Cornwell-Arquitt Robert L, Nigh Riley, Hathaway Michael T, Yesselman Joseph D, Hendrix David A
Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97333, United States.
Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, NE 68503, United States.
Nucleic Acids Res. 2025 Jun 20;53(12). doi: 10.1093/nar/gkaf565.
RNA molecules adopt complex structures that perform essential biological functions across all forms of life, making them promising candidates for therapeutic applications. However, our ability to design new RNA structures remains limited by an incomplete understanding of their folding principles. While global metrics such as the minimum free energy are widely used, they are at odds with naturally occurring structures and incompatible with established design rules. Here, we introduce local stability compensation (LSC), a principle that RNA folding is governed by the local balance between destabilizing loops and their stabilizing adjacent stems, challenging the focus on global energetic optimization. Analysis of over 100 000 RNA structures revealed that LSC signatures are particularly pronounced in bulges and their adjacent stems, with distinct patterns across different RNA families that align with their biological functions. To validate LSC experimentally, we systematically analyzed thousands of RNA variants using DMS chemical mapping. Our results demonstrate that stem folding, as measured by reactivity, correlates with LSC (R² = 0.458 for hairpin loops) and that instabilities show no significant effect on folding for distal stems. These findings demonstrate that LSC can be a guiding principle for understanding RNA function and for the rational design of custom RNAs.
RNA分子会形成复杂的结构，这些结构在所有生命形式中执行着至关重要的生物学功能，这使得它们成为有前景的治疗应用候选物。然而，我们设计新RNA结构的能力仍然受到对其折叠原理理解不完整的限制。虽然诸如最小自由能等全局指标被广泛使用，但它们与天然存在的结构不一致，并且与既定的设计规则不兼容。在这里，我们引入了局部稳定性补偿（LSC），这一原理认为RNA折叠受去稳定环与其稳定相邻茎之间的局部平衡支配，这对专注于全局能量优化提出了挑战。对超过100000个RNA结构的分析表明，LSC特征在凸起及其相邻茎中尤为明显，不同RNA家族有不同的模式，这些模式与其生物学功能相符。为了通过实验验证LSC，我们使用DMS化学图谱系统地分析了数千个RNA变体。我们的结果表明，通过反应性测量的茎折叠与LSC相关（发夹环的R² = 0.458），并且不稳定性对远端茎的折叠没有显著影响。这些发现表明，LSC可以作为理解RNA功能和合理设计定制RNA的指导原则。
