Low-resolution models for nucleic acids from small-angle X-ray scattering with applications to electrostatic modeling

Abstract

Several algorithms are available to reconstruct low-resolution electron density maps of biological macromolecules from small-angle solution scattering data. These algorithms have been extensively applied to proteins and protein complexes. Here, we demonstrate their applicability to nucleic acids by reconstructing a set of RNA and DNA molecules of known three-dimensional structure from their small-angle X-ray scattering profiles. The overall size and shape of the molecules get reproduced well in all tested cases. Furthermore, we show that the generated bead models can be used as inputs for electrostatic calculations. The number of ions bound under different solution conditions computed from numerical solutions of the Poisson–Boltzmann equation for bead models agrees very well with results of calculations on all atom models derived from crystallography. The predictions from Poisson–Boltzmann theory also agree generally well with experimentally determined ion binding numbers.