Experimental approaches for investigating ion atmospheres around nucleic acids and proteins

Lipfert, 2014, Understanding nucleic acid-ion interactions, Annu Rev Biochem, 83, 813, 10.1146/annurev-biochem-060409-092720 Okur, 2017, Beyond the Hofmeister Series: Ion-Specific Effects on Proteins and Their Biological Functions, J Phys Chem B, 121, 1997, 10.1021/acs.jpcb.6b10797 Record, 1998, Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts, Adv Protein Chem, 51, 281, 10.1016/S0065-3233(08)60655-5 Yu, 2020, Dynamics of ionic interactions at protein–nucleic acid interfaces, Acc Chem Res, 53, 1802, 10.1021/acs.accounts.0c00212 Zhang, 2010, Chemistry of Hofmeister anions and osmolytes, Annu Rev Phys Chem, 61, 63, 10.1146/annurev.physchem.59.032607.093635 Burley, 2021, RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences, Nucleic Acids Res, 49, D437, 10.1093/nar/gkaa1038 Ross, 1964, Electrophoresis of DNA. II. Specific interactions of univalent and divalent cations with DNA, Biopolymers, 2, 79, 10.1002/bip.1964.360020111 Shapiro, 1969, The binding of small cations to deoxyribonucleic acid. Nucleotide specificity, Biochemistry, 8, 3233, 10.1021/bi00836a015 Skerjanc, 1968, Interactions of polyelectrolytes with simple electrolytes. III. The binding of magnesium ion by deoxyribonucleic acid, J Am Chem Soc, 90, 3081, 10.1021/ja01014a017 Zubay, 1958, Nucleic acid interactions with metal ions and amino acids, BBA - Biochimica et Biophysica Acta, 29, 47, 10.1016/0006-3002(58)90145-8 Bret, 1984, Distribution of counterions around a cylindrical polyelectrolyte and manning's condensation theory, Biopolymers, 23, 287, 10.1002/bip.360230209 Manning, 1969, Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions. I. Colligative Properties, J Chem Phys, 51, 924, 10.1063/1.1672157 Record, 1976, Ion effects on ligand-nucleic acid interactions, J Mol Biol, 107, 145, 10.1016/S0022-2836(76)80023-X Anderson, 1990, Ion distributions around DNA and other cylindrical polyions: theoretical descriptions and physical implications, Annu Rev Biophys Biophys Chem, 19, 423, 10.1146/annurev.bb.19.060190.002231 Manning, 1978, Molecular theory of polyelectrolyte solutions with applications to electrostatic properties of polynucleotides, Q Rev Biophys, 11, 179, 10.1017/S0033583500002031 Record, 1978, Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity, Q Rev Biophys, 11, 103, 10.1017/S003358350000202X Manning, 1969, Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions. 3. An Analysis Based on Mayer Ionic Solution Theory, J Chem Phys, 51, 3249, 10.1063/1.1672502 Manning, 1969, Limiting Laws and Counterion Condensation in Polyelectrolyte Solutions. 2. Self-Diffusion of Small Ions, J Chem Phys, 51, 934, 10.1063/1.1672158 Dehaseth, 1977, Nonspecific Interaction of Lac Repressor with DNA - Association Reaction Driven by Counterion Release, Biochemistry, 16, 4783, 10.1021/bi00641a004 Record, 1977, Interpretation of monovalent and divalent cation effects on the lac repressor-operator interaction, Biochemistry, 16, 4791, 10.1021/bi00641a005 Stigter, 1995, Evaluation of the counterion condensation theory of polyelectrolytes, Biophys J, 69, 380, 10.1016/S0006-3495(95)79910-6 Privalov, 2011, Interpreting protein/DNA interactions: distinguishing specific from non-specific and electrostatic from non-electrostatic components, Nucleic Acids Res, 39, 2483, 10.1093/nar/gkq984 Record, 1991, Analysis of equilibrium and kinetic measurements to determine thermodynamic origins of stability and specificity and mechanism of formation of site-specific complexes between proteins and helical DNA, Methods Enzymol, 208, 291, 10.1016/0076-6879(91)08018-D Bai, 2007, Quantitative and comprehensive decomposition of the ion atmosphere around