Unwinding of circular helicoidal molecules vs. size

Zoli, Marco

doi:10.1209/0295-5075/110/18001

Cited by 3 publications

(3 citation statements)

References 43 publications

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“…In some recent papers [26,27], the thermodynamic stability of a set of double stranded mini-circles has been investigated via path integral techniques and, by computation of the free energy, the stablest helicoidal conformations have been selected as a function of N.…”

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confidence: 99%

J-factors of short DNA molecules

Zoli

2016

The Journal of Chemical Physics

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The propensity of short DNA sequences to convert to the circular form is studied by a mesoscopic Hamiltonian method which incorporates both the bending of the molecule axis and the intrinsic twist of the DNA strands. The base pair fluctuations with respect to the helix diameter are treated as path trajectories in the imaginary time path integral formalism. The partition function for the sub-ensemble of closed molecules is computed by imposing chain end boundary conditions both on the radial fluctuations and on the angular degrees of freedom. The cyclization probability, the J-factor, proves to be highly sensitive to the stacking potential, mostly to its nonlinear parameters. We find that the J-factor generally decreases by reducing the sequence length (N) and, more significantly, below N = 100 base pairs. However, even for very small molecules, the J-factors remain sizeable in line with recent experimental indications. Large bending angles between adjacent base pairs and anharmonic stacking appear as the causes of the helix flexibility at short length scales.

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confidence: 99%

J-factors of short DNA molecules

Zoli

2016

The Journal of Chemical Physics

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“…However, h j * 's increment as a function of N is not linear suggesting that the equilibrium helical repeat should saturate at ∼10, for chains in the range of hundreds of bps (albeit not studied here). While h j * 's are the most probable twist conformations selected by free energy minimization, our plots indicate that, because of thermal fluctuations, the chains may assume also h j 's conformations which are close to h j * on the energy scale [27].…”

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confidence: 81%

Short DNA persistence length in a mesoscopic helical model

Zoli¹

2018

EPL

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The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available to base pair fluctuations and derive the partition function. The apparent persistence lengths of a set of short chains have been computed as a function of the twist conformation both in the over-twisted and the untwisted regimes, whereby the equilibrium twist is selected by free energy minimization. The obtained values are significantly lower than those generally attributed to kilo-base long DNA. This points to an intrinsic helix flexibility at short length scales, arising from large fluctuational effects and local bending, in line with recent experimental indications. The interplay between helical untwisting and persistence length has been discussed for a heterogeneous fragment by weighing the effects of the sequence specificities through the non-linear stacking potential. 1The DNA double helical structure is stable enough to preserve genetic information encoded in the Watson-Crick paired bases and also loose enough to allow for those transient base pair (bp) openings [1] which make the code accessible to enzymes during the processes of replication, transcription and repair. At physiological temperatures DNA molecules fluctuate between a variety of random coil conformations in which even distant segments along the helical axis can be brought in close proximity [2]. This points to an inherent flexibility of the DNA chain which has been widely probed over the last twenty five years [3]. While these experiments demonstrate that stretch and twist elasticity are intertwined [4], they also call for models in which bp fluctuations and stacking interactions are considered as dependent on the specific twist conformation of the molecule. Modeling of the helix and its conformational states can be carried out at different levels of resolution ranging from all-atom simulations to continuous worm-like chain (WLC) models which simply treat DNA as a homogeneous and inextensible rod [5], not accounting for the interplay between twist and bp fluctuations. This may explain the shortcomings of the WLC model emerged in the analysis of the cyclization properties [6,7] at those short length scales in which the details of the bp interactions matter. In this regard, mechanical models such as the Dauxois-Peyrard-Bishop (DPB) model

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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].…”

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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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Unwinding of circular helicoidal molecules vs. size

Cited by 3 publications

References 43 publications

J-factors of short DNA molecules

J-factors of short DNA molecules

Short DNA persistence length in a mesoscopic helical model

Mesoscopic helical models for nucleic acids

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