Controlling Nanopore Size, Shape, and Stability

Abstract

Solid-state nanopores are considered a promising tool for the study of biological polymers such
as DNA and RNA, due largely to their flexibility in size, potential in device integration and
robustness. Here, we show that the precise shape of small nanopores (~5 nm diameter in 20 nm
SiN membranes) can be controlled by using transmission electron microscope (TEM) beams of
different sizes. However, when some of these small nanopores are immersed in an aqueous
solution, their resistance is observed to decrease over time. By comparing nanopores of
different shapes using (scanning) TEM both before and after immersion in aqueous solution, we
demonstrate that the stability of small nanopores is related to their three-dimensional geometry,
which depends on the TEM beam size employed during pore fabrication. Optimal stability is
obtained using a TEM beam size of approximately the same size as the intended nanopore
diameter. In addition, we show that thermal oxidation can serve as a means to independently
control nanopore size following TEM fabrication. These observations provide key guidelines
for the fabrication of stable solid-state nanopores on the scale of nucleic acids and small
proteins.