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Title: Critical behavior of megabase-size DNA toward the transition into a compact state.
Authors: Yoshikawa, Yuko
Suzuki, Yuki  KAKEN_id
Yamada, Kozo
Fukuda, Wakao
Yoshikawa, Kenichi
Takeyasu, Kunio
Imanaka, Tadayuki
Author's alias: 吉川, 研一
Keywords: atomic force microscopy
biochemistry
DNA
fluorescence
molecular biophysics
molecular configurations
optical microscopy
segregation
Issue Date: 14-Dec-2011
Publisher: American Institute of Physics
Journal title: The Journal of chemical physics
Volume: 135
Issue: 22
Thesis number: 225101
Abstract: We studied the changes in the higher-order structure of a megabase-size DNA (S120-1 DNA) under different spermidine (SPD) concentrations through single-molecule observations using fluorescence microscopy (FM) and atomic force microscopy (AFM). We examined the difference between the folding transitions in S120-1 DNA and sub-megabase-size DNA, T4 DNA (166 kbp). From FM observations, it is found that S120-1 DNA exhibits intra-chain segregation as the intermediate state of transition, in contrast to the all-or-none nature of the transition on T4 DNA. Large S120-1 DNA exhibits a folding transition at lower concentrations of SPD than T4 DNA. AFM observations showed that DNA segments become aligned in parallel on a two-dimensional surface as the SPD concentration increases and that highly intense parallel alignment is achieved just before the compaction. S120-1 DNA requires one-tenth the SPD concentration as that required by T4 DNA to achieve the same degree of parallel ordering. We theoretically discuss the cause of the parallel ordering near the transition into a fully compact state on a two-dimensional surface, and argue that such parallel ordering disappears in bulk solution.
Rights: © 2011 American Institute of Physics
URI: http://hdl.handle.net/2433/152375
DOI(Published Version): 10.1063/1.3666845
PubMed ID: 22168726
Appears in Collections:Journal Articles

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