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Research contents - Ichikawa Laboratory

    Soft Matter Physics

    Nonlinear Physics under Nonequilibrium Conditions

    Structure and functions of macromolecules (DNA)




Soft Matter Physics

    Direct observations of transition dynamics from macro- to micro-phase separation in asymmetric lipid bilayers induced by externally added glycolipids

    Non-periodic oscillatory deformation of an actomyosin microdroplet encapsulated within a lipid interface

    Coupling between pore formation and phase separation in charged lipid membranes

    Wrinkling of a spherical lipid interface induced by actomyosin cortex

    Droplet-shooting and size-filtration (DSSF) method for synthesis of cell-sized liposomes with controlled lipid compositions

    Molecular behavior of DNA in a cell-sized compartment coated by lipids

    Direct measurement of DNA-mediated adhesion between lipid bilayers

    Quantification of the influence of endotoxins on the mechanics of adult and neonatal red blood cells

    Emergence of DNA-Encapsulating Liposomes from a DNA–Lipid Blend Film

    Dynamical formation of lipid bilayer vesicles from lipid-coated droplets across a planar monolayer at an oil/water interface

    Emergence of a thread-like pattern with charged phospholipids on an oil/water interface

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Direct observations of transition dynamics from macro- to micro-phase separation in asymmetric lipid bilayers induced by externally added glycolipids

In general, phase separation in binary liquid mixtures completes by relaxation below the transition temperature. However, it is also well known that the competition between local attractive and long-ranged repulsive interactions between two phases leads to stable micro-phase separation. The coarsening dynamics from a homogeneous phase to macro- or micro-phase has been extensively investigated in binary mixture systems of polymeric and/or low-molecular-weight molecules. In contrast, the dynamics from macro- to micro-phase separation remains poorly understood because no appropriate experiments and models exist for investigating this phenomenon (figure a). In this letter, We present the first direct observations of morphological transitions from macro- to micro-phase separation using micrometer-sized asymmetric lipid vesicles exposed to externally added glycolipids (GM1:monosialotetrahexosylganglioside). The transition occurs via an intermediate stripe morphology state. During the transition, monodisperse micro-domains emerge through repeated scission events of the stripe domains (figure b,c). By numerically analyzing the bending elastic model and the time-dependent Ginzburg-Landau equation (figure b), we gained insights into the mechanism of the novel transitions, which is apparently governed by the local spontaneous curvature induced by the local asymmetric composition. Our findings could provide important mechanistic clues for new material designs and for understanding the dynamics of the heterogeneities existing in cell membranes.

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Reference
"Direct observations of transition dynamics from macro- to micro-phase separation in asymmetric lipid bilayers induced by externally added glycolipids" Shunsuke F. Shimobayashi, Masatoshi Ichikawa and Takashi Taniguchi, Europhysics Letters, 113, 56005 (2016).

Non-periodic oscillatory deformation of an actomyosin microdroplet encapsulated within a lipid interface

Active force generation in living organisms, which is mainly involved in actin cytoskeleton and myosin molecular motors, plays a crucial role in various biological processes. Although the contractile properties of actomyosin have been extensively investigated, their dynamic contribution to a deformable membrane remains unclear because of the cellular complexities and the difficulties associated with in vitro reconstitution. Here, by overcoming these experimental difficulties, we demonstrate the dynamic deformation of a reconstituted lipid interface coupled with self-organized structure of contractile actomyosin. Therein, the lipid interface repeatedly oscillates without any remarkable periods. The oscillatory deformation of the interface is caused by the aster-like three-dimensional hierarchical structure of actomyosin inside the droplet, which is revealed that the oscillation occurs stochastically as a Poisson process.

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Reference
"Non-periodic oscillatory deformation of an actomyosin microdroplet encapsulated within a lipid interface", Y. Nishigami, H. Ito, S. Sonobe and M. Ichikawa, Sci. Rep., 6, 18964 (2016).

