Nanochannel-Confined TAMRA-Polypyrrole Stained DNA Stretching by Varying the Ionic Strength from Micromolar to Millimolar Concentrations
Seonghyun Lee,
Yelin Lee,
Yongkyun Kim,
Cong Wang,
Jungyul Park,
Gun Young Jung,
Yenglong Chen,
Rakwoo Chang,
Shuji Ikeda,
Hiroshi Sugiyama,
Kyubong Jo
Affiliations
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
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.
