title: Understanding nucleic acid-ion interactions.
abstract: Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions' electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid-ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid-ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid-ion interactions.
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, 2628 CJ Delft, Netherlands; email: Jan.Lipfert@lmu.de.
authors.forename: Jan
authors.initials: J
authors.lastname: Lipfert
authors.forename: Sebastian
authors.initials: S
authors.lastname: Doniach
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.forename: Daniel
authors.initials: D
authors.lastname: Herschlag
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D002412:Cations; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D007477:Ions / Q000737:chemistry*; D008274:Magnesium / Q000737:chemistry; D008670:Metals / Q000737:chemistry; D008962:Models, Theoretical; D009690:Nucleic Acid Conformation; D009696:Nucleic Acids / Q000737:chemistry*; D016012:Poisson Distribution; D012313:RNA / Q000737:chemistry; D012984:Software; D055672:Static Electricity; D013816:Thermodynamics
chemical_list: D002412:Cations; D007477:Ions; D008670:Metals; D009696:Nucleic Acids; D012313:RNA; D004247:DNA; D008274:Magnesium
keywords: Hill equation; Manning condensation; Poisson–Boltzmann; RNA/DNA; electrostatics; free energy; ions