Bend-Induced Twist Waves and the Structure of Nucleosomal DNA

Skoruppa, Enrico; Nomidis, Stefanos K.; Marko, John F.; Carlon, Enrico

doi:10.1103/physrevlett.121.088101

Cited by 58 publications

(75 citation statements)

References 36 publications

(41 reference statements)

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“…The oscillations in the bending densities Ω 1 and Ω 2 arise from the geometrical constraints of the system, which in turn induce oscillations in the twist density Ω 3 from the presence of twist-bend coupling (G = 0). These twist waves have been indeed observed in X-ray crystallographic structures of DNA bound to histone proteins [18]. While Eq.…”

Section: Dna Elasticity and Twist-bend Couplingmentioning

confidence: 59%

“…We focused particularly on the effect of twist-bend coupling, which is an interaction arising from the DNA grooves asymmetry [15]. As recently discussed in the case of DNA minicircles and nucleosomal DNA [18], we found that also in DNA loops the bending deformation induces twist waves, i.e., twist oscillations following the periodicity of the helical pitch. Differently from the minicircle case, in the loops discussed here twist waves have a modulated amplitude, which is maximal at the loop apex and vanishes at the two ends.…”

Section: Discussionmentioning

confidence: 85%

“…The advantage of the variational solution is that it involves simple trigonometric functions, from which various properties of the loop can be easily obtained. Combining with the results of previous work [18], we have extended the variational solution to more complex DNA models, with anisotropic bending and twist-bend coupling. The comparison with numerical simulations of various coarsegrained model of DNA shows that the harmonic-loop approximation performs extremely well in all cases.…”

Section: Introductionmentioning

confidence: 79%

“…This description fails to account for a coupling interaction present in real DNA, that connects the bending and twisting degrees of freedom, and originates from the asymmetry of the DNA grooves [15]. The effect of such a twist-bend coupling interaction on the behavior of DNA at various scales has been recently discussed [16][17][18][19][20]. The aim of this paper is to investigate its influence on the structure of short DNA loops.…”

Section: Introductionmentioning

confidence: 99%

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Twist-bend coupling, twist waves, and the shape of DNA loops

et al. 2019

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By combining analytical and numerical calculations, we investigate the minimal-energy shape of short DNA loops of approximately 100 base pairs (bp). We show that in these loops the excess twist density oscillates as a response to an imposed bending stress, as recently found in DNA minicircles and observed in nucleosomal DNA. These twist oscillations, here referred to as twist waves, are due to the coupling between twist and bending deformations, which in turn originates from the asymmetry between DNA major and minor grooves. We introduce a simple analytical variational shape, that reproduces the exact loop energy up to the fourth significant digit, and is in very good agreement with shapes obtained from coarse-grained simulations. We, finally, analyze the loop dynamics at room temperature, and show that the twist waves are robust against thermal fluctuations. They perform a normal diffusive motion, whose origin is briefly discussed.

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Section: Dna Elasticity and Twist-bend Couplingmentioning

confidence: 59%

Section: Discussionmentioning

confidence: 85%

Section: Introductionmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Twist-bend coupling, twist waves, and the shape of DNA loops

et al. 2019

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“…The physical implications of this coupling are profound and mechanically akin to those described in §3. For instance, if a protein such as RNAP ( figure 5 ) bends the DNA locally, this mechanical deformation propagates in the form of mechanical twist waves down the chain [ 138 ]. These waves are reminiscent of soliton solutions in the PB-like models described above and have important implications for the stability of nucleosomes, the complex of DNA and histone proteins, which makes the chromatin in eukaryotic cells [ 138 ].…”

Section: Computational Challenges and Models For Dna Dynamicsmentioning

confidence: 99%

A review on nonlinear DNA physics

et al. 2020

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The study and the investigation of structural and dynamical properties of complex systems have attracted considerable interest among scientists in general and physicists and biologists in particular. The present review paper represents a broad overview of the research performed over the nonlinear dynamics of DNA, devoted to some different aspects of DNA physics and including analytical, quantum and computational tools to understand nonlinear DNA physics. We review in detail the semi-discrete approximation within helicoidal Peyrard–Bishop model and show that localized modulated solitary waves, usually called breathers, can emerge and move along the DNA. Since living processes occur at submolecular level, we then discuss a quantum treatment to address the problem of how charge and energy are transported on DNA and how they may play an important role for the functioning of living cells. While this problem has attracted the attention of researchers for a long time, it is still poorly understood how charge and energy transport can occur at distances comparable to the size of macromolecules. Here, we review a theory based on the mechanism of ‘self-trapping’ of electrons due to their interaction with mechanical (thermal) oscillation of the DNA structure. We also describe recent computational models that have been developed to capture nonlinear mechanics of DNA in vitro and in vivo , possibly under topological constraints. Finally, we provide some conjectures on potential future directions for this field.

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Dynamics of a DNA minicircle: Poloidal rotation and in‐plane circular vibration

Kim

Hong

Lee

et al. 2022

Bulletin Korean Chem Soc

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We investigated the dynamics of a 90-base pair-long DNA minicircle with the sequence of (AT) 45 /(AT) 45 using the all-atom molecular dynamics (MD) simulation. The simulation was run for a duration of 5 μs and the internal dynamics was analyzed in terms of the poloidal rotation and the in-plane circular vibration. The poloidal rotation was defined by the directional variation of each base pair relative to the plane of the DNA minicircle, and its correlation time was estimated to be 61 ns. The in-plane circular vibration was measured as the radial distance variation of each base pair from the center-of-mass of the DNA, and the correlation time was 6.3 ns. The characteristic time scales determined for the poloidal rotation and the radial fluctuation suggest that the internal motion of a small DNA minicircle is highly dynamic. This work provides a new set of dynamic information for small DNA minicircles, available for future applications.

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Bend-Induced Twist Waves and the Structure of Nucleosomal DNA

Cited by 58 publications

References 36 publications

Twist-bend coupling, twist waves, and the shape of DNA loops

Twist-bend coupling, twist waves, and the shape of DNA loops

A review on nonlinear DNA physics

Dynamics of a DNA minicircle: Poloidal rotation and in‐plane circular vibration

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