title: Determining the Locations of Ions and Water around DNA from X-Ray Scattering Measurements.
abstract: Nucleic acids carry a negative charge, attracting salt ions and water. Interactions with these components of the solvent drive DNA to condense, RNA to fold, and proteins to bind. To understand these biological processes, knowledge of solvent structure around the nucleic acids is critical. Yet, because they are often disordered, ions and water evade detection by x-ray crystallography and other high-resolution methods. Small-angle x-ray scattering (SAXS) is uniquely sensitive to the spatial correlations between solutes and the surrounding solvent. Thus, SAXS provides an experimental constraint to guide or test emerging solvation theories. However, the interpretation of SAXS profiles is nontrivial because of the difficulty in separating the scattering signals of each component: the macromolecule, ions, and hydration water. Here, we demonstrate methods for robustly deconvoluting these signals, facilitating a more straightforward comparison with theory. Using SAXS data collected on an absolute intensity scale for short DNA duplexes in solution with Na(+), K(+), Rb(+), or Cs(+) counterions, we mathematically decompose the scattering profiles into components (DNA, water, and ions) and validate the decomposition using anomalous scattering measurements. In addition, we generate a library of physically motivated ion atmosphere models and rank them by agreement with the scattering data. The best-fit models have relatively compact ion atmospheres when compared to predictions from the mean-field Poisson-Boltzmann theory of electrostatics. Thus, the x-ray scattering methods presented here provide a valuable measurement of the global structure of the ion atmosphere that can be used to test electrostatics theories that go beyond the mean-field approximation.
authors.affiliation: School of Applied and Engineering Physics, Cornell University, Ithaca, New York.
authors.forename: Steve P
authors.initials: SP
authors.lastname: Meisburger
authors.affiliation: School of Applied and Engineering Physics, Cornell University, Ithaca, New York.
authors.forename: Suzette A
authors.initials: SA
authors.lastname: Pabit
authors.affiliation: School of Applied and Engineering Physics, Cornell University, Ithaca, New York. Electronic address: lp26@cornell.edu.
authors.forename: Lois
authors.initials: L
authors.lastname: Pollack
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D057927:Hydrophobic and Hydrophilic Interactions; D008672:Metals, Alkali / Q000737:chemistry*; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data; D053838:Scattering, Small Angle; D014867:Water / Q000737:chemistry; D014961:X-Ray Diffraction
chemical_list: D008672:Metals, Alkali; D014867:Water; D004247:DNA