Coupling between pore formation and phase separation in charged lipid membranes

We investigated the effect of charge on the membrane morphology of giant unilamellar vesicles (GUVs) composed of various mixtures containing charged lipids. We observed the membrane morphologies by fluorescent and confocal laser microscopy in lipid mixtures consisting of a neutral unsaturated lipid (DOPC), a neutral saturated lipid (DPPC), a charged unsaturated lipid (DOPG(∁E), a charged saturated lipid (DPPG(∁E), and cholesterol (Chol). In binary mixtures of neutral DOPC-DPPC and charged DOPC-DPPG(∁E, spherical vesicles were formed. On the other hand, pore formation was often observed with GUVs consisting of DOPG(∁E and DPPC. In a DPPC-DPPG(∁E-Chol ternary mixture, pore-formed vesicles were also frequently observed. The percentage of pore-formed vesicles increased with the DPPG(∁E concentration. Moreover, when the head group charges of charged lipids were screened by the addition of salt, pore-formed vesicles were suppressed in both the binary and ternary charged lipid mixtures. We discuss the mechanisms of pore formation in charged lipid mixtures and the relationship between phase separation and the membrane morphology. Finally, we reproduce the results seen in experimental systems by using coarse-grained molecular dynamics simulations.

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Reference
"Coupling between pore formation and phase separation in charged lipid membranes", H. Himeno, H. Ito, Y. Higuchi, T. Hamada, N. Shimokawa, and M. Takagi, Phys. Rev. E, 92, 062713 (2015).

Wrinkling of a spherical lipid interface induced by actomyosin cortex

Actomyosin actively generates contractile forces that provide the plasma membrane with the deformation stresses essential to carry out biological processes. Although the contractile property of purified actomyosin has been extensively studied, to understand the physical contribution of the actiomyosin contractile force on a deformable membrane is still a challenging problem and of great interest in the field of biophysics. Here, we reconstituted a model system with a cell-sized deformable interface that exhibits anomalous curvature dependent wrinkling caused by actomyosin cortex underneath the spherical closed interface. Through the shape analysis of the wrinkling deformation, we found that the dominant contributor on the wrinkled shape changes from bending elasticity to stretching elasticity of the reconstituted cortex by increasing the droplet curvature radius of the order of the cell-size, i.e., tens of micrometer. The observed curvature dependence was explained by the theoretical description of the cortex elasticity and contractility. Our present results provide a fundamental insight on the deformation of a curved membrane induced by the actomyosin cortex.

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Reference
"Wrinkling of a spherical lipid interface induced by actomyosin cortex", H. Ito, Y. Nishigami, S. Sonobe, and M. Ichikawa, Phys. Rev. E, 92, 062711 (2015).

Droplet-shooting and size-filtration (DSSF) method for synthesis of cell-sized liposomes with controlled lipid compositions

We report a centrifugal microfluidic method, droplet-shooting and size-filtration (DSSF), for the production of cell-sized liposomes with controlled lipid compositions. This involves the generation of large and small droplets from the tip of a glass capillary and the selective transfer of small droplets through an oil-water interface, thus resulting in the generation of cell-sized liposomes. We demonstrate control of the microdomain formation as well as the formation of asymmetric lipid bilayer liposomes of uniform size by the control of lipid composition. The DSSF method involves simple microfluidics and is easy to use. In addition, only a small volume (0.5 E mL) of sample solution is required for the formation of hundreds of cell-sized liposomes. We believe that this method can be applied to generate cell-sized liposomes for a wide variety of uses, such as the construction of artificial cell-like systems.

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Reference
"Droplet-shooting and size-filtration (DSSF) method for synthesis of cell-sized liposomes with controlled lipid compositions", M. Morita, H. Onoe, M. Yanagisawa, H. Ito, M. Ichikawa, K. Fujiwara, H. Saito, and M. Takinoue, ChemBioChem, 16, 2029 (2015).

Molecular behavior of DNA in a cell-sized compartment coated by lipids

The behavior of long DNA molecules in a cell-sized confined space was investigated. We prepared water-in-oil droplets covered by phospholipids, which mimic the inner space of a cell, following the encapsulation of DNA molecules with unfolded coil and folded globule conformations. Microscopic observation revealed that the adsorption of coiled DNA onto the membrane surface depended on the size of the vesicular space. Globular DNA showed a cell-size-dependent unfolding transition after adsorption on the membrane. Furthermore, when DNA interacted with a two-phase membrane surface, DNA selectively adsorbed on the membrane phase, such as an ordered or disordered phase, depending on its conformation. We discuss the mechanism of these trends by considering the free energy of DNA together with a polyamine in the solution. The free energy of our model was consistent with the present experimental data. The cooperative interaction of DNA and polyamines with a membrane surface leads to the size-dependent behavior of molecular systems in a small space. These findings may contribute to a better understanding of the physical mechanism of molecular events and reactions inside a cell.

