UC Santa Barbara

The strong negative charge of nucleic acids adds additional complexity to their behavior, beyond what would be expected for neutral polymers, through the addition of long-range self-repulsive interactions and through the screening of those interactions by ions in solution. Among the techniques that can probe the electrostatic behavior of a charged polymer are single-molecule force spectroscopy, which reports on the elasticity of the polymer (i.e., extension as a function of applied force), and ion counting, which reports on the stoichiometry of positive and negative ions constituting the polymer’s “ion atmosphere”. While extensive studies of both types have been made of double-stranded DNA, a strongly charged and moderately stiff polymer, less is known about the single-stranded nucleic acids (ssNAs), which are also strongly charged but are comparatively flexible.

In my dissertation, I use single-molecule magnetic tweezers to measure the elasticity of ssRNA as a function of monovalent and divalent salt concentration under 0.1–10 pN applied force and observe behavior characteristic of flexible polyelectrolytes. I then extend the measurements up to 100 pN to probe the intermediate-force domain connecting behavior dominated by electrostatics and by the chemical structure of the backbone. These new data allow the critical testing of a wormlike chain-derived model treating electrostatics through a mean-field, salt-dependent tension. This model is shown to quantitatively account for the data and to bridge the established behaviors at lower and higher force. I also quantify the ion atmosphere stoichiometry of both ssDNA and ssRNA using three complementary experimental techniques, including both bulk and single-molecule approaches. These results are compared with Poisson-Boltzmann models incorporating varying degrees of structural complexity, demonstrating the inherently short-ranged (i.e., sub-Debye screening length) nature of nucleic acid-ion interactions.