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1
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Cheng S, Wang P, Tao C, Zhang D, Li Z, Yamaguchi Y. The effect of electrophoretic parameters on separation performance of short DNA fragments. Anal Biochem 2018; 556:99-103. [PMID: 29969583 DOI: 10.1016/j.ab.2018.06.031] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 06/26/2018] [Accepted: 06/29/2018] [Indexed: 11/17/2022]
Abstract
Effective separation of short DNA fragments is important for the identification of PCR or LAMP products. We investigated the effect of electric field strength, sample plug width, effective length of the capillary, concentration and molecular weight of polymer on the separation performance of small DNA. Results demonstrated that the sample plug played a non-negligible role in the peak broadening. The migration time of DNA was exponentially decreased with the increase of electric field strength. Increasing effective length of capillary, concentration or molecular weight of HEC may improve the separation performance, but it was at the cost of long migration time.
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Affiliation(s)
- Shuyi Cheng
- Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, No. 516 JunGong Road, Shanghai, 200093, China
| | - Ping Wang
- Department of Clinical Laboratory, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, 1665 Kongjiang Road, Shanghai, 200092, China
| | - Chunxian Tao
- Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, No. 516 JunGong Road, Shanghai, 200093, China
| | - Dawei Zhang
- Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, No. 516 JunGong Road, Shanghai, 200093, China
| | - Zhenqing Li
- Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, No. 516 JunGong Road, Shanghai, 200093, China.
| | - Yoshinori Yamaguchi
- Photonics and Bio-medical Research Institute, Department of Physics Faculty of Science, East China University of Science and Technology, No. 130 Meilong Road, Shanghai, 200237, China; Department of Applied Physics, Graduate School of Engineering, Osaka University, Yamadaoka Suita-city, Osaka, 565-0871, Japan.
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2
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Zhu Y, Li Z, Wang P, Shen L, Zhang D, Yamaguchi Y. Factors affecting the separation performance of proteins in capillary electrophoresis. J Chromatogr B Analyt Technol Biomed Life Sci 2018. [DOI: 10.1016/j.jchromb.2018.03.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Kubo T, Nishimura N, Furuta H, Kubota K, Naito T, Otsuka K. Tunable separations based on a molecular size effect for biomolecules by poly(ethylene glycol) gel-based capillary electrophoresis. J Chromatogr A 2017. [DOI: 10.1016/j.chroma.2017.06.043] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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4
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Capillary electrophoresis of RNA in hydroxyethylcellulose polymer with various molecular weights. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1011:114-20. [DOI: 10.1016/j.jchromb.2015.12.057] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 12/22/2015] [Accepted: 12/28/2015] [Indexed: 11/17/2022]
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5
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Affiliation(s)
- Rachel K Harstad
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Alexander C Johnson
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Megan M Weisenberger
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
| | - Michael T Bowser
- University of Minnesota , Department of Chemistry, 207 Pleasant Street South East, Minneapolis, Minnesota 55455, United States
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6
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Yamaguchi Y, Li Z, Zhu X, Liu C, Zhang D, Dou X. Polyethylene Oxide (PEO) and Polyethylene Glycol (PEG) Polymer Sieving Matrix for RNA Capillary Electrophoresis. PLoS One 2015; 10:e0123406. [PMID: 25933347 PMCID: PMC4416823 DOI: 10.1371/journal.pone.0123406] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 02/18/2015] [Indexed: 11/18/2022] Open
Abstract
The selection of sieving polymer for RNA fragments separation by capillary electrophoresis is imperative. We investigated the separation of RNA fragments ranged from 100 to 10,000 nt in polyethylene glycol (PEG) and polyethylene oxide (PEO) solutions with different molecular weight and different concentration. We found that the separation performance of the small RNA fragments (<1000 nt) was improved with the increase of polymer concentration, whereas the separation performance for the large ones (>4000 nt) deteriorated in PEG/PEO solutions when the concentration was above 1.0%/0.6%, respectively. By double logarithmic plot of mobility and RNA fragment size, we revealed three migration regimes for RNA in PEG (300-500k) and PEO (4,000k). Moreover, we calculated the smallest resolvable nucleotide length (Nmin) from the resolution length analysis.