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Reference
"Molecular behavior of DNA in a cell-sized compartment coated by lipids", Tsutomu Hamada, Rie Fujimoto, Shunsuke F. Shimobayashi, Masatoshi Ichikawa and Masahiro Takagi, Physical Review E, 91(6), 062717 (2015).
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Direct measurement of DNA-mediated adhesion between lipid bilayers

Multivalent interactions between deformable mesoscopic units are ubiquitous in biology, where membrane macromolecules mediate the interactions between neighbouring living cells and between cells and solid substrates. Lately, analogous artificial materials have been synthesised by functionalising the outer surface of compliant Brownian units, for example emulsion droplets and lipid vesicles, with selective linkers, in particular short DNA sequences. This development extended the range of applicability of DNA as a selective glue, originally applied to solid nano and colloidal particles. On very deformable lipid vesicles, the coupling between statistical effects of multivalent interactions and mechanical deformation of the membranes gives rise to complex emergent behaviours, as we recently contributed to demonstrate [Parolini et al., Nature Communications, 2015, 6, 5948]. Several aspects of the complex phenomenology observed in these systems still lack a quantitative experimental characterisation and fundamental understanding. Here we focus on the DNA-mediated multivalent interactions of a single liposome adhering to a flat supported bilayer. This simplified geometry enables the estimate of the membrane tension induced by the DNA-mediated adhesive forces acting on the liposome. Our experimental investigation is completed by morphological measurements and the characterisation of the DNA-melting transition, probed by in-situ Förster Resonant Energy Transfer spectroscopy. Experimental results are compared with the predictions of an analytical theory that couples the deformation of the vesicle to a full description of the statistical mechanics of mobile linkers. With at most one fitting parameter, our theory is capable of semi-quantitatively matching experimental data, confirming the quality of the underlying assumptions.

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Reference
"Direct measurement of DNA-mediated adhesion between lipid bilayers", Shunsuke F. Shimobayashi, B. M. Mognetti, L. Parolini, D. Orsi, P. Cicuta and L. Di Michele, Physical Chemistry Chemical Physics , 17(24),15615-15628 (2015).
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Quantification of the influence of endotoxins on the mechanics of adult and neonatal red blood cells

We physically modeled the influence of endotoxin-induced sepsis symptoms on human red blood cells (RBCs) by quantifying the impact of endotoxins on the cell mechanics by the analysis of Fourier-transformed mean square amplitude of shape fluctuation, called flicker spectroscopy. With the aid of a microfluidic diffusion chamber, we noninvasively determined principal mechanical parameters of human RBCs in the absence and presence of endotoxins for individual RBCs for the first time. Because of the elongation of saccharide chain length of endotoxins, we found an increase in the morphological transition from discocytes to echinocytes, and monotonic changes in the mechanical parameters. Since septic shocks often cause lethal risks of neonates, we measured the mechanical parameters of neonatal RBCs, and compared them to those of adult RBCs. The quantitative comparison reveals that neonatal RBCs are more susceptible to the effect of endotoxins than adult RBCs. Furthermore, coincubation with the antiseptic peptide P19-2.5 (Aspidasept) with endotoxin results in a slight suppression of the impact of the endotoxin. The strategy proposed in our study can potentially be applied for the quantitative diagnosis of RBCs based on mechanical readouts.

