Supporting information
Analysis of Small Interfering RNA by Capillary Electrophoresis
in Hydroxyethylcellulose Solutions
Chenchen Liu1, Yoshinori Yamaguchi2, 3, Xifang Zhu4, Zhenqing Li1, Yi Ni2,
Xiaoming Dou2,4
1Engineering
Research Center of Optical Instrument and System, University of Shanghai for
Science and Technology, 516 Jungong Road, Shanghai 200093, China
2Institute
of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China
University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
3Department
of Applied Physics, Graduate School of Engineering, Osaka University, Yamadaoka,
Suita-city, Osaka, 565-0871, Japan
4School
of Optoelectronic Engineering, ChangZhou Institute of Technology, 299 South Tongjiang
Road, Changzhou, Jiangsu 213002, China
Correspondence: Dr. Yoshinori Yamaguchi, Department of Applied Physics, Graduate School of
Engineering, Osaka University, Yamadaoka, Suita-city, Osaka, 565-0871, Japan
Dr. Xiaoming Dou, Graduate School of Science, East China University of Science and
Technology, 130 Meilong Road, Shanghai 200237, China
Email: yoshi.yamaguchi@ap.eng.osaka-u.ac.jp; xiaomingdou@yeah.net
S1. Noncoding siRNA ladder marker contained 10 dsRNA fragments: 20 bp, 30 bp,
40 bp, 50 bp, 100 bp, 200 bp, 300 bp, 400 bp, 500 bp and 1,000 bp. dsDNA
sample contained 13 dsDNA fragments which were 20 bp, 40 bp, 60 bp, 80 bp,
100 bp, 120 bp, 140 bp, 160 bp, 180 bp, 200 bp, 300 bp, 400 bp and 500 bp.
S2. To examine the RL difference between dsRNA and dsDNA, we calculated RL
between the adjacent dsRNA fragments of 20 bp, 40 bp, 100 bp, 200 bp, 300 bp,
400 bp and 500 bp. As shown in Fig. S1(a)
Figure S1. (a) The plot of RL versus dsRNA/dsDNA fragment size in different concentrations of
250k HEC solution. (b) The double logarithmic plot of the mobility versus dsRNA/dsDNA
fragment size in different concentrations of 250k HEC solution. CE conditions were the same as in
Figure 1.
S3. Mobility, resolution and resolution length
Mobility (μ), resolution(Rs) and resolution length (RL) were employed to evaluate
the separation performances for CE. The mobility and resolution are defined as
following:
μ =v/E=Le/(t E)
(s1)
where, v is the migrating velocity of nucleic acid fragments, Le is the effective length
of the capillary, t is the migration time and E is the electric field strength applied on
the capillary. And
Rs =2 x / (w1 + w2)
(s2)
where x is the difference of migration time between two peaks in electropherogram,
w is the full width of half-maximum of these two peaks (w1, w2). Peak width and
migration time (t) from the electropherogram were determined by Gaussian fitting and
the author’s observation when asymmetry appeared. Baseline separation is defined
when Rs equaled to 1.5 in this paper. When Rs equals to 1, the adjacent two peaks are
overlapped at about 0.3 of full height of peak.
In this paper, we employed RL. Mathematically, RL is the “natural unit”
normalized from Rs (Equation (3)), which is:
RL= n/Rs
(s3)
where, n is the size difference between two adjoined peaks. RL represents the
“resolution per base”, and RL theoretically describes the size difference that can be
resolved as Rs equal to 1. Small value of RL indicates good separation performance.