Soft Matter and Biophysics

Nucleic acid deformations play important roles in many biological processes. The physical understanding of nucleic acid deformation by environmental stimuli is limited due to the challenge in the precise measurement of RNA and DNA deformations and the complexity of interactions in RNA and DNA. Magnetic tweezers experiments provide an excellent opportunity to precisely measure DNA and RNA twist changes induced by environmental stimuli. In this work, we applied magnetic tweezers to measure double-stranded RNA twist changes induced by salt and temperature changes. We observed RNA unwinds when lowering salt concentration, or increasing temperature. Our molecular dynamics simulations revealed the mechanism: lowering salt concentration or increasing temperature enlarges RNA major groove width, which causes twist decrease through twist-groove coupling. Combining these results with previous results, we found some universality in RNA and DNA deformations induced by three different stimuli: salt change, temperature, and stretching force. For RNA, these stimuli first modify the major groove width, which is transduced into twist change through twist-groove coupling. For DNA, these stimuli first modify diameter, which is transduced into twist change through twist-diameter coupling. Twist-groove coupling and twist-diameter coupling appear to be utilized by protein binding to reduce DNA and RNA deformation energy cost upon protein binding.

Read more at Proceedings of the National Academy of Sciences USA:
https://www.pnas.org/doi/10.1073/pnas.2218425120

Solid-state cooling employing barocaloric materials, especially plastic crystals, paves a promising way for eco-friendly refrigeration. However, inadequate understanding of the thermal properties hinders their practical applications. Here, we take α-pentaerythritol crystals as an example and reveal that the thermal transport is anisotropic, and the lattice dynamics is highly anharmonic. More importantly, we find that the two lowest-energy resonant phonon modes, associated with two mutually perpendicular molecular rotations, play critical roles in thermal conductivity and phase stability. The two optical modes suppress the acoustic branches by the avoided-crossing effect and hybridize with and strongly scatter acoustic phonons, further hindering thermal transport in α-pentaerythritol crystals. Furthermore, pressure can largely tune the rotational dynamics, reduce the resonance, and increase the phonon transmission and by adjusting the pressure from 0 MPa to 3500 MPa, an increase of 108% and 103% in in-plane and out-of-plane thermal conductivity, respectively, can be achieved. Our work provides a microscopic understanding of the rotational dynamics in α-pentaerythritol crystals, which can facilitate designing molecules to achieve a better barocaloric effect with more excellent thermal properties.

Read more at Journal of Materials Chemistry C:
https://pubs.rsc.org/en/content/articlelanding/2022/tc/d2tc02878f

Ferrofluids (FFs) can adapt their shape to a magnetic field. However, they cannot maintain their shape when the magnetic field is removed. Here, with a magneto-responsive and reconfigurable interfacial self-assembly (MRRIS) process, we show that FFs can be structured by a magnetic field and maintain their shape, like solids, after removing the magnetic field. The competing self-assembly of magnetic and nonmagnetic nanoparticles at the liquid interface endow FFs with both reconfigurability and structural stability. By manipulating the external magnetic field, we show that it is possible to “write” and “erase” the shape of the FFs remotely and repeatedly. To gain an in-depth understanding of the effect of MRRIS on the structure of FFs, we systematically study the shape variation of these liquids under both the static and dynamic magnetic fields. Our study provides a simple yet novel way of manipulating FFs and opens opportunities for the fabrication of all-liquid devices.

Read more at Nano Letters:
https://pubs.acs.org/doi/full/10.1021/acs.nanolett.2c01721

Double-helix structures, such as DNA, are formed in nature to realize many unique functions. Inspired by this, researchers are pursuing strategies to design such structures from polymers. A key question is whether the double helix can be formed from the self-folding of a single polymer chain without specific interactions. Here, using Langevin dynamics simulation and theoretical analysis, we find that a stable double-helix phase can be achieved by the self-folding of single semiflexible polymers as a result of the cooperation between local structure and nonlocal attraction. The critical temperature of double-helix formation approximately follows T^cri∼ln(k_θ) and T^cri∼ln(k_τ ), where k_θ and k_τ are the polymer bending and torsion stiffness, respectively. Furthermore, the double helix can exhibit major and minor grooves due to symmetric break for better packing. Our results provide a novel guide to the experimental design of the double helix.

Read more at Physical Review Letters:
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.128.197801

DNA deformations upon environmental changes, e.g., salt and temperature, play crucial roles in many biological processes  and  material  applications.  Here,  our  magnetic  tweezers  experiments  observed  that  the  increase  in  NaCl, KCl, or RbCl concentration leads to substantial DNA overwinding. Our simulations and theoretical calcula-tion quantitatively explain the salt-induced twist change through the mechanism: More salt enhances the screening of interstrand electrostatic repulsion and hence reduces DNA diameter, which is transduced to twist increase through twist-diameter coupling. We determined that the coupling constant is 4.5 ±  0.8 kBT/(degrees∙nm) for one base pair. The coupling comes from the restraint of the contour length of DNA backbone. On the basis of this coupling con-stant and diameter-dependent DNA conformational entropy, we predict the temperature dependence of DNA twist ≈ −0.01 degree/°C, which agrees with our and previous experimental results. Our analysis suggests that twist-diameter coupling is a common driving force for salt- and temperature-induced DNA twist changes.

Read more at Science Advances:
https://www.science.org/doi/epdf/10.1126/sciadv.abn1384

When stretched, both DNA and RNA duplexes change their twist angles through twist-stretch coupling. The coupling is negative for DNA but positive for RNA, which is not yet completely understood. Here, our magnetic tweezers experiments show that the coupling of RNA reverses from positive to negative by multivalent cations. Combining with the previously reported tension-induced negative-to-positive coupling reversal of DNA, we propose a unified mechanism of the couplings of both RNA and DNA based on molecular dynamics simulations. Two deformation pathways are competing when stretched: shrinking the radius causes positive couplings but widening the major groove causes negative couplings. For RNAwhose major groove is clamped by multivalent cations and canonical DNA, their radii shrink when stretched, thus exhibiting positive couplings. For elongated DNA whose radius already shrinks to the minimum and canonical RNA, their major grooves are widened when stretched, thus exhibiting negative couplings.

Read more at Physical Review Letters:
https://journals.aps.org/prl/abstract/10.1103/PhysRevLett.128.108103

The paper was featured in CityU Research Stories:
https://www.cityu.edu.hk/research/stories/2022/06/02/physical-mechanisms-explaining-dna-and-rna-twist-changes