The Snakelike Chain Character of Unstructured RNA

Abstract

The three-dimensional conformation of RNA is governed by a number of physical and chemical factors. However, in the absence of base-pairing and tertiary structure, unstructured RNA assumes a random-walk conformation dominated by the electrostatic self-repulsion of its charged, flexible backbone. This behavior is often modeled as a “wormlike chain” (WLC) with an electrostatics-dependent persistence length. However, through measurements of the end-to-end extension and ion atmosphere of poly(U) RNA stretched by 0.1-10 pN applied force, we find that the WLC model does not adequately describe the behavior of unstructured RNA. Instead, we find that our data are well described by a “snakelike chain” (SLC) model. The SLC model is characterized by smooth bending on long length scales and ion-stabilized crumpling on short length scales. We see signatures of both regimes in our extension vs. force data: a low-force power-law characteristic of a chain of swollen blobs on long length scales and a high-force region of increasing compliance with ion valence, consistent with increased conformational stabilization, on short length scales. In monovalent salt, we find the crossover between the two regimes (SLC blob size) to scale with the Debye screening length, indicating the determining importance of electrostatics. By systematically varying force and bulk salt concentration, we measure the change in the number of ions associated with the RNA as it is stretched. We find that ions are liberated during stretching. This is consistent with the SLC picture: ions that stabilize the short-length-scale crumples are released when those crumples are mechanically straightened. Additionally, we observe the number of ions liberated increases with increasing bulk salt concentration; this is consistent with the SLC model, but contradicts the WLC model with electrostatics-dependent persistence length.