Influence of decreased solvent permittivity on the structure and magnesium(II)-binding properties of the catalytic domain 5 of a group II intron ribozyme

Skilandat

Cadmium: From Toxicity to Essentiality

et al. 2012

Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromaticnitrogen sites (e.g., N7 of purines) over oxygen sites (like sugar-hydroxyl groups). However, matters are not that simple, though it is true that the affinity of Cd(2+) towards ribose-hydroxyl groups is very small; yet, a correct orientation brought about by a suitable primary binding site and a reduced solvent polarity, as it is expected to occur in a folded nucleic acid, may facilitate metal ion-hydroxyl group binding very effectively. Cd(2+) prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH(2) group in the adenine residue. This Cd(2+)-(N7) interaction in a guanine moiety leads to a significant acidification of the (N1)H meaning that the deprotonation reaction occurs now in the physiological pH range. N3 of the cytosine residue, together with the neighboring (C2)O, is also a remarkable Cd(2+) binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd(2+) dramatically, giving in addition rise to the deprotonation of the (C4)NH(2) group. The phosphodiester bridge is only a weak binding site but the affinity increases further from the mono-to the di-and the triphosphate. The same also holds for the corresponding nucleotides. Complex stability of the pyrimidine-nucleotides is solely determined by the coordination tendency of the phosphate group(s), whereas in the case of purine-nucleotides macrochelate formation takes place by the interaction of the phosphate-coordinated Cd(2+) with N7. The extents of the formation degrees of these chelates are summarized and the effect of a non-bridging sulfur atom in a thiophosphate group (versus a normal phosphate group) is considered. Mixed ligand complexes containing a nucleotide and a further mono-or bidentate ligand are covered and it is concluded that in these species N7 is released from the coordination sphere of Cd(2+). In the case that the other ligand contains an aromatic residue (e.g., 2,2'-bipyridine or the indole ring of tryptophanate) intramolecular stack formation takes place. With buffers like Tris or Bistris mixed ligand complexes are formed. Cd(2+) coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd(2+) and nucleic acids. Cd(2+) binding to oligonucleotides follows the principles of coordination to its units. The available crystal studies reveal that N7 of purines is the prominent binding site followed by phosphate oxygens and other heteroatoms in nucleic acids. Due to its high thiophilicity, Cd(2+) is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.

Section: The Metal Ion Affinity Of Ribose-hydroxyl Groups Is Smallmentioning

confidence: 99%

Complex Formation of Cadmium with Sugar Residues, Nucleobases, Phosphates, Nucleotides, and Nucleic Acids

Skilandat

Cadmium: From Toxicity to Essentiality

et al. 2012

“…Studies in an aqueous solution of 1,4-dioxane have been used to simulate the reduced permittivity of such conditions and found an overall increased Mg 2+ affinity to a short RNA hairpin [331]. Such an increase was also observed for the binding of Cu 2+ to single nucleotides in dioxane-enriched solutions [332].…”

Section: Effects Of Solvent Permittivity and Co-solutes To Mimic Macrmentioning

confidence: 97%

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

Pechlaner

Metal Ions in Life Sciences

2011

Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.

“…Further factors can influence the metal ion affinity considerably: Both, ionic strengths [14] and solvent polarity [15][16][17][18] are well known factors. In addition, it is important to use buffers that are not good ligands for metal ions at the same time.…”

Section: Prerequisits To the Rna And The Experimental Conditionsmentioning

confidence: 99%

“…Unfortunately, the low gyromagnetic ratio of nitrogen leads to a rather low signal of directly observed 15 N nuclei, and thus, extensive recording times (10 -20 h) are needed to obtain a simple 1D spectrum. Also spectral assignments of larger RNAs are complicated.…”

Section: [ 31 P]-nmrmentioning

confidence: 99%

Methods to Detect and Characterize Metal Ion Binding Sites in RNA

Erat

Structural and Catalytic Roles of Metal Ions in RNA

2011

Metal ions are inextricably associated with RNAs of any size and control their folding and activity to a large part. In order to understand RNA mechanisms, also the positioning, affinities and kinetics of metal ion binding must be known. Due to the spectroscopic silence and relatively fast exchange rates of the metal ions usually associated with RNAs, this task is extremely challenging and thus numerous methods have been developed and applied in the past. Here we provide an overview on the different metal ions and methods applied in RNA (bio)chemistry: The physical-chemical properties of important metal ions are presented and briefly discussed with respect to their application together with RNA. Each method ranging from spectroscopic over biochemical to computational approaches is briefly described also mentioning caveats that might occur during the experiment and/or interpretation of the results