nucleic acids, J Am Chem Soc, 129, 14981, 10.1021/ja075020g Gebala, 2015, Cation-anion interactions within the nucleic acid ion atmosphere revealed by ion counting, J Am Chem Soc, 137, 14705, 10.1021/jacs.5b08395 Fogolari, 2002, The Poisson-Boltzmann equation for biomolecular electrostatics: a tool for structural biology, J Mol Recognit, 15, 377, 10.1002/jmr.577 Honig, 1995, Classical electrostatics in biology and chemistry, Science, 268, 1144, 10.1126/science.7761829 Baker, 2001, Electrostatics of nanosystems: application to microtubules and the ribosome, Proc Natl Acad Sci U S A, 98, 10037, 10.1073/pnas.181342398 Gilson, 1988, Calculating the electrostatic potential of molecules in solution: Method and error assessment, J Comput Chem, 9, 327, 10.1002/jcc.540090407 Li, 2019, DelPhi Suite: New Developments and Review of Functionalities, J Comput Chem, 40, 2502, 10.1002/jcc.26006 Grochowski, 2008, Continuum molecular electrostatics, salt effects, and counterion binding—A review of the Poisson-Boltzmann theory and its modifications, Biopolymers, 89, 93, 10.1002/bip.20877 Netz, 2000, Beyond Poisson-Boltzmann: Fluctuation effects and correlation functions, Eur Phys J E, 1, 203, 10.1007/s101890050023 Chu, 2007, Evaluation of ion binding to DNA duplexes using a size-modified Poisson-Boltzmann theory, Biophys J, 93, 3202, 10.1529/biophysj.106.099168 Granot, 1983, Effect of finite ionic size on the solution of the Poisson-Boltzmann equation: Application to the binding of divalent metal ions to DNA, Biopolymers, 22, 1831, 10.1002/bip.360220715 Gavryushov, 2008, Electrostatics of B-DNA in NaCl and CaCl2 Solutions: Ion Size, Interionic Correlation, and Solvent Dielectric Saturation Effects, J Phys Chem B, 112, 8955, 10.1021/jp711339d Borukhov, 1997, Steric Effects in Electrolytes: A Modified Poisson-Boltzmann Equation, Phys Rev Lett, 79, 435, 10.1103/PhysRevLett.79.435 Das, 2005, Determining the Mg2+ Stoichiometry for Folding an RNA Metal Ion Core, J Am Chem Soc, 127, 8272, 10.1021/ja051422h Gebala, 2019, Quantitative studies of an RNA duplex electrostatics by ion counting, Biophys J, 117, 1116, 10.1016/j.bpj.2019.08.007 Gebala, 2019, Ion counting demonstrates a high electrostatic field generated by the nucleosome, Elife, 8, 10.7554/eLife.44993 Pabit, 2010, Counting Ions around DNA with Anomalous Small-Angle X-ray Scattering, J Am Chem Soc, 132, 16334, 10.1021/ja107259y Yu, 2021, Quantifying and visualizing weak interactions between anions and proteins, Proc Natl Acad Sci U S A, 118, 10.1073/pnas.2015879118 Gebala, 2016, Does cation size affect occupancy and electrostatic screening of the nucleic acid ion atmosphere?, J Am Chem Soc, 138, 10925, 10.1021/jacs.6b04289 Andresen, 2004, Spatial Distribution of Competing Ions around DNA in Solution, Phys Rev Lett, 93, 10.1103/PhysRevLett.93.248103 Andresen, 2008, Mono- and Trivalent Ions around DNA: A Small-Angle Scattering Study of Competition and Interactions, Biophys J, 95, 287, 10.1529/biophysj.107.123174 Bleam, 1980, Relative binding affinities of monovalent cations for double-stranded DNA, Proc Natl Acad Sci U S A, 77, 3085, 10.1073/pnas.77.6.3085 Pletka, 2020, Detecting counterion dynamics in DNA-protein association, Angew Chem Int Ed Engl, 59, 1465, 10.1002/anie.201910960 Das, 2003, Counterion distribution around DNA probed by solution X-ray scattering, Phys Rev Lett, 90, 10.1103/PhysRevLett.90.188103 Hud, 1997, Localization of divalent metal ions in the minor groove of DNA A-tracts, J Am Chem Soc, 119, 5756, 10.1021/ja9704085 Denisov, 2000, Sequence-specific binding of counterions to B-DNA, Proc Natl Acad Sci U S A, 97, 629, 10.1073/pnas.97.2.629 Pabit, 2009, Using Anomalous Small Angle X-Ray Scattering to Probe the Ion Atmosphere Around Nucleic