Twist-stretch profiles of DNA chains

Zoli, Marco

doi:10.1088/1361-648x/aa6c50

Cited by 14 publications

(11 citation statements)

References 92 publications

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“…In this limit, h → ∞ and the ladder Hamiltonian model is meaningful. The overall experimental pattern, here summarized, can be explained by a three dimensional model which treats the helical repeat of short molecules as a variable whose average value is computed by minimizing the free energy of the molecular system subjected to a tunable load [109][110][111].…”

Section: Fixed Planes Representationmentioning

confidence: 99%

Mesoscopic helical models for nucleic acids

Zoli

2021

Preprint

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Nucleic acids physical properties can be investigated by theoretical methods which range from fully atomistic representations to coarse grained models, e.g. the worm-like-chain, taken from polymer physics. Here I take an intermediate approach, usually named mesoscopic, and show how to build a three dimensional Hamiltonian model which accounts for the main interactions responsible for the stability of the helical molecules. While the 3D mesoscopic model yields a sufficiently detailed description of the helix at the level of the base pair, it also provides a convenient approach to extract information regarding the thermodynamics and structure of molecules in solution. The main features of a computational method developed over the last years are discussed together with some applications to the calculation of DNA flexibility properties.

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Section: Fixed Planes Representationmentioning

confidence: 99%

Mesoscopic helical models for nucleic acids

Zoli

2021

Preprint

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“…In general, to perform such calculations, one has first to minimize the free energy over a broad range of possible twist angles and then select the equilibrium twist conformation, as explained in detail in ref. [70]. As a result, this procedure can be significantly time consuming even for short fragments [71].…”

Section: Modelmentioning

confidence: 99%

Base pair fluctuations in helical models for nucleic acids

Zoli

2021

Preprint

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A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian motion for a particle embedded in a stable helical structure. The probability to return to the initial position is computed, as a function of time, by integrating over the particle paths consistent with the physical properties of the model potential. The zero time condition for the first-passage probability defines the constraint to select the integral cutoff for various macroscopic helical conformations, obtained by tuning the twist, the bending and the slide motion between adjacent base pairs along the molecule stack. Applying the method to a short homogeneous chain at room temperature, we obtain meaningful estimates for the maximum fluctuations in the twist conformation with ∼ 10.5 base pairs per helix turn, typical of double stranded DNA helices. Untwisting the double helix, the base pair fluctuations broaden and the integral cutoff grows. The cutoff is found to increase also in the presence of a sliding motion which shortens the helix contour length, a situation peculiar of dsRNA molecules.

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“…c) In terms of the twist variable, the code generates a large number of possible conformations, each identified by a value for the average helical repeat, i.e., the number of base pairs per helix turn [52]. The gist of the method lies in the determination of the equilibrium twist conformation and in the computation of the helical properties as a function of the twist conformation as shown below.…”

Section: A Helixmentioning

confidence: 99%

DNA size in confined environments

Zoli

2019

Phys. Chem. Chem. Phys.

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For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The ds-DNA is modeled by a mesoscopic Hamiltonian which accounts for the three dimensional helical structure and incorporates fluctuational effects at the level of the base pair. The computational method assumes that the base pair fluctuations are temperature dependent trajectories whose amplitudes can be spatially modulated according to the crowders distribution. We show that the molecule elongation, as measured by the end-to-end distance varies non-monotonically with the strength of the confinement. Furthermore it is found that, if the crowders mostly confine the DNA mid-chain, the helix over-twists and its end-to-end distance grows in the strong confinement regime. Instead, if the crowders mostly pin one chain end, the helix untwists while the molecule stretches for large confinement strengths. Thus, our results put forward a peculiar relation between stretching and twisting which significantly depends on the crowders profile. The method could be applied to disegn specific DNA shapes by controlling the environment which constrains the molecule.

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Twist-stretch profiles of DNA chains

Cited by 14 publications

References 92 publications

Mesoscopic helical models for nucleic acids

Mesoscopic helical models for nucleic acids

Base pair fluctuations in helical models for nucleic acids

DNA size in confined environments

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