From toroidal to rod-like condensates of semiflexible polymers

Hoang, Trinh Xuan; Giacometti, Andrea; Podgornik, Rudolf; Nguyen, Nhung; Banavar, Jayanth R.; Maritan, Amos

doi:10.1063/1.4863996

Cited by 32 publications

(24 citation statements)

References 59 publications

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“…1) are the hexagonal structures of ds DNA LCD particles, which do not possess abnormal bands in the CD spectra. The local structure in this case consists of straight ds DNA chains with parallel nematic alignment minimizing the bending energy [53].…”

Section: The CD Spectra Of Ds Dna Lcd Particlesmentioning

confidence: 99%

“…The dispersions can be obtained by the phase exclusion (condensation) of linear ds DNA molecules from aqueous-salt-poly(ethyleneglycol) (PEG) solutions [15,16] or mixtures of PEG with a mineral oil [17]. This process, depending on the molecular mass of ds DNA molecules, is realized as the intramolecular or the intermolecular assembling of molecules [6][7][8][9][10][11][12][13][14][15][16][17][18] into the dispersion particles, driven by packing constrains and enforced by the van der Waals, hydrophobic and electrostatic interactions. Note that the particles of the low molecular mass ds ≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡≡ DNA dispersions are "microscopic droplets of concentrated DNA solution".…”

Section: Introductionmentioning

confidence: 99%

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Double-Stranded DNA Packing in Particles of Liquid-Crystalline Dispersions and Liquid-Crystalline Phases Obtained from These Particles

Yevdokimov¹,

Skuridin²,

Salyanov³

et al. 2018

Liq. Cryst. and their Appl.

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In this research we compared the optical properties of liquid-crystalline DNA dispersion particles formed as a result of the phase exclusion of double-stranded (ds) DNA molecules from aqueous-salt of poly(ethylene glycol) solutions and the phases obtained from these dispersions. It is shown that the liquid-crystalline dispersions with cholesteric packing of double-stranded DNA molecules are characterized by an intense (abnormal) negative band in the circular dichroism (CD) spectrum. The phases obtained from these dispersions possess «fingerprint» texture at both room and elevated temperatures. The CD spectra without abnormal band are found for double-stranded DNA dispersions with an initial hexagonal packing of molecules, which are formed at room temperatures. However, the temperature increase results in the appearance of an abnormal band in the CD spectrum of the hexagonal double-stranded DNA dispersion particles. The observed optical effect corresponds to a new "hexagonal → re-entrant cholesteric" phase transition in the case of the particles formed by both the semi-rigid and flexible ds DNA molecules. Unlike the dispersion particles, the textures of phases obtained from these particles do not demonstrate any attributes typical of conventional cholesteriсs. These textures present anisotropic domains with beautiful colors at room and elevated temperatures. In the agreement with the measured magnitude of the abnormal CD band, the colors can reveal a very small helical pitch well below the values known for classical cholesterics.

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Section: The CD Spectra Of Ds Dna Lcd Particlesmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Double-Stranded DNA Packing in Particles of Liquid-Crystalline Dispersions and Liquid-Crystalline Phases Obtained from These Particles

Yevdokimov¹,

Skuridin²,

Salyanov³

et al. 2018

Liq. Cryst. and their Appl.

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“…For x = 1, one recovers the power law of L 1/3 [19]. For x = 0.5, the transition line would become independent of L, but for this limiting case, both the toroid phase and the rod-like phase disappear (see below).…”

mentioning

confidence: 99%

“…A recent study of the ground states of a chain molecule [19] using the WLC together with different types of interactions promoting compaction resulted in a phase diagram with toroidal and rod-like ground states. Furthermore, the combination of analytical calculations and computer simulations showed that the shape of the phase diagram was quite insensitive to the microscopic details.…”