Acids, Methods in Enzymology: Academic Press, 19, 391, 10.1016/S0076-6879(09)69019-4 Pollack, 2011, SAXS studies of ion-nucleic acid interactions, Annu Rev Biophys, 40, 225, 10.1146/annurev-biophys-042910-155349 Pabit, 2009, Both helix topology and counterion distribution contribute to the more effective charge screening in dsRNA compared with dsDNA, Nucleic Acids Res, 37, 3887, 10.1093/nar/gkp257 Rouzina, 1997, Competitive electrostatic binding of charged ligands to polyelectrolytes: practical approach using the non-linear Poisson-Boltzmann equation, Biophys Chem, 64, 139, 10.1016/S0301-4622(96)02231-4 Rouzina, 1996, Competitive Electrostatic Binding of Charged Ligands to Polyelectrolytes: Planar and Cylindrical Geometries, J Phys Chem, 100, 4292, 10.1021/jp9525898 Rouzina, 1996, Influence of Ligand Spatial Organization on Competitive Electrostatic Binding to DNA, J Phys Chem, 100, 4305, 10.1021/jp9525907 Kirmizialtin, 2012, RNA and its ionic cloud: solution scattering experiments and atomically detailed simulations, Biophys J, 102, 819, 10.1016/j.bpj.2012.01.013 Greenfeld M, Herschlag D. Probing Nucleic Acid–Ion Interactions with Buffer Exchange-Atomic Emission Spectroscopy. Biophysical, Chemical, and Functional Probes of RNA Structure, Interactions and Folding: Part B2009. p. 375-89. Jacobson, 2017, Counting the ions surrounding nucleic acids, Nucleic Acids Res, 45, 1596 Giambasu, 2015, Competitive interaction of monovalent cations with DNA from 3D-RISM, Nucleic Acids Res, 43, 8405, 10.1093/nar/gkv830 Giambasu, 2019, Predicting Site-Binding Modes of Ions and Water to Nucleic Acids Using Molecular Solvation Theory, J Am Chem Soc, 141, 2435, 10.1021/jacs.8b11474 Giambasu, 2014, Ion counting from explicit-solvent simulations and 3D-RISM, Biophys J, 106, 883, 10.1016/j.bpj.2014.01.021 Cavanagh, 2007 Anderson, 1978, Sodium-23 NMR studies of cation-DNA interactions, Biophys Chem, 7, 301, 10.1016/0301-4622(78)85007-8 Reuben, 1975, The alkali ion-DNA interaction as reflected in the nuclear relaxation rates of Na and Rb, Proc Natl Acad Sci U S A, 72, 245, 10.1073/pnas.72.1.245 Hud, 1999, Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex, J Mol Biol, 285, 233, 10.1006/jmbi.1998.2327 Hud, 1999, Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending, J Mol Biol, 286, 651, 10.1006/jmbi.1998.2513 Clore, 2009, Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes, Chem Rev, 109, 4108, 10.1021/cr900033p Iwahara, 2021, Discrete-state stochastic kinetic models for target DNA search by proteins: Theory and experimental applications, Biophys Chem, 269, 10.1016/j.bpc.2020.106521 Schreiber, 1996, Rapid, electrostatically assisted association of proteins, Nat Struct Biol, 3, 427, 10.1038/nsb0596-427 Zhou, 2018, Electrostatic Interactions in Protein Structure, Folding, Binding, and Condensation, Chem Rev, 118, 1691, 10.1021/acs.chemrev.7b00305 Ha, 1992, Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the “glutamate effect” on protein-DNA interactions, J Mol Biol, 228, 252, 10.1016/0022-2836(92)90504-D Leirmo, 1987, Replacement of potassium chloride by potassium glutamate dramatically enhances protein-DNA interactions in vitro, Biochemistry, 26, 2095, 10.1021/bi00382a006 Lombardo, 2020, Structural Characterization of Biomaterials by Means of Small Angle X-rays and Neutron Scattering (SAXS and SANS), and Light Scattering Experiments, Molecules, 25, 10.3390/molecules25235624 Hass, 2015, Contemporary NMR Studies of Protein Electrostatics, Annu Rev Biophys, 44, 53, 10.1146/annurev-biophys-083012-130351 Nguyen, 2019, NMR methods for characterizing the basic side chains of proteins: electrostatic interactions, hydrogen bonds, and conformational dynamics, Methods Enzymol, 615, 285, 10.1016/bs.mie.2018.08.017