AI Article Synopsis
- - RNA molecules can form different structures, and stem-loops are a common one; this study analyzed 15 RNA stem-loop sequences using molecular dynamics simulations.
- - The analysis revealed that the stem regions generally adopt a stable A-form structure, but the loop regions are more variable and require adjustments for accurate modeling.
- - Current models for simulating RNA are still challenging, but the findings from this study could serve as a benchmark for testing new RNA modeling techniques in the future.
Article Abstract
Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here, we present a systematic analysis of 15 RNA stem-loop sequences simulated with molecular dynamics simulations in an implicit solvent environment. Analysis of RNA cluster ensembles showed that the stem-loop structures can generally adopt the A-form RNA in the stem region. Loop structures are more sensitive, and experimental structures could only be reproduced with modification of CH···O interactions in the force field, combined with an implicit solvent nonpolar correction to better model base stacking interactions. Accurately modeling RNA with current atomistic physics-based models remains challenging, but the RNA systems studied herein may provide a useful benchmark set for testing other RNA modeling methods in the future.
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|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC11584990 | PMC |
| http://dx.doi.org/10.1021/acs.jcim.4c00756 | DOI Listing |
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