Solid-state membranes with nanometer-sized pores (nanopores) have drawn great attention because of its promising application potential, such as DNA or RNA sensing or sequencing with single-molecule resolution. Nowadays, individual nanopores can be routinely fabricated one by one by TEM-drilling. But to enable parallel sequencing with high throughput an array of nanopores is required.
Here, we present a simple but reliable approach to fabricate nanopore arrays in silicon with nanometer precision by means of standard semiconductor cleanroom processes . Free-standing Si membranes, 100 µm in diameter and 300 nm thick, were fabricated on an SOI wafer using the Bosch process of inductively-coupled plasma (ICP) etching. Then, using either optical or e-beam lithography sub-micro-scale patterns with controlled pitch distance were defined on the membrane front side which were subsequently etched by KOH anisotropic etching. Thus, inverted pyramidal openings formed. Then, the pyramidal openings were shrunk by dry thermal oxidation at 850 °C. The shrinkage rate of the openings with initial widths ranging from 58 nm to 345 nm slowed down significantly with time and saturated after 4 hours. In the saturation regime, the shrinkage rate is within ±2 nm/h, which gives us nanometer precision to tune the pore size. Thus oxidized pores with diameters as small as 8 nm were obtained with prefect circular shape. In addition, the pore size distribution did not get broadened by the thermal oxidation process, in most cases the spread of pore size distribution even decreased due to the stress-related retardation in oxidation of the non-planar silicon structures. Investigation of cross sections of the pores suggests that the initial inverted pyramidal structure is most probably the cause of self-limiting shrinkage, while the circular shape is probably formed due to the oxide flow at the pyramid tips.
Further DNA translocation experiments were carried out on the silicon nanopore arrays. Oligonucleotides with different lengths, labeled with ATTO532 and DY521-XL fluorophores respectively, were inserted into the cis-chamber. By diffusion or driven by bias, the labeled oligonucleotides passed through the nanopores and were excited by a single laser source at the trans-chamber side. A beam splitter was mounted in the optical path between the microscope and the CCD camera to split the incident beam into two channels by wavelengths, thereby single molecule translocation with two colors was studied simultaneously on the nanopore arrays.
 Zhang M, Schmidt T, Sangghaleh F, Roxhed N, Sychugov I and Linnros J, Oxidation of nanopores in a silicon membrane: self-limiting formation of sub-10 nm circular openings (submitted to Nanotechnology)