Supplementary information for
Ultrafast and Wide Range Analysis of DNA Molecules Using
Rigid Network Structure of Solid Nanowires
Sakon Rahonga, Takao Yasuib*, Takeshi Yanagidaa*, Kazuki Nagashimaa, Masaki Kanaia,
Annop Klamchuena, Gang Menga, Yong Hea, Fuwei Zhugea, Noritada Kajib, Tomoji Kawaia*
and Yoshinobu Babab,c*
a
Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka-cho, Ibaraki,
Osaka 567-0047, Japan
b
Department of Applied Chemistry, Graduate School of Engineering, Nagoya University, and
FIRST Research Center for Innovative Nanobiodevices, Nagoya University, Furo-cho, Chikusaku, Nagoya 464-8603, Japan
c
Health Research Institute, National Institute of Advanced Industrial Science and Technology
(AIST), Takamatsu 761-0395, Japan
*Corresponding authors: (T. Yasui) Phone: +81-52-789-4611; Fax: +81-52-789-4666; E-mail:
yasui@apchem.nagoya-u.ac.jp; (T. Yanagida) Phone: +81-06-6879-4294; Fax: +81-06-68794295; E-mail: yanagi32@sanken.osaka-u.ac.jp; (T. Kawai) Phone: +81-06-6879-4307; Fax: +8106-6879-4307; E-mail: kawai@sanken.osaka-u.ac.jp; (Y. Baba) Phone: +81-52-789-4664; Fax:
+81-52-789-4666; E-mail: babaymtt@apchem.nagoya-u.ac.jp
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Figure S1 Detailed scheme of the fabrication procedure. (a) A 250 nm Cr layer is prepared on
fused quartz substrate by RF sputtering. (b) Then, the microchannel pattern is prepared by a
photolithography process and the Cr layer is etched with Cr etchant solution. (c) After that, the
substrate is etched (to a 2 m depth) by the RIE process and (d) a 10 nm Cr layer is prepared by
RF sputtering. (e) Next, an electron beam resist coating is applied, (f) the nanowire area is drawn
by electron beam lithography and the Cr layer is lifted off with the Cr etchant solution to open
the area for the nanowire growth. (g) After that, a 3 nm Au layer is deposited as a catalyst for
nanowire growth on the substrate by DC sputtering, (h) the electron beam resist is lifted off with
dimethylformamide (DMF) solution, leaving the Au catalyst in the microchannel pattern. (i) The
nanowires are grown in the microchannel using a pulse laser deposition (PLD) system and (j) the
Cr layer is lifted off with Cr etchant solution. (k) Then, the 1-cycle growth nanowire device is
sealed with a fused quartz cover glass using hexafluorosilisic acid (H2SiF6) at 75 deg C for 24 h.
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(l, m, n, and o) After the 1-cycle growth nanowires are achieved, further growths of 2 and 3
cycles can be achieved by depositing a 3 nm Au catalyst layer on the substrate and growing the
nanowires by PLD for the desired number of cycles. (p) After that, the Cr layer and the
nanowires on the surface substrate are lifted off with the Cr etchant solution (q) the 1-cycle
growth nanowire device is sealed with a fused quartz cover glass as in the previous process (10),
and the 3-cycle nanowire device is obtained. (r, s, t, and u) To prepare the 5-cycle growth
nanowire device, the 3 nm Au catalyst layer is deposited on the substrate and the nanowires are
grown by PLD for 2 more cycles. (v) After that, the Cr layer and nanowires on the surface
substrate are lifted off with Cr etchant solution; then the device is covered and sealed with a
cover glass (10). (w) Thus, the 5-cycle growth nanowire device is achieved.
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Figure S2 Peak identification in the network structure. (a) Peak identification of 166 kbp DNA
(20 ng/µL) and 48.5 kbp DNA (50 ng/µL) in the nanowire network structure with the (I) 1-cycle
growth nanowires, (II) 3-cycle growth nanowires, and (III) 5-cycle growth nanowires. The
applied DC electric field in the separation channel was 500 V/cm. (b) Peak identification of (I)
48.5 kbp DNA (20 ng/µL) and 10 kbp DNA (40 ng/µL) in the nanowire network structure with
1-cycle growth nanowires at the applied DC electric field of 500 V/cm, (II) 10 kbp DNA (30
ng/µL) and 5 kbp DNA (30 ng/µL) in the nanowire network structure with 3-cycle growth
nanowires at the applied DC electric field of 500 V/cm, and (III) 1 kbp DNA (30 ng/µL) and 100
bp DNA (30 ng/µL) in the nanowire network structure with 5-cycle growth nanowires at the
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applied DC electric field of 500 V/cm. The electropherograms in (a) and (b) were obtained at 1
mm from the entrance of the microchannel with the nanowire network structure.
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Figure S3 Separation data in the network structure. (a) Separation of 166 kbp DNA (20 ng/µL)
and 48.5 kbp DNA (50 ng/µL) in the nanowire network structure with the (I) 1-cycle growth
nanowires, (II) 3-cycle growth nanowires, and (III) 5-cycle growth nanowires. The applied DC
electric field in the separation channel was 500 V/cm. (b) Separation of (I) 48.5 kbp DNA (20
ng/µL) and 10 kbp DNA (40 ng/µL) in the nanowire network structure with 1-cycle growth
nanowires at the applied DC electric field of 500 V/cm, (II) 10 kbp DNA (30 ng/µL) and 5 kbp
DNA (30 ng/µL) in the nanowire network structure with 3-cycle growth nanowires at the applied
DC electric field of 500 V/cm, and (III) 1 kbp DNA (30 ng/µL) and 100 bp DNA (30 ng/µL) in
the nanowire network structure with 5-cycle growth nanowires at the applied DC electric field of
500 V/cm. The electropherograms in (a) and (b) were obtained at 1 mm from the entrance of the
microchannel with the nanowire network structure.
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Figure S4 Fitting curves for mobility vs. DNA size, mobility vs. number of growth cycles, and
time vs. DNA size. (a) Natural logarithm of mobility vs. DNA size ranging from 0 to 5 kbp in
the nanowire network structure with the 5-cycle growth nanowires. The dotted line is a linear fit
to data points of DNA size from 0 to 1 kbp. This fit demonstrated Ogston behavior in shorter
DNA molecules. (b) Natural logarithm of mobility vs. number of growth cycles. The dotted line
is a linear fit to data points of growth cycles. This fit also demonstrated Ogston behavior in
shorter DNA molecules.
(c) Transportation time and diffusion time vs. DNA size in the
nanowire network structure with the 5-cycle growth nanowires. Both dotted lines are linear fits
to data points of DNA size. These fits showed the transportation time is smaller than the
diffusion time.
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