Journal
BIOPHYSICAL JOURNAL
Volume 105, Issue 11, Pages 2569-2576Publisher
CELL PRESS
DOI: 10.1016/j.bpj.2013.10.019
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Funding
- National Science Foundation [DMR-1006737]
- NSF graduate research fellowship [DGE-1144085]
- Direct For Mathematical & Physical Scien [1006737] Funding Source: National Science Foundation
- Direct For Mathematical & Physical Scien
- Division Of Materials Research [1309414] Funding Source: National Science Foundation
- Division Of Materials Research [1006737] Funding Source: National Science Foundation
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In the absence of base-pairing and tertiary structure, ribonucleic acid (RNA) assumes a random-walk conformation, modulated by the electrostatic self-repulsion of the charged, flexible backbone. This behavior is often modeled as a Kratky-Porod wormlike chain'' (WLC) with a Barrat-Joanny scale-dependent persistence length. In this study we report measurements of the end-to-end extension of poly(U) RNA under 0.1 to 10 pN applied force and observe two distinct elastic-response regimes: a low-force, power-law regime characteristic of a chain of swollen blobs on long length scales and a high-force, salt-valence-dependent regime consistent with ion-stabilized crumpling on short length scales. This short-scale structure is additionally supported by force- and salt-dependent quantification of the RNA ion atmosphere composition, which shows that ions are liberated under stretching; the number of ions liberated increases with increasing bulk salt concentration. Both this result and the observation of two elastic-response regimes directly contradict the WLC model, which predicts a single elastic regime across all forces and, when accounting for scale-dependent persistence length, the opposite trend in ion release with salt concentration. We conclude that RNA is better described as a snakelike chain,'' characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. In monovalent salt, these two regimes are separated by a characteristic length that scales with the Debye screening length, highlighting the determining importance of electrostatics in RNA conformation.
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