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Critical behavior of megabase-size DNA toward the transition into a compact state
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Image of FIG. 1.

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FIG. 1.

FM images of S120-1 DNA (a)–(d) and T4 DNA molecules (e) on a glass surface in aqueous environment, and an AFM image of S120-1 DNA on a mica surface in dry state (f). (a)–(e) DNAs are extended by inducing weak convective flow with a pipette in 10 mM Tris-HCl buffer at pH 7.6 and fixed on a glass surface, (f) DNA sample is gently adsorbed on a mica surface in 10 mM Tris-HCl buffer with 0.01 mM SPD at pH 7.6, and then rinsed with water and dried before the measurement.

Image of FIG. 2.

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FIG. 2.

Real-time monitoring of a single DNA molecule in bulk solution with various concentrations of SPD and corresponding quasi-three-dimensional profile of the fluorescence intensity. Total observation time is 1 s for all of the successive pictures. In (a), (b), (d), and (e), Brownian fluctuations are seen for both translational and intra-chain motions. In (c) and (f), the images of the compact state are situated at the center of each frame by shifting the position of the objects because of their significant translational Brownian motion; on the order of 5–10 μm for 1 s.

Image of FIG. 3.

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FIG. 3.

FM images of T4 DNA (a) and (b) and S120-1 DNA (c) in the presence of 0.1 mM SPD and corresponding quasi-three-dimensional profile of the fluorescence intensity. (a) and (c) On a glass surface in aqueous environment and (b) in bulk solution. In (b), the coexistence of coil and globule DNAs is observed, where only 0.5%–1% of T4 DNA molecules exhibit a compacted globule state.

Image of FIG. 4.

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FIG. 4.

AFM images of DNA molecules at various concentrations of SPD in dry state. All of the specimens are gently adsorbed on the mica surface without shear stress.

Image of FIG. 5.

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FIG. 5.

AFM images of S120-1 DNA in the presence of 0.1 mM SPD. (a) Megabase-size DNA (an enlarged image of Fig. 4(g)), and (b) short fragments produced by mechanical agitation (pipetting and shaking) of S120-1 DNA.

Image of FIG. 6.

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FIG. 6.

Dependence of the degree of parallel ordering, S = 〈cos 2Δθ i 〉, on the logarithm of the SPD concentration (top graph). The illustration shows how we evaluated the degree of ordering from the AFM image. In the actual procedure, the S value is averaged for the data set of cross-sectional lines with different angles. Detail of the procedure to calculate S value is given in the text.

Image of FIG. 7.

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FIG. 7.

Schematic illustrations of different intermediate states between coil and compact conformations of DNA.

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/content/aip/journal/jcp/135/22/10.1063/1.3666845
2011-12-08
2014-04-17

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.

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Scitation: Critical behavior of megabase-size DNA toward the transition into a compact state
http://aip.metastore.ingenta.com/content/aip/journal/jcp/135/22/10.1063/1.3666845
10.1063/1.3666845
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