Solid-State Nanopores: Methods of Fabrication and Integration, and Feasibility Issues in DNA Sequencing - Nanopores: Sensing and Fundamental Biological Interactions - page 187

Fig. 8.8 A silicon chip etched from both sides into V-grooves. The dashed lines indicate the
V-grooves from the backside. The pore sizes can be controlled down to 20 nm by optimizing
the etching rate and etching time. (Images taken by S.R. Park, unpublished, 2004)

begins with a 100 oriented). First, a silicon nitride Si 3 N 4

protective layer is deposited, about 200 nm in thickness, on both sides of the wafer
using PECVD (Plasma Enhanced Chemical Vapor Deposition). One then spin-coats
PMMA, bake, and make a two sets of parallel lines using e-beam lithography on
both sides. The two sets of line are perpendicular to each other. The patterns are
developed in PMMA developer (MIBK:IPA 1:1). The PMMA pattern is transferred
onto the silicon nitride layer using RIE (Reactive Ion Etcher). Repeat the same RIE
procedure on the other side of the wafer. Now one has a silicon wafer sandwiched
by silicon nitride films having patterns of vertical lines on one side and horizontal
lines on the other side. KOH anisotropic etch is carried out at 85 C with 45%
(KOH) solution using silicon nitride as a mask. This gives about 0.8

m m thick Si wafer ( < 100 >

m m/min

etching rate. Approximately one hour later, the pores are opened.
It was found by Adam Politzer [ 16 ] that the inhomogeneous wafer thickness can
pose a serious problem in fabricating large number of nanopores in a single chip.
A careful analysis of the pore openings showed that the pore sizes are not directly
correlated with the lithography feature sizes [ 16 ]. To overcome this problem, it has
been suggested by Robert Riehn [ 17 ] that instead of using a regular silicon wafer,
a thin crystalline silicon membrane on a SOI wafer should be used as the starting
material. Since the thickness of the silicon layer on a SOI wafter can be precisely
controlled, the issue of inhomogeneities may be avoided.

8.4 Considerations on Using Solid-State Nanopores
for DNA Sequencing

The challenge of DNA sequencing is due to the simple fact that the basic units of
the nucleic acids, the four nucleotides of adenine, cytosine, guanine, and thymine,
are spaced at a very short physical distance, about 4 ˚

(0.4 nm) apart, on the