mentioning

confidence: 99%

Phase diagram of the ground states of DNA condensates

et al. 2015

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Phase diagram of the ground states of DNA in a bad solvent is studied for a semi-flexible polymer model with a generalized local elastic bending potential characterized by a nonlinearity parameter x and effective self-attraction promoting compaction. x = 1 corresponds to the worm-like chain model. Surprisingly, the phase diagram as well as the transition lines between the ground states are found to be a function of x. The model provides a simple explanation for the results of prior experimental and computational studies and makes predictions for the specific geometries of the ground states. The results underscore the impact of the form of the microscopic bending energy at macroscopic observable scales.The non-linear elasticity of DNA at short length scales, probed by non-equilibrium DNA cyclization experiments [1,2], AFM imaging on surfaces [3], as well as by equilibrium mechanically constrained DNA experiments [4][5][6], is still not well understood. While the conclusions regarding the first two methods for probing non-linear ds-DNA elasticity have been criticized [7], the experiments on stressed DNA ring molecules are performed by a different methodology based on thermodynamic methods via DNA high-curvature states through partial hybridization of a ss-DNA loop with a linear complementary strand [6]. This methodology does not depend on thermal fluctuations to realize high-curvature states and thus appears to have a far better accuracy and reliability. The non-linearity in this latter case is clearly present and is captured in a single parameter describing the onset of DNA kink formation. This clearly exhibited elastic nonlinearity is taken as the motivation for the present study that attempts to derive the macroscopic consequences of this interesting microscopic elastic behavior of DNA.Another interesting facet of DNA behavior is that under specific solution conditions, it condenses into highly compact structures with pronounced symmetry [8][9][10][11]. This condensation phenomenon serves as an example of high polymer density packing in biology and of polymer phase transitions and phase separations in general, being relevant also for artificial gene delivery [12,13]. Several distinct morphologies of the DNA condensates have been observed including a toroid, a spheroid as well as a rodlike configuration [10,[14][15][16]. Our principal goal is to explore the rich interplay between the strong tendency for compactness, arising from the presence of multivalent cations or osmolytes in the solution, and the intrinsic stiffness of the DNA molecule promoting the chain to be locally straight. In the absence of stiffness, one would expect the chain to adopt a densely compact spheroidal globule configuration. The key issue is to understand how local stiffness and the detailed way it enters the elastic energy result in the spheroidal configuration becoming unstable w.r.t. other lower energy configurations. In particular, one would like to map out a phase diagram and understand the different condensate geometries.The topolog...

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“…Despite of the fact that there are current theoretical attempts [37,38] to describe this pattern of DNA condensation, a universal theory that explains the formation of DNA toroidal condensates does not exist.…”

Section: Introductionmentioning

confidence: 99%

Liquid-Crystalline Dispersions of Double-Stranded DNA

et al. 2019

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In this review, we compare the circular dichroism (CD) spectra of liquid-crystalline dispersion (LCD) particles formed in PEG-containing aqueous-salt solutions with the purpose of determining the packing of ds DNA molecules in these particles. Depending on the osmotic pressure of the solution, the phase exclusion of ds DNA molecules at room temperature results in the formation of LCD particles with the cholesteric or the hexagonal packing of molecules. The heating of dispersion particles with the hexagonal packing of the ds DNA molecules results in a new phase transition, accompanied by an appearance of a new optically active phase of ds DNA molecules. Our results are rationalized by way of a concept of orientationally ordered “quasinematic” layers formed by ds DNA molecules, with a parallel alignment in the hexagonal structure. These layers can adopt a twisted configuration with a temperature increase; and as a result of this process, a new, helicoidal structure of dispersion particle is formed (termed as the “re-entrant” cholesteric phase). To prove the cholesteric pattern of ds DNA molecules in this phase, the “liquid-like” state of the dispersion particles was transformed into its “rigid” counterpart.

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From toroidal to rod-like condensates of semiflexible polymers

Cited by 32 publications

References 59 publications

Double-Stranded DNA Packing in Particles of Liquid-Crystalline Dispersions and Liquid-Crystalline Phases Obtained from These Particles

Double-Stranded DNA Packing in Particles of Liquid-Crystalline Dispersions and Liquid-Crystalline Phases Obtained from These Particles

Phase diagram of the ground states of DNA condensates

Liquid-Crystalline Dispersions of Double-Stranded DNA

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