Flexibility of short DNA helices under mechanical stretching

Zoli, Marco

doi:10.1039/c6cp02981g

Cited by 22 publications

(17 citation statements)

References 101 publications

(129 reference statements)

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“…The method followed here is similar in spirit to the procedure reported in different earlier publications. [6,9,10,12,21,[47][48][49][50][51][52]].…”

Section: Calculation Of the Persistence Length (L P )mentioning

confidence: 99%

Ionic liquids make DNA rigid

Garai

Ghoshdastidar

Senapati

et al. 2018

The Journal of Chemical Physics

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Persistence length of double-stranded DNA (dsDNA) is known to decrease with an increase in ionic concentration of the solution. In contrast to this, here we show that the persistence length of dsDNA increases dramatically as a function of ionic liquid (IL) concentration. Using all atom explicit solvent molecular dynamics simulations and theoretical models, we present, for the first time, a systematic study to determine the mechanical properties of dsDNA in various hydrated ILs at different concentrations. We find that dsDNA in 50 wt % ILs have lower persistence length and stretch modulus in comparison to 80 wt % ILs. We further observe that both the persistence length and stretch modulus of dsDNA increase as we increase the concentration of ILs. The present trend of the stretch modulus and persistence length of dsDNA with IL concentration supports the predictions of the macroscopic elastic theory, in contrast to the behavior exhibited by dsDNA in monovalent salt. Our study further suggests the preferable ILs that can be used for maintaining DNA stability during long-term storage.

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“…The method followed here is similar in spirit to the procedure reported in different earlier publications. [6,9,10,12,21,[47][48][49][50][51][52]].…”

Section: Calculation Of the Persistence Length (L P )mentioning

confidence: 99%

Ionic liquids make DNA rigid

Garai

Ghoshdastidar

Senapati

et al. 2018

The Journal of Chemical Physics

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“…To address these issues we have recently applied a mesoscopic Hamiltonian model, which treats the dsDNA at the level of the base pair [26,27], to the analysis of the looping probabilities in short molecules: the obtained J-factors fit the order of magnitude of the experimental data and reproduce the observed trend as a function of the fragment size [28]. Importantly, radial fluctuations between the pair mates and large bending angles between adjacent base pairs have been incorporated in the computational method thus allowing for the formation of kinks which locally unstack the helix [29][30][31][32], enhance the cyclization efficiency and may reduce the persistence length [23,[33][34][35].…”

Section: Analysis Of Looping Probability Induced By T4 Ligase Enzymesmentioning

confidence: 99%

End-to-end distance and contour length distribution functions of DNA helices

Zoli

2018

The Journal of Chemical Physics

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I present a computational method to evaluate the end-to-end and the contour length distribution functions of short DNA molecules described by a mesoscopic Hamiltonian. The method generates a large statistical ensemble of possible configurations for each dimer in the sequence, selects the global equilibrium twist conformation for the molecule, and determines the average base pair distances along the molecule backbone. Integrating over the base pair radial and angular fluctuations, I derive the room temperature distribution functions as a function of the sequence length. The obtained values for the most probable end-to-end distance and contour length distance, providing a measure of the global molecule size, are used to examine the DNA flexibility at short length scales. It is found that, also in molecules with less than ∼60 base pairs, coiled configurations maintain a large statistical weight and, consistently, the persistence lengths may be much smaller than in kilo-base DNA.

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“…This has also been suggested more recently by molecular dynamics simulations [78] and analysis of (un)looping probabilities in short chains based on single molecule fluorescence resonance energy transfer [79]. While the polymer flexibility can be directly related to the average bending angles between any two distant monomers [80,81], computation of persistence length has shown that linear short sequences have an intrinsic flexibility mainly ascribed to their terminal base pairs [42,82].…”

Section: Methodsmentioning

confidence: 86%

Twist-stretch profiles of DNA chains

Zoli

2017

J. Phys.: Condens. Matter

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Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are applied to generate a large ensemble of possible configurations for the base pairs of the sequence. The model also accounts for the bending and twisting fluctuations between adjacent base pairs along the molecules stack. Simulating a broad range of twisting conformation, we compute the helix structural parameters by averaging over the ensemble of base pairs configurations. The method selects, for any applied force, the average twist angle which minimizes the molecule's free energy. It is found that the chains generally over-twist under an applied stretching and the over-twisting is physically associated to the contraction of the average helix diameter, i.e. to the damping of the base pair fluctuations. Instead, assuming that the maximum amplitude of the bending fluctuations may decrease against the external load, the DNA molecule first over-twists for weak applied forces and then untwists above a characteristic force value. Our results are discussed in relation to available experimental information albeit for kilo-base long molecules.

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Flexibility of short DNA helices under mechanical stretching

Cited by 22 publications

References 101 publications

Ionic liquids make DNA rigid

Ionic liquids make DNA rigid

End-to-end distance and contour length distribution functions of DNA helices

Twist-stretch profiles of DNA chains

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