Twist-stretch relations in nucleic acids

Zoli, Marco

doi:10.1007/s00249-023-01669-6

Cited by 3 publications

(1 citation statement)

References 76 publications

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“…In the solution, due to the influence of thermal motion, large molecules like polymer molecules are constantly twisted, bent, and vibrated. 44 The radius of gyration (ROG) is a physical quantity that describes the result of this motion. The ROG decreases with the increase in simulation time.…”

Section: Resultsmentioning

confidence: 99%

Efficient Fabrication of Self-Assembled Polylactic Acid Colloidosomes for Pesticide Encapsulation

Payizila,

Teng,

Huang

et al. 2024

ACS Omega

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Colloidosomes are microcapsules whose shells are composed of cumulated or fused colloidal particles. When colloidosomes are used for in situ encapsulation, it is still a challenge to achieve a high encapsulation efficiency and controllable release by an effective fabrication method. Herein, we present a highly efficient route for the large-scale preparation of colloidosomes. The biodegradable polylactic acid (PLA) nanoparticles (NPs) as shell materials can be synthesized using an antisolvent precipitation method, and the possible formation mechanism was given through the molecular dynamics (MD) simulation. The theoretical values are basically consistent with the experimental results. Through the use of the modified and unmodified PLA NPs, the colloidosomes with controllable shell porosities can be easily constructed using spray drying technology. We also investigate the mechanism of colloidosomes successfully self-assembled by PLA NPs with various factors of inlet temperature, feed rate, and flow rates of compressed air. Furthermore, avermectin (AVM) was used as a model for in situ encapsulation and a controllable release. The spherical modified colloidosomes encapsulating AVM not only achieve a small mean diameter of 1.57 μm but also realize a high encapsulation efficiency of 89.7% and impermeability, which can be further verified by the MD simulation. AVM molecules gather around and clog the shell pores during the evaporation of water molecules. More importantly, the PLA colloidosomes also reveal excellent UV-shielding properties, which can protect AVM from photodegradation.

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Section: Resultsmentioning

confidence: 99%

Efficient Fabrication of Self-Assembled Polylactic Acid Colloidosomes for Pesticide Encapsulation

Payizila,

Teng,

Huang

et al. 2024

ACS Omega

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Mechanical response of double-stranded DNA: Bend, twist, and overwind

Mou,

Liu,

et al. 2024

The Journal of Chemical Physics

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We employed all-atom molecular dynamics simulations to explore the mechanical response of bending, twisting, and overwinding for double-stranded DNA (dsDNA). We analyzed the bending and twisting deformations, as well as their stiffnesses, using the tilt, roll, and twist modes under stretching force. Findings indicate that the roll and twist angles vary linearly with the stretching force but show opposite trends. The tilt, roll, and twist elastic moduli are considered constants, while the coupling between roll and twist modes slightly decreases under stretching force. The effect of the stretching force on the roll and twist modes, including both their deformations and elasticities, exhibits sequence-dependence, with symmetry around the base pair step. Furthermore, we examined the overwinding path and mechanism of dsDNA from the perspective of the stiffness matrix, based on the tilt, roll, and twist modes. The correlations among tilt, roll, and twist angles imply an alternative overwinding pathway via twist–roll coupling when dsDNA is stretched, wherein entropic contribution prevails.

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Fluctuations cutoff in a 1D Hamiltonian model for DNA

Zoli

2024

Phys. Scr.

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Considering a one dimensional mesoscopic model for DNA, we focus on the upper bound for the base pair ﬂuctuations, a relevant parameter in computer simulations for which contrasting estimates have been reported. Noticing that the free energy of the model can be obtained analytically in the thermodynamic limit, we derive a relation for the ﬂuctuations upper bound in terms of temperature and elastic force constant of the stacking potential. At room temperature, the ﬂuctuation cutoﬀ is constrained to values ∼ 2˚A in fair agreement with the threshold above which hydrogen bonds break and base pairs dissociate.

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Twist-stretch relations in nucleic acids

Cited by 3 publications

References 76 publications

Efficient Fabrication of Self-Assembled Polylactic Acid Colloidosomes for Pesticide Encapsulation

Efficient Fabrication of Self-Assembled Polylactic Acid Colloidosomes for Pesticide Encapsulation

Mechanical response of double-stranded DNA: Bend, twist, and overwind

Fluctuations cutoff in a 1D Hamiltonian model for DNA

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