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Reference
"Quantification of the influence of endotoxins on the mechanics of adult and neonatal red blood cells", H. Ito, N. Kuss, Bastian E. Rapp, Masatoshi Ichikawa, Thomas Gutsmann, Klaus Brandenburg, Johannes M. B. Poeschl, and Motomu Tanaka, J. Phys. Chem. B, 119, 7837 (2015).
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Emergence of DNA-Encapsulating Liposomes from a DNA–Lipid Blend Film

Spontaneous generation of DNA-enclosing liposomes from a DNA–lipid blend film is investigated. The special properties of the lipid vesicles, namely, micrometer size, unilamellarity, and dense polymer encapsulation acquired by the dehydration–rehydration process, are physicochemically revealed. We found that the formation of giant unilamellar vesicles encapsulating DNAs are governed by micropatterns of the films, such as dots and network patterns. From the results, we proposed a plausible physical mechanism for the dehydration–rehydration process, making it possible to optimize the encapsulation of any agent.

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Reference
"Emergence of DNA-Encapsulating Liposomes from a DNA–Lipid Blend Film", Shunsuke F. Shimobayashi, and Masatoshi Ichikawa The Journal of Physical Chemistry B, 118 (36), 10688-10694 (2014).
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Dynamical formation of lipid bilayer vesicles from lipid-coated droplets across a planar monolayer at an oil/water interface

Recently, the transfer method has been shown to be useful for preparing cell-sized phospholipid bilayer vesicles, within which desired substances at desired concentrations can be encapsulated, with a desired asymmetric lipid composition. Here, we investigated the transfer process of water-in-oil (W/O) droplets coated by phospholipid monolayers across an oil/water interface by both experimental observation and theoretical modeling. Real-time experimental observation of the transfer revealed that the transfer process is characterized by three kinetic regimes: a precontact process (approaching regime), an early fast process (entering regime), and a late slow process (relaxation regime). In addition, bigger droplets require much more time to transfer than smaller droplets. We propose a theoretical model to interpret this kinetic process. Our theoretical model reproduces the essential aspects of the transfer kinetics, including its size-dependence.

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Reference
"Dynamical formation of lipid bilayer vesicles from lipid-coated droplets across a planar monolayer at an oil/water interface", H. Ito, T. Yamanaka, S. Kato, T. Hamada, M. Takagi, M. Ichikawa, and K. Yoshikawa, Soft Matter, 9, 9539-9547 (2013).
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Emergence of a thread-like pattern with charged phospholipids on an oil/water interface

The spontaneous formation of a thread-like pattern with negatively charged lipids on an oil/water interface is reported. An analysis of the time-dependent change at the interface observed by fluores- cence microscopy revealed that the thread-like pattern is generated through a two-step mechanism. First, inverted lipid micelles in the bulk-oil phase gradually diffuse onto the oil/water interface. Next, the micelles are adsorbed on the interface and self-assemble to form the thread-like pattern. The essential characteristics of this pattern formation are theoretically reproduced by a simple Monte Carlo simulation that takes into account the kinetics in the coalescence of charged micelles on a 2D interface.

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Reference
"Emergence of a thread-like pattern with charged phospholipids on an oil/water interface", H. Ito, M. Yanagisawa, M. Ichikawa, and K. Yoshikawa, J. Chem. Phys. , 136, 204903 (2012).
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Nonlinear Physics under Nonequilibrium Conditions

    Oscillation and collective conveyance of water-in-oil droplets by microfluidic bolus flow

    Novel Micro-scale DC Motor: Noise Induces Regular Rhythmic Motion

    Spontaneous mode-selection in the self-propelled motion of a solid/liquid composite driven by interfacial instability

    Utilizing the eikonal relationship in strategies for reentrant wave termination in excitable media

    Travelling wave of segregation in a highly filled rotating drum

    Contribution of convection to spatiotemporal stripe patterns formed by Ag and Sb coelectrodeposition

    Rotary motion driven by a direct current electric field

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Oscillation and collective conveyance of water-in-oil droplets by microfluidic bolus flow

Microfluidic techniques have been extensively developed to realize micro-total analysis systems in a small chip. For microanalysis, electro-magnetic forces have generally been utilized for the trapping of objects, but hydrodynamics has been little explored despite its relevance to pattern formation. Here, we report that water-in-oil (W/O) droplets can be transported in the grid of an array of other large W/O droplets. As each droplet approaches an interspace of the large droplet array, while exhibiting persistent back-and-forth motion, it is conveyed at a velocity equal to the droplet array. We confirm the appearance of closed streamlines in a numerical simulation, suggesting that a vortex-like stream is involved in trapping the droplet. Furthermore, more than one droplet is also conveyed as an ordered cluster with dynamic reposition.

