A Stability Concept for Metal Ion Coordination to Single-Stranded Nucleic Acids and Affinities of Individual Sites

摘要

Tnhe three-dimensional architecture and function ofnnucleic acids strongly depend on the presence ofnmetal ions, among other factors. Given the negativencharge of the phosphate sugar backbone, positivelyncharged species, mostly metal ions, are necessary forncompensation. However, these ions also allow andninduce folding of complicated RNA structures. Further-nmore, metal ions bind to specific sites, stabilizing localnmotifs and positioning themselves correctly to aid (orneven enable) a catalytic mechanism, as, for example, innribozymes. Many nucleic acids thereby exhibit large dif-nferences in folding and activity depending not only onnthe concentration but also on the kind of metal ionninvolved. As a consequence, understanding the role ofnmetal ions in nucleic acids requires knowing not only the exact positioning and coordination sphere of each specifically boundnmetal ion but also its intrinsic site affinity. However, the quantification of metal ion affinities toward certain sites in a single-nstranded (though folded) nucleic acid is a demanding task, and few experimental data exist.