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Lee S, Lee Y, Kim Y, Wang C, Park J, Jung GY, Chen Y, Chang R, Ikeda S, Sugiyama H, Jo K. Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations. Polymers (Basel) 2018; 11:E15. [PMID: 30959999 PMCID: PMC6401831 DOI: 10.3390/polym11010015] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/17/2018] [Accepted: 12/17/2018] [Indexed: 12/19/2022] Open
Abstract
Large DNA molecules have been utilized as a model system to investigate polymer physics. However, DNA visualization via intercalating dyes has generated equivocal results due to dye-induced structural deformation, particularly unwanted unwinding of the double helix. Thus, the contour length increases and the persistence length changes so unpredictably that there has been a controversy. In this paper, we used TAMRA-polypyrrole to stain single DNA molecules. Since this staining did not change the contour length of B-form DNA, we utilized TAMRA-polypyrrole stained DNA as a tool to measure the persistence length by changing the ionic strength. Then, we investigated DNA stretching in nanochannels by varying the ionic strength from 0.06 mM to 47 mM to evaluate several polymer physics theories proposed by Odijk, de Gennes and recent papers to deal with these regimes.
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Affiliation(s)
- Seonghyun Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yelin Lee
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Yongkyun Kim
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
| | - Cong Wang
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Jungyul Park
- Department of Mechanical Engineering, Sogang University, Seoul 04107, Korea.
| | - Gun Young Jung
- School of Material Science and Engineering, GIST, Gwangju 61005, Korea.
| | - Yenglong Chen
- Institute of Physics, Academia Sinica and Department of Chemical Engineering, National Tsing-Hua University and Department of Physics, National Taiwan University, Taipei 10617, Taiwan.
| | - Rakwoo Chang
- Department of Chemistry, Kwangwoon University, Seoul 01897, Korea.
| | - Shuji Ikeda
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Hiroshi Sugiyama
- Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-Ku, Kyoto 606-8501, Japan.
| | - Kyubong Jo
- Department of Chemistry and Integrated Biotechnology, Sogang University, Seoul 04107, Korea.
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