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Affiliation(s)
- Yoshinori Yamaguchi
- Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, No. 516 Jungong Road, Shanghai 200093, China
- Department of Applied Physics, Graduate School of Engineering, Osaka University, Yamadaoka, Suita-city, Osaka, 565–0871, Japan
| | - Zhenqing Li
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
- * E-mail: (ZL); (XD)
| | - Xifang Zhu
- College of Photoelectric Engineering, Changzhou Institute of Technology, No.299, Tongjiangnan Road, Changzhou, 213002, China
| | - Chenchen Liu
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Dawei Zhang
- Institute of Photonics and Bio-medicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), 130 Meilong Road, Shanghai 200237, China
| | - Xiaoming Dou
- Engineering Research Center of Optical Instrument and System, Ministry of Education, Shanghai Key Lab of Modern Optical System, University of Shanghai for Science and Technology, No. 516 Jungong Road, Shanghai 200093, China
- * E-mail: (ZL); (XD)
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7
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Liu C, Yamaguchi Y, Zhu X, Li Z, Ni Y, Dou X. Analysis of small interfering RNA by capillary electrophoresis in hydroxyethylcellulose solutions. Electrophoresis 2015; 36:1651-7. [PMID: 25867445 DOI: 10.1002/elps.201500018] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 03/18/2015] [Accepted: 03/18/2015] [Indexed: 11/10/2022]
Abstract
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.
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Affiliation(s)
- Chenchen Liu
- Engineering Research Center of Optical Instrument and System, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Yoshinori Yamaguchi
- Institute of Photonics and Biomedicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, P. R. China.,Department of Applied Physics, Graduate School of Engineering, Osaka University, Yamadaoka, Suita-city, Osaka, Japan
| | - Xifang Zhu
- School of Optoelectronic Engineering, Changzhou Institute of Technology, Changzhou, Jiangsu, P. R. China
| | - Zhenqing Li
- Engineering Research Center of Optical Instrument and System, University of Shanghai for Science and Technology, Shanghai, P. R. China
| | - Yi Ni
- Institute of Photonics and Biomedicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, P. R. China
| | - Xiaoming Dou
- Institute of Photonics and Biomedicine (IPBM), Graduate School of Science, East China University of Science and Technology (ECUST), Shanghai, P. R. China.,School of Optoelectronic Engineering, Changzhou Institute of Technology, Changzhou, Jiangsu, P. R. China
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8
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Li Z, Yang R, Wang Q, Zhang D, Zhuang S, Yamaguchi Y. Electrophoresis of periodontal pathogens in poly(ethyleneoxide) solutions with uncoated capillary. Anal Biochem 2015; 471:70-2. [DOI: 10.1016/j.ab.2014.11.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 11/04/2014] [Accepted: 11/05/2014] [Indexed: 11/17/2022]
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9
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Update on Robotic Versus Laparoscopic Sacrocolpopexy: Outcomes and Costs. CURRENT OBSTETRICS AND GYNECOLOGY REPORTS 2014. [DOI: 10.1007/s13669-014-0099-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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Su Y, Mu X, Qi L. A new chiral ligand exchange capillary electrophoresis system based on Zn(ii)–l-leucine complexes coordinating with β-cyclodextrin and its application in screening tyrosinase inhibitors. RSC Adv 2014. [DOI: 10.1039/c4ra09433f] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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11
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Li Z, Chen S, Liu C, Zhang D, Dou X, Yamaguchi Y. Quantification of Periodontal Pathogens Cell Counts by Capillary Electrophoresis. J Chromatogr A 2014; 1361:286-90. [DOI: 10.1016/j.chroma.2014.07.100] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2014] [Revised: 07/31/2014] [Accepted: 07/31/2014] [Indexed: 10/24/2022]
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12
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Li Z, Li D, Zhang D, Yamaguchi Y. Determination and quantification of Escherichia coli by capillary electrophoresis. Analyst 2014; 139:6113-7. [DOI: 10.1039/c4an01649a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Capillary electrophoresis (CE) is widely employed for the separation of nucleic acids or protein, but it is rarely applied in the quantification ofEscherichia coli(E. coli).
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Affiliation(s)
- Zhenqing Li
- Engineering Research Center of Optical Instrument and System
- Ministry of Education
- Shanghai Key Lab of Modern Optical System
- University of Shanghai for Science and Technology
- Shanghai 200093, China
| | - De Li
- Engineering Research Center of Optical Instrument and System
- Ministry of Education
- Shanghai Key Lab of Modern Optical System
- University of Shanghai for Science and Technology
- Shanghai 200093, China
| | - Dawei Zhang
- Engineering Research Center of Optical Instrument and System
- Ministry of Education
- Shanghai Key Lab of Modern Optical System
- University of Shanghai for Science and Technology
- Shanghai 200093, China
| | - Yoshinori Yamaguchi
- Photonics and Bio-medical Research Institute
- Department of Physics Faculty of Science
- East China University of Science and Technology
- Shanghai 200237, China
- Department of Applied Physics
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