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Reference
"Oscillation and collective conveyance of water-in-oil droplets by microfluidic bolus flow", T. Ohmura, M. Ichikawa, K. Kamei, and Y.T. Maeda, Applied Physics Letters, 107, 074102 (2015).
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Novel Micro-scale DC Motor: Noise Induces Regular Rhythmic Motion

We demonstrated that a micro scale water droplet shows regular oscillatory motion under DC voltage of several volts. Interestingly, we also found that external noise stabilizes the periodic motion. In our earlier studies (PRE 74,046301 (2006) and APL 96,104105(2010)), it has been reported that oscillatory motion of a droplet is generated under DC voltage on the order of 100V without any switching device. Here, we show that one-order smaller DC voltage induces oscillatory motion and it is stable against noise. Such significant development in this study on the micro droplet motion suggests the possibility to construct a new Nano-scale motor driven by DC less than a volt, working under Brownian noise, in a near future; mimicking the essence of molecular motor in living system.

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Reference
“Micro back-and-forth motion under DC electronic Field E T. Kurimura, M. Takinoue, K. Yoshikawa and M. Ichikawa, Physical Review E, 88, 042918/1-5 (2013).
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Spontaneous mode-selection in the self-propelled motion of a solid/liquid composite driven by interfacial instability

Spontaneous motion of a solid/liquid composite induced by a chemical Marangoni effect, where an oil droplet attached to a solid soap is placed on a water phase, was investigated. The composite exhibits various characteristic motions, such as revolution (orbital motion) and translational motion. The results showed that the mode of this spontaneous motion switches with a change in the size of the solid scrap. The essential features of this mode-switching were reproduced by ordinary differential equations by considering nonlinear friction with proper symmetry.

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Reference
"Spontaneous mode-selection in the self-propelled motion of a solid/liquid composite driven by interfacial instability", F. Takabatake, N. Magome, M. Ichikawa, and K. Yoshikawa, J. Chem. Phys., 134, 114704 (2011).
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Utilizing the eikonal relationship in strategies for reentrant wave termination in excitable media

Obstacle-anchored vortices can be terminated by the application of high-frequency wave-trains in excitable media as we have shown in Isomura et al., PRE, 2008. We theoretically derived the dependency between the obstacle radius and the maximum unpinning period through reinterpretation of the well-known eikonal equation. Figure a) shows the restitution curves for three different excitabilities and the minimum velocity on obstacles with size between 0.4 and 2.0cm. The fit of the minimum velocity (dashed line) provides all information to derive the minimum unpinning period (Tmin) to unpin an obstacle bounded spiral wave. Figure b) shows the comparison of numerically and theoretically obtained minimum unpinning period for each excitability, respectively. Our theoretical result was confirmed by experiments with cardiomyocyte monolayers. This result may be useful for improving the stimulation protocol of implantable cardiac pacemakers.

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Reference
"Utilizing the eikonal relationship in strategies for reentrant wave termination in excitable media", M. Hörning, A. Isomura, Z. Jia, E. Entcheva, and K. Yoshikawa, Phys. Rev. E, 81, 056202 (2010).
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Travelling wave of segregation in a highly filled rotating drum

The dynamics of a segregation pattern for a granular mixture in a highly filled rotating drum were studied. A spontaneously segregated band pattern traveled laterally, and was accompanied by the repeated creation of new bands near the center of the drum and annihilation at both of its ends. The presence of nearly stationary convection plays an essential role in causing this travelling wave. Based on direct observations of both the interior and exterior of the segregation pattern, this spatio-temporal pattern is interpreted in terms of a one-dimensional Cahn-Hilliard equation by including the effect of stationary convection.

