatially offset line-confocal detectors. We successfully separated single molecules of FITC, FITC-tagged glutamate, and FITC-tagged glycine.

Diffusion limitation: a possible source for the occurrence of doughnut patterns on DNA microarrays

Doughnut shaped hybridization patterns on DNA microarrays are mainly allocated to spotting or drying artifacts. The present study reports on results obtained from four different approaches that when combined generate a better view on the occurrence of these patterns. This study points out that doughnuts are not only formed during the spotting and drying process, but the hybridization process itself can be considered as an important cause. A combination of computer simulations, theoretical, optical, and experimental techniques shows how ring-shaped hybridization patterns occur when diffusion-limited conditions are present during the hybridization process. The theoretical assumptions as well as the simulations indicate that, for the basic geometry of a microarray hybridization experiment, a large amount of binding molecules reach the spot from the sides (and not from above the spot), leading to a preferential binding on the rims of the spot. These patterns seem to occur especially during hybridization with short oligonucleotides that have a very high binding probability and fast hybridization kinetics. Longer target DNA molecules lead to a more evenly distributed intensity signal. Furthermore, the diffusion-limited conditions also lead to pronounced hybridization intensity patterns on the scale of a whole spot block, where larger intensities are obtained on the edges of the block compared with the spots laying in the center of the block.

Detection enhancement in nano-channels using micro-machined silicon groove

The present paper reports on an experimental study of the possibility to use a micro-machined detection groove to enhance the detection sensitivity in flat-rectangular nano-channels for ultra-rapid liquid chromatography separations. Transversally running detection grooves with three different axial widths (respectively, 2, 4 and 6 microm) and one depth (4.75 microm) were tested in glass and silicon channels for the whole range of detectable fluorescein isothiocyanate isomer I, FITC, concentrations. The groove with the most square-like cross-section (i.e., 4 microm wide and 4.75 microm deep) yielded the best combination of detection gain and minimal additional band broadening. In a 1cm long channel, the effective plate loss caused by the 4 microm wide groove would only be of the order of 20%, while the gain in S/N-ratio was of the order of a factor of 5. The detection groove concept yields larger gains in silicon channel substrates than in glass channel substrates, due to the larger stray light losses occurring in the latter.

An automated injection system for sub-micron sized channels used in shear-driven-chromatography

This paper describes a method to automatically and reproducibly inject sharply delimited sample plugs in the shallow (i.e., sub-micron) channels typically used in shear driven chromatography. The formation of asymmetric plugs, which typically occurs during loading of the sample in wide channels, is circumvented by etching a slit in the middle of the channel that is connected to a micro-well and a vacuum system with syringes for the supply of both the analyte and the mobile phase. The design of the injection slit was supported by a series of CFD simulations to optimize its shape and that of the corresponding injection well. The system was intensively tested experimentally and showed good reproducibility, both for the width and the area of the injected peaks (relative standard deviations are max. 4 and 6%, respectively). The concentration of the injected plug was found to be approximately 80% of the original sample concentration. It was also observed that with the current setup the lower limit of the peak width was about 120 microm. This is a consequence of the fact that the peak width originating from the convection filling step becomes negligible to the contribution of diffusion during the filling and flushing time. Being fully automated and perfectly closed, the presently proposed injection system also paves the way to integrate other functionalities in shear driven chromatography, i.e. gradient elution and parallelization.

A dimensionless number analysis of the hybridization process in diffusion- and convection-driven DNA microarray systems

The present theoretical analysis aims at providing a general understanding of the combined effect the many different process variables have on the hybridization rate in diffusion- and convection-driven DNA microarray systems. It is shown that all process variables can be grouped into only four different dimensionless numbers (the Damkohler number Da, the dimensionless association constant kappa(A), the dimensionless initial concentration C'(0) and a geometrical ratio alpha). These four numbers have a straightforward physical meaning and only contain easily measurable parameters. Reducing the solution space from 7D to 4D, the dimensionless number representation greatly facilitates the insight in the conditions leading to the occurrence of diffusion-limited hybridization rates in both diffusion- and convection-driven DNA microarray systems. This in turn simplifies their design and the interpretation of the experimental results that are obtained with these systems.

Ultra-rapid separation of an angiotensin mixture in nanochannels using shear-driven chromatography

The present paper reports on the separation of a mixture of fluorescein isothiocyanate-labeled angiotensin I and II peptides in a shear-driven nanochannel with a C18-coating and using an eluent consisting of 5% acetonitrile in 0.02 M aqueous phosphate buffer at pH 6.5. The flat-rectangular nanochannel in fused silica consisted of an etched structure in combination with a flat moving wall. The very fast separation kinetics that can be achieved in a nanochannel allowed to separate the angiotensin peptides in less then 0.2 s in a distance of only 1.8 mm. Plate heights as small as 0.4 microm were calculated after substraction of the injection effect.