Parallelized single-molecule translocations in arrayed silicon nanopores coated with a lipid bilayer

• Solid-state nanopores have been recognized as a versatile tool for single-molecule detection with high sensitivity. They have been extensively studied for analysis by nanopore translocation of biomolecules, such as DNA, RNA, and proteins. As a complement to the electrical sensing readout, optical sensing of labeled molecules on a solid-state nanopore array can notably enhance the sensing capacity with high throughput. However, the widely used silicon nitride (SiNx) nanopore produces significant photoluminescence (PL) background under blue-green laser illumination, which can severely limit, e.g., multicolor sensing for DNA barcode discrimination. In addition, the occasionally occurring irreversible DNA clogging in a solid-state nanopore, because of DNA molecules interacting with the nanopore channel wall during translocation, can seriously affect the sensing efficacy and accuracy. To address these problems, we have developed an optical sensing system dedicated to nanopore arrays fabricated in a free-standing silicon membrane with its surface functionalized by lipid bilayer coating.A silicon nanopore array with pores of sub-20 nm diameter is fabricated in a silicon-on-insulator wafer using electron beam lithography in combination with anisotropic etching. The 55 nm thick free-standing silicon membrane shows negligible PL emission in the 550 to 800 nm spectral range under blue-green laser illumination, which greatly improves the optical signal-to-background ratio for single-molecule detection in comparison with standard SiNx devices. The formation of a lipid bilayer on the nanopore walls is successful as inferred by monitoring in situ the stepwise reduction of the nanopore conductance of ionic current and subsequently by observing ex situ the homogenous fluorescence emitted from a labeled lipid bilayer. As a demonstration, we perform the optical sensing measurements with a conventional wide-field microscope to detect the translocation of fluorophore-labeled DNA strands (120 kbp). With the low background PL of the silicon membrane, the optical signal of individual DNA translocation events is more clearly identified than when using similarly processed SiNx nanopore devices. Moreover, the coated fluidic lipid bilayer provides a nonstick surface to minimize the non-specific interaction of DNA molecules with the silicon pore walls. The results show that the DNA clogging is substantially reduced in the lipid bilayer coated nanopores as compared to uncoated nanopores. These results demonstrate that using silicon nanopores coated by a lipid bilayer is a promising strategy to realizing massively-parallel single-molecule optical detection.

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TEKNIK OCH TEKNOLOGIER  -- Elektroteknik och elektronik -- Annan elektroteknik och elektronik (hsv//swe)

ENGINEERING AND TECHNOLOGY  -- Electrical Engineering, Electronic Engineering, Information Engineering -- Other Electrical Engineering, Electronic Engineering, Information Engineering (hsv//eng)

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