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Reference
"Travelling wave of segregation in a highly filled rotating drum", Shio Inagaki and Kenichi Yoshikawa, Phys. Rev. Lett., 105, 118001 (2010).
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Contribution of convection to spatiotemporal stripe patterns formed by Ag and Sb coelectrodeposition

Various spatiotemporal patterns of dark and light stripes are formed on the surface of an electrode put in an electrolyte solution in a Ag and Sb coelectrodeposition system. In this study, we investigate the effect of natural convection of the solution on these spatiotemporal patterns. When the electrode is placed vertically, natural convection generally emerges in the electrolyte solution in the vicinity of the electrode surface during electrodeposition and flows upward along the electrode surface. When convective flow along the electrode surface was eliminated by placing the electrode horizontally, the configuration of the one-directional traveling waves (anisotropic shape) changed to an isotropic shape. This indicates that the formation of an anisotropic shape for one-directional traveling waves is due to upward convective flow along the electrode surface.

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Reference
"Contribution of convection to spatiotemporal stripe patterns formed by Ag and Sb coelectrodeposition", Yuko Nagamine and Kenichi Yoshikawa, Chaos, 20, 023117 (2010).
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Rotary motion driven by a direct current electric field

A water-in-oil (w/o) micro-droplet exhibits a spontaneous rotary motion under a stationary direct current electric field. The rotary motion appears above a certain critical electric potential and its frequency increases with an increase in the potential. A simple theoretical model including an over-damped equation of motion and dissipation of electric charge can describe the occurrence of the rotary motion. This rotary motion of w/o microdroplet is believed to be a novel spatiotemporal order under a electrochemical nonequilibrium open system.

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Reference
"Rotary motion driven by a direct current electric field", M. Takinoue, Y. Atsumi, and K. Yoshikawa, Appl. Phys. Lett., 96, 104105 (2010).
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Structure and functions of macromolecules (DNA)

    Probability of double-strand breaks in genome-sized DNA by γ -ray decreases markedly as the DNA concentration increases

    Confinement causes opposite effects on the folding transition of a single polymer chain depending on its stiffness

    Torsional effect on the wrapping transition of a semiflexible polymer around a core as a model of nucleosome

    Protamine-induced DNA compaction but not aggregation shows effective radioprotection against double-strand breaks

    Chain length dependence of folding transition in a semiflexible homo-polymer chain: Appearance of a core-shell structure

    Cleavage pattern of DNA caused by endonuclease: Theoretical modeling and experimental verification

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Probability of double-strand breaks in genome-sized DNA by γ -ray decreases markedly as the DNA concentration increases

By use of the single-molecule observation, we count the number of DNA double-strand breaks caused by γ-ray irradiation with genome-sized DNA molecules (166 kbp). We find that P 1, the number of double-strand breaks (DSBs) per base pair per unit Gy, is nearly inversely proportional to the DNA concentration above a certain threshold DNA concentration. The inverse relationship implies that the total number of DSBs remains essentially constant. We give a theoretical interpretation of our experimental results in terms of attack of reactive species upon DNA molecules, indicating the significance of the characteristics of genome-sized giant DNA as semiflexible polymers for the efficiency of DSBs.

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Reference
"Probability of double-strand breaks in genome-sized DNA by γ -ray decreases markedly as the DNA concentration increases" Shunsuke F. Shimobayashi, Takafumi Iwaki, Toshiaki Mori and Kenichi Yoshikawa, Journal of Chemical Physics, 138 (17), 174907/1-5 (2013).


Confinement causes opposite effects on the folding transition of a single polymer chain depending on its stiffness

We investigated the folding transition between an elongated coil state and a compact state on a single polymer chain confined in a small space with different stiffness with the aid of Monte Carlo simulation. In a flexible polymer, the folding transition is retarded in a confined space. In contrast, the transition is promoted for a semiflexible chain, in which the discontinuity of the volume change occupied by a single chain is diminished by confinement. This unique confinement effect is interpreted in terms of conformational entropy and self-avoiding repulsive interaction.

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Reference
"Confinement causes opposite effects on the folding transition of a single polymer chain depending on its stiffness", Yuji Higuchi, Takafumi Iwaki, and Kenichi Yoshikawa, Phys. Rev. E. , 84, 021924 (2011).
Related papers
"Conformational transition of giant DNA in a confined space surrounded by a phospholipid membrane", Ayako Kato, Eri Shindo, Takahiro Sakaue, Akihiko Tsuji and Kenichi Yoshikawa, Biophysical Journal, 97, 1678(2009).
"Stepwise Collapse of Polyelectrolyte Chains Entrapped in a Finite Space As Predicted by Theoretical Considerations", Seiji Takagi and Kenichi Yoshikawa, Langmuir, 15, 4143 (1999).


