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

Type of publication Peer-reviewed
Publikationsform Contribution to book (peer-reviewed)
Publication date 2013
Author Sigel Roland K. O., Skilandat Miriam, Sigel Astrid, Operschall Bert P., Sigel Helmut,
Project Metal Ion-Guided Assembly and Structures of the Catalytic Core of Ribozymes
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Contribution to book (peer-reviewed)

Book Metal Ions Life Science,
Editor , Sigel Astrid
Publisher Springer Netherlands, Dordrecht
Page(s) 191 - 274
ISBN 978-94-007-5178-1
Title of proceedings Metal Ions Life Science,
DOI 10.1007/978-94-007-5179-8

Abstract

Cadmium(II), commonly classified as a relatively soft metal ion, prefers indeed aromatic-nitrogen 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 Cd2+ 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. Cd2+ prefers the guanine(N7) over the adenine(N7), mainly because of the steric hindrance of the (C6)NH2 group in the adenine residue. This Cd2+-(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 Cd2+ binding site, though replacement of (C2)O by (C2)S enhances the affinity towards Cd2+ dramatically, giving in addition rise to the deprotonation of the (C4)NH2 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 Cd2+ 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 Cd2+. 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. Cd2+ coordination to dinucleotides and to dinucleoside monophosphates provides some insights regarding the interaction between Cd2+ and nucleic acids. Cd2+ 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, Cd2+ is regularly used in so-called thiorescue experiments, which lead to the identification of a direct involvement of divalent metal ions in ribozyme catalysis.
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