title: Studies of the B-Z transition of DNA: The temperature dependence of the free-energy difference, the composition of the counterion sheath in mixed salt, and the preparation of a sample of the 5'-d[T-(m(5) C-G)12 -T] duplex in pure B-DNA or Z-DNA form.
abstract: It is often envisioned that cations might coordinate at specific sites of nucleic acids and play an important structural role, for instance in the transition between B-DNA and Z-DNA. However, nucleic acid models explicitly devoid of specific sites may also exhibit features previously considered as evidence for specific binding. Such is the case of the "composite cylinder" (or CC) model which spreads out localized features of DNA structure and charge by cylindrical averaging, while sustaining the main difference between the B and Z structures, namely the better immersion of the B-DNA phosphodiester charges in the solution. Here, we analyze the non-electrostatic component of the free-energy difference between B-DNA and Z-DNA. We also compute the composition of the counterion sheath in a wide range of mixed-salt solutions and of temperatures: in contrast with the large difference of composition between the B-DNA and Z-DNA forms, the temperature dependence of sheath composition, previously unknown, is very weak. In order to validate the model, the mixed-salt predictions should be compared to experiment. We design a procedure for future measurements of the sheath composition based on Anomalous Small-Angle X-ray Scattering and complemented by (31) P NMR. With due consideration for the kinetics of the B-Z transition and for the capacity of generating at will the B or Z form in a single sample, the 5'-d[T-(m(5) C-G)12 -T] 26-mer emerges as a most suitable oligonucleotide for this study. Finally, the application of the finite element method to the resolution of the Poisson-Boltzmann equation is described in detail. © 2016 Wiley Periodicals, Inc. Biopolymers 105: 369-384, 2016.
authors.affiliation: Physique de la Matière Condensée, Ecole Polytechnique, CNRS, 91128, Palaiseau, France.
authors.forename: Maurice
authors.initials: M
authors.lastname: Guéron
authors.affiliation: Laboratoire de Biochimie, Ecole polytechnique, CNRS, Université Paris-Saclay, 91128, Palaiseau Cedex, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Plateau
authors.affiliation: Physique de la Matière Condensée, Ecole Polytechnique, CNRS, 91128, Palaiseau, France.
authors.forename: Marcel
authors.initials: M
authors.lastname: Filoche
mesh_terms: D059371:DNA, B-Form / Q000737:chemistry*; D043542:DNA, Z-Form / Q000737:chemistry*; D007700:Kinetics; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D012492:Salts / Q000737:chemistry; D053838:Scattering, Small Angle; D012996:Solutions; D013696:Temperature; D013816:Thermodynamics; D014961:X-Ray Diffraction
chemical_list: D059371:DNA, B-Form; D043542:DNA, Z-Form; D009841:Oligonucleotides; D012492:Salts; D012996:Solutions
keywords: ASAXS; B-DNA/Z-DNA transition; composite cylinder model; counterion sheath composition; mixed salt solution