Torsional effect on the wrapping transition of a semiflexible polymer around a core as a model of nucleosome

We investigated the effect of the torsional rigidity of a semiflexible chain on the wrapping transition around a spherical core, as a model of a nucleosome, the fundamental unit of chromatin. Through molecular dynamics simulation, we show that the torsional effect has a crucial effect on the chain wrapping around the core under the topological constraints. In particular, the torsional stress (i) induces the wrapping/unwrapping transition, and (ii) leads to a unique complex structure with an antagonistic wrapping direction which never appears without the topological constraints. We further examine the effect of the stretching stress for the nucleosome model in relation to the unique characteristic effect of the torsional stress on the manner of wrapping.

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Reference
"Torsional effect on the wrapping transition of a semiflexible polymer around a core as a model of nucleosome", Yuji Higuchi, Takahiro Sakaue, and Kenichi Yoshikawa, Phys. Rev. E. , 82, 031909 (2010).


Protamine-induced DNA compaction but not aggregation shows effective radioprotection against double-strand breaks

Protamine, an arginine-rich protein, is essential for the compaction of sperm DNA. We performed single-molecule observations of DNA double-strand breaks caused by 60Co -ray irradiation and quantitatively evaluated the protective effect of protamine. It was shown that double-strand breaks were significantly protected for the tightly compact DNA, whereas there is no apparent decrease on the damage for loosely aggregated DNA molecules. Our findings suggest that the densely packed structure of DNA reduces the ability of radiolytic reactive oxygen species to access DNA and thus protects DNA from double-strand breaks.

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References
"Protamine-induced DNA compaction but not aggregation shows effective radioprotection against double-strand breaks", Mari Suzuki, Cecile Crozatier, Kenichi Yoshikawa, Toshiaki Mori, and Yuko Yoshikawa, Chemical Physics Letters, 480, 113 (2009).
"DNA compaction plays key role in radioprotection against double-strand breaks as revealed by single-molecule observation", Yuko Yoshikawa, Toshiaki Mori, Nobuyuki Magome, Kumiko Hibino, and Kenichi Yoshikawa, Chemical Physics Letters, 456, 80 (2008).
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Chain length dependence of folding transition in a semiflexible homo-polymer chain: Appearance of a core-shell structure

The folding transition of single, long semiflexible polymers was studied with special emphasis on the chain length effect using Monte Carlo simulations. While a relatively short chain (10-25 Kuhn segments) undergoes a large discrete transition between swollen coil and compact toroid conformations, a long chain (50 Kuhn segments) exhibits an intrachain segregated state between the disordered coil and ordered toroid.

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Reference
"Chain length dependence of folding transition in a semiflexible homo-polymer chain: Appearance of a core-shell structure", Yuji Higuchi, Takahiro Sakaue, and Kenichi Yoshikawa, Chemical Physics Letters, 461, 42 (2008).
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Cleavage pattern of DNA caused by endonuclease: Theoretical modeling and experimental verification

In apoptotic cells, genomic DNA molecules are fragmented into multiple fragments with lengths that are integer multiples of ca. 180-200 base pairs (bp), i.e., the size of a single nucleosome. Here we propose a simple mathematical model for interpreting this cleavage pattern of DNA. Under the condition of a purely stochastic cleavage process, we derive a time evolution of the probability distribution of the fragment length by a Poisson distribution. We examine the applicability of our model by analyzing experimental results with apoptotic cells. Our model enables us to satisfactorily interpret the experimental trends. Interestingly, this theoretical fitting of the experimental data provides kinetic information for the cleavage reaction.

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Reference
"Cleavage pattern of DNA caused by endonuclease: Theoretical modeling and experimental verification", Shio Inagaki, Li Liu, Masahiro Takinoue, and Kenichi Yoshikawa, Applied Physics Letters, 96, 063701 (2005).
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