Analysis of small interfering RNA by capillary electrophoresis in hydroxyethylcellulose solutions

The analysis of small interfering RNA (siRNA) is important for gene function studies and drug developments. We employed CE to study the separation of siRNA ladder marker, which were ten double‐stranded RNA (dsRNA) fragments ranged from 20 to 1000 bp, in solutions of hydroxyethylcellulose (HEC) polym...

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Bibliographic Details
Published in:Electrophoresis 2015-07, Vol.36 (14), p.1651-1657
Main Authors: Liu, Chenchen, Yamaguchi, Yoshinori, Zhu, Xifang, Li, Zhenqing, Ni, Yi, Dou, Xiaoming
Format: Article
Language:English
Subjects:
Capillary electrophoresis
Cellulose - analogs & derivatives
Cellulose - chemistry
double-stranded DNA
double-stranded RNA
Electrophoresis
Electrophoresis, Capillary - methods
Fragments
Genes
Hydroxyethylcellulose
Ladders
Markers
Migration
Molecular weight
Ribonucleic acids
RNA, Small Interfering - chemistry
small interfering RNA
Solutions
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Summary:The analysis of small interfering RNA (siRNA) is important for gene function studies and drug developments. We employed CE to study the separation of siRNA ladder marker, which were ten double‐stranded RNA (dsRNA) fragments ranged from 20 to 1000 bp, in solutions of hydroxyethylcellulose (HEC) polymer with different concentrations and molecular weights (Mws). Migration mechanism of dsRNA during CE was studied by the mobility and resolution length (RL) plots. We found that the RL depended on not only the concentration of HEC, but also the Mw of HEC. For instance, RL of small dsRNA fragment was more influenced by concentration of high Mw HEC than large dsRNA fragment and RL of large dsRNA fragment was more influenced by concentration of low Mw HEC than small dsRNA fragment. In addition, we found electrophoretic evidence that the structure of dsRNA was more compact than dsDNA with the same length. In practice, we succeeded to separate the glyceraldehyde 3‐phosphate dehydrogenase siRNA in the mixture of the siRNA ladder marker within 4 min.
ISSN:0173-0835
1522-2683
DOI:10.1002/elps.201500018