Support Information: Nanoparticle Aggregation Logic Computing Controlled by
DNA Branch Migration
Cheng Zhang (张成),1, a) Jingjing Ma (麻晶晶),1,
Schlaberg,2 Shi Liu (刘石),2 and Jin Xu (许进)1, a)
b)
Jing Yang (杨静),2 H. Inaki
1
Institute of Software, School of Electronics Engineering and Computer Science, Key
Laboratory of High Confidence Software Technologies of Ministry of Education,
Peking University, Beijing 100871, People’s Republic of China
2
North China Electric Power University, School of Control and Computer
Engineering, Beijing 102206, People’s Republic of China
a)
b)
Electronic mail: zhangcheng369@pku.edu.cn and jxu@pku.edu.cn
Cheng Zhang and Jingjing Ma contributed equally to this work.
1. DNA sequences used in experiment
The sequences of the oligonucleotides are listed in Table S1.
NO.
B
abd
abc
2A1
2A2
efh
egh
2A4
2B1
2B2
Da
Dc
D1
D2
Sequence (from 5’ to 3’)
TAGTGCCAGATTTTT-SH
ATTCATCTAGTGCCAGAGGTATCC
ATTCATCTCGCTTGTCAGGTATCC
TCTGGCACTATGACAAGCGA
TCTGGCACTATCGCTTGTCA
CTAATCACCCTGCTTCGGGGAACTGG
CTAATCACATACGCATTCCGAACTGG
CCCGAAGCAGGGGGAATGCGTATG
CCCTGCTTCGTCGCTTGTCA
TCTGGCACTACATACGCATT
GGTTTGTATTGGCATATCACTCTTTTTTTTTTTT-SH
GCCTTACGAGTCTTCTTTTTTTTTTTT-SH
GAGTGATATGCCAATACAAACC CACAACTCAGTA
GAAGACTCGTAAGGCTACTGAGTTGTG
(-SH: thoilated DNA)
Table S1. DNA sequences
2. Materials
The main materials and chemicals used in our experiments are as follows: gold
nanoparticles
(AuNPs)
with
diameter
of
5
and
15
nm
from
Ted
Pella;
Bis(p-sulfonatophenyl)phenylphosphinedipotassium salt dihydrate (BSPP) from Strem
Chemical; Tris-Borate-EDTA buffer (TBE) and Tris-Acetic-EDTA buffer (TAE) from
Solarbio; disulfide protected thiolated oligonucleotides by purification of HPLC from Sangon
China; agarose from BIOWEST; methylenebisacrylamide and acrylamide monomer from
TCI, Stains-All from SIGMA ALORICH.
3. PAGE gel analysis of DNA strands
Before starting the experiment, the hybridizations of DNA strands were tested by PAGE
gel, to determine whether they would work well in strand displacement reactions. The gel
experiments were performed with TAE buffer by a mini gel device (Bio-rad). Then gels were
stained with Stain all for 20 min.
4. Multivalent DNA/AuNPs conjugations
The key method used in this work is conjugation of DNA and AuNP. 15 nm AuNP and
thiol-DNA strands were used in the experiment. The specific steps were as follows: (1) The
thiol-DNA strands were activated by dithio- threitol (DTT) and then extracted twice by ethyl
acetate. (2) The “activated” thiol-DNA samples were added to the AuNP solution directly to
(3) Then, an
“Aging process” was carried out. Sodium polyphosphate buffer (pH 7.0) was added to 0.01
M. Later, NaCl was gradually added to a concentration to 0.2 M. The samples were then
incubated for 40 h.
(4) Unbound DNA was removed by centrifugation at
30 min.
(5) The obtained DNA/AuNP conjugates were redissolved in sodium polyphosphate
The main materials are as follows: Disodium hydrogen
phosphate, sodium dihydrogen phosphate, NaCl, DTT, ethyl acetate (All chemicals were of
analytical grade); 15 nm AuNP from Tedpella; All DNA samples were from Shang- hai
Sangon. The equipment: Alpha Imager, Anke TGL-16G centrifuge, Bio photometer
(eppendorf), ELGA Ultra-Pure Water System, Sartorius electronic balance. Tne AuNPs
concentration was detected using extinction coefficients: ε520 (5 nm) = 9.3 x 106 M-1cm-1.
5. Triggering the aggregation of nanoparticles
In each reaction system, the volume of AuNP solution labeled by specific DNA strands
was 100 μL. NaCl was added to 0.2 M, and products of DNA displacement were gradually
added to the solution of AuNPs (adding small volumes for 4-8 times). At the end of the
reaction, the experimental results were detected by absorbance at 520 nm. All reactions were
performed in triplicate with independent samples.
6. TEM images
TEM images were obtained using a Tecnai G20. To increase surface hydrophilicity, TEM
grids were ionized for 20-30 s using oxygen plasma cleaner (Harrick Plasma PDC-32). Then
2-4 μL of purified sample was spotted on the surface and left on the grid for 3 min. Later,
added 10 μL of 0.5X TBE buffer for washing and used filter paper to wick off excess buffer.
After repeating washing for 1-2 times, grids were air-dried for analyzing. In the transmission
electron micrographs, there were many typical products as shown in Fig S1. Scale bars 100
nm, 50 nm and 20 nm. In Fig S1A, simple unit: 5 nm nanoparticles surrounded one 15 nm
particle to form a particle shell. In Fig S1B, many simple units aggregated to form a large
cluster.
Figure S1. TEM Analysis of AuNPs /DNA conjugates products