Non-planar nanofluidic devices for single molecule analysis fabricated using nanoglassblowing


Elizabeth A. Strychalski

Department of Physics, Cornell University, Ithaca, NY 14853, USA


 “Nanoglassblowing”1 was developed as a method to fabricated integrated micro- and nanofluidic fused silica devices with wide, shallow nanochannels and areas of gradual channel depth change.  Using this method, channels were constructed with out-of-plane curvature of channel covers from over ten micrometers to a few nanometers, nanochannel aspect ratios smaller than 2x10-5:1 (depth:width), and nanochannels as shallow as 7 nm.  These low aspect ratios and shallow channel depths are difficult to obtain using other fabrication techniques without collapsing the channel cover.  The gradual changes in channel depth also eliminate abrupt free energy barriers at the transition from microfluidic to nanofluidic regions, facilitating loading of double-stranded deoxyribonucleic acid (DNA) molecules.  The nanochannel depths and aspect ratios formed by nanoglassblowing allowed measurements of the radius of gyration, , of single l DNA molecules confined to slit-like nanochannels with depths, , ranging from 11 nm to 507 nm.


Nanofluidic devices are used for a variety of research applications, including biomolecular analysis, and interest in slit-like nanochannels in particular continues to grow.  The utility of these structures remains limited, however, by planar device architectures as well as the need for high-resolution nanofabrication processes.  A simple fabrication method termed “nanoglassblowing” is presented here that enables control over out-of-plane curvature of channel surfaces and improves attainable aspect ratios of shallow nanochannels in device regions without curvature.  This method results in continuous nanoscale channel depth variation, which arises due to the outward deflection of a softened glass channel cover by increased air pressure during annealing of a bonded device.


Because this method enables device bonding without the collapse of low aspect ratio, slit-like nanochannels, contact photolithography can be used to pattern wide precursor trenches.  This facilitates the fabrication of nanochannels that are both shallow and wide, a combination needed to prevent hydrodynamic or other nanochannel edge interactions that could hinder dynamic physical measurements, such as observation of long DNA molecules in constrained environments or continuous flow molecular analysis.  The ability to subsequently fabricate variable nanochannel depths from this single layer of photolithography and etch depth obviates the need for multiple levels of aligned lithography.  These fabrication benefits permit the seamless integration of device features across the centimeter to nanometer length scales relevant to miniaturized fluidic systems, including the critical micrometer-to-nanometer transition.  When combined with the desirable optical and chemical properties of fused silica, the resulting devices are well suited to the manipulation and observation of single biomolecules.


To make devices using nanoglassblowing, 500 mm thick fused silica channel substrate wafers (7980 fused silica, Corning Inc., Canton, NY; Mark Optics, Santa Ana, CA) were patterned using contact lithography, wet etched at 22 °C without agitation using 100:1 buffered oxide etch with surfactant (Ultra Etch, Air Products and Chemicals Inc., Allentown, PA), and fusion bonded to 170 μm thick fused silica cover wafers.  Nanoglassblowing occurred while bonded devices were annealed at atmosphere using the following process: ramp from room temperature at 150 °C/h to 1050 °C, dwell 6 h at 1050 °C, and cool to room temperature.  The amount of out-of-plane curvature of the channel cover was observed to be influenced reproducibly by the presence of access holes during annealing, channel width, channel etch depth, and device geometry. 


Figure 2(a) shows fluorescence micrographs of l DNA molecules in a 3 mm wide loading channel of a device with 7 nm deep nanochannels.  The out-of-plane deflection was sufficient to accommodate DNA molecules in their bulk radius of gyration.  Figure 2(b) shows two DNA molecules loaded into the 7 nm deep, 300 μm wide slit-like nanochannel and confined by the dense matrix of surface roughness features.  DNA molecules often remained stretched around these features upon removal of the applied electric field, which may be useful for applications requiring DNA elongation and observation, such as single molecule genomic mapping.  Radius of gyration, , measurements are plotted in figure 2(c) versus channel depth. 


Nanoglassblowing has the potential to extend the availability and utility of glass microfluidic and nanofluidic devices, by providing a simple means to fabricate and integrate non-planar device features, continuous changes in channel depth ranging from tens of micrometers to a few nanometers, and wide, shallow nanochannels.


Certain commercial equipment and materials are identified to foster understanding.  Such identification does not imply recommendation or endorsement by the National Institute of Standards and Technology, nor does it imply that the materials and equipment identified are necessarily the best available for the purpose.




Figure 1: (a) Illustrated side-views of otherwise identical channels annealed without and with access holes demonstrate the effects of these holes on nanoglassblowing.  The dashed lines 1 and 2 in (a) and (b) correspond to the locations of scanned height measurements 1 and 2 in (c).  (b) White light interference patterns are visible in this photograph of adjacent channels with (32 ± 2) nm etch depths (scale bar: 1.25 mm).  The left channel has no access hole, while the right channel has an access hole through which air could pass during bonding and annealing.  (c) Out-of-plane curvature varies smoothly across the channel widths, as seen in these single representative scanned height measurements.



Figure 2: (a) l DNA molecules in their bulk conformation in a deep, curved loading region (scale bar: 10 μm).  (b) l DNA molecules electrophoresing through a 7 nm deep and 300 μm wide slit-like nanochannel (scale bar: 10 μm).  (a) and (b) show unprocessed image data.  (c) Radius of gyration, , is plotted against nanochannel depth, .  Each data point combines the results from ten l DNA molecules and is corrected for the effects of diffraction limited optical resolution and image pixelation.  Error bars represent the addition of one standard deviation of the mean and estimates of error from optical resolution, image pixelation, digital filtering, and noise thresholding.  Uncertainty values for the nanochannel depths are smaller than the data symbols.  Brochard’s predicted theoretical scaling is shown as a dashed line overlaid on the experimental data.




1                      E. A. Strychalski, S. M. Stavis, and H. G. Craighead, Nanotechnology  (2008).