Molecular dynamics study of ways of RNA base-pair formation

Duan, Qiangqiang; Tao, Peng; Wang, Jun; Xiao, Yi

doi:10.1103/physreve.102.032403

Cited by 5 publications

(2 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…We found that many base pairs have been broken (Figure S4, Supporting Information), and this may be the reason why the functions of these NANPs cannot be restored because the original base pairing interaction cannot be easily formed due to the complicated base pair formation mechanisms in RNA. [ 58 ] To further confirm it, we have added water molecules to the structures after the vacuum simulation and performed another 100 ns simulations. We have found that RMSD has increased even higher (Figure S5, Supporting Information), and the broken base pairs cannot be restored (Figure S4, Supporting Information), indicating that the NANP structures have undergone irreversible deformation in the vacuum simulations.…”

Section: Resultsmentioning

confidence: 99%

Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures

Tran

Chandler

Halman

et al. 2022

Small

View full text Add to dashboard Cite

Recent advances in nanotechnology now allow for the methodical implementation of therapeutic nucleic acids (TNAs) into modular nucleic acid nanoparticles (NANPs) with tunable physicochemical properties which can match the desired biological effects, provide uniformity, and regulate the delivery of multiple TNAs for combinatorial therapy. Despite the potential of novel NANPs, the maintenance of their structural integrity during storage and shipping remains a vital issue that impedes their broader applications. Cold chain storage is required to maintain the potency of NANPs in the liquid phase, which greatly increases transportation costs. To promote long‐term storage and retention of biological activities at higher temperatures (e.g., +50 °C), a panel of representative NANPs is first exposed to three different drying mechanisms—vacuum concentration (SpeedVac), lyophilization (Lyo), and light‐assisted drying (LAD)—and then rehydrated and analyzed. While SpeedVac primarily operates using heat, Lyo avoids temperature increases by taking advantage of pressure reduction and LAD involves a near‐infrared laser for uniform drying in the presence of trehalose. This work compares and defines refinements crucial in formulating an optimal strategy for producing stable, fully functional NANPs and presents a forward advancement in their development for clinical applications.

show abstract

Section: Resultsmentioning

confidence: 99%

Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures

Tran

Chandler

Halman

et al. 2022

Small

View full text Add to dashboard Cite

show abstract

“…The folding process of RNA is generally hierarchical, with the formation of the double helix first, followed by the folding of the tertiary structure under the interaction of tertiary contacts. The most straightforward idea is to use traditional all-atom molecular dynamics (AAMD) simulations to study RNA folding, − but the problem is that even with state-of-the-art computing resources, it is still difficult for an unfolded RNA conformation to fold with AA force fields. Some alternative prediction models have been proposed.…”

mentioning

confidence: 99%

Ribonucleic Acid Folding Prediction Based on Iterative Multiscale Simulation

Zhang

Zhong

et al. 2022

J. Phys. Chem. Lett.

View full text Add to dashboard Cite

RNA folding prediction is a challenge. Currently, many RNA folding models are coarse-grained (CG) with the potential derived from the known RNA structures. However, this potential is not suitable for modified and entirely new RNA. It is also not suitable for the folding simulation of RNA in the real cellular environment, including many kinds of molecular interactions. In contrast, our proposed model has the potential to address these issues, which is a multiscale simulation scheme based on all-atom (AA) force fields. We fit the CG force field using the trajectories generated by the AA force field and then iteratively perform molecular dynamics (MD) simulations of the two scales. The all-atom molecular dynamics (AAMD) simulation is mainly responsible for the correction of RNA structure, and the CGMD simulation is mainly responsible for efficient conformational sampling. On the basis of this scheme, we can successfully fold three RNAs belonging to a hairpin, a pseudoknot, and a four-way junction.

show abstract