From nucleotides to ribozymes—A comparison of their metal ion binding properties

Abstract

It is undisputable that the fates of metal ions and nucleic acids are inescapably interwoven. Metal ions are essential for charge compensation of the negatively charged phosphate-sugar backbone, they are instrumental for proper folding, and last but not least they are crucial cofactors for ribozyme catalysis. Considerable progress has been achieved in the past few years on the identification of metal ion binding sites in large DNA and RNA molecules, like in ribozymes including the ribosome. Hereby, most information was gained from crystallography, which fails to explain metal ion binding equilibria in solution as well as the factors that determine the coordination of a metal ion to a specific site. In contrast, such information is readily available for the low-molecular building blocks of large nucleic acids, i.e. for mononucleotides and to some extent also dinucleotides. In this review, we combine and compare for the first time both sets of information. The focus is thereby set on Mg2+, Ca2+, Mn2+, and Cd2+ because these four metal ions are either freely available in cells, have a large impact on the catalytic rate of ribozymes, and/or are often applied in RNA biochemistry. Our comparisons show that results obtained from small molecules can be directly transposed to the findings in large RNA structures like the ribosome. For example, the basic coordination-chemical properties of the different metal ions are reflected in their binding to large nucleic acid structures: macrochelate formation, e.g. the simultaneous intranucleotide coordination of a Mg2+ ion to the phosphate unit and the N7 site of a purine nucleobase (be it inner-or outersphere), is well known for mononucleotides. We show that the frequency of occurrence of this type of coordination is the same for mononucleotides and the ribosome.

Metal Ion–RNA Interactions Studied via Multinuclear NMR

“…However it has been shown that around 10 % of the total negative charge is compensated by metal ions that are site specifically bound (5). In order to be active, RNA molecules need to adopt complex three dimensional structures, stabilized by a large number and variety of tertiary contacts.…”

“…In order to be active, RNA molecules need to adopt complex three dimensional structures, stabilized by a large number and variety of tertiary contacts. In this folding process, localized pockets of accumulated negative charge are formed, that strongly bind positively charged ions, that is Na + , K + , Ca 2+ and Mg 2+ , the most abundant solvated metal ions in cells (5). In particular, Mg 2+ has been shown to perform both a structural and a catalytical role.…”

“…The biologically most relevant metal ion in RNA biochemistry is Mg 2+ , which is commonly considered as spectroscopically silent (5). It is however worth mentioning that Mg 2+ is NMR active, and, despite its low sensitivity, low natural abundance and its large quadrupolar moment, a few reports have been published dealing with the use of this "exotic" nucleus in the study of NTPs-Mg 2+ as well as nucleic acids-Mg 2+ interactions (for a recent review, see (10)).…”

“…mediated through the hydrogen bonds of the coordinated water molecule (Fig. 2) (5). It is worth noting that the coordination properties of metal ions to single nucleotides can be directly translated to large nucleic acids (5 However, the chemical exchange within RNA-metal ions system mostly prevents direct observation of J-coupling (18).…”

“…2) (5). It is worth noting that the coordination properties of metal ions to single nucleotides can be directly translated to large nucleic acids (5 However, the chemical exchange within RNA-metal ions system mostly prevents direct observation of J-coupling (18). Lastly, also 31 P chemical shift perturbation can be used to explore RNA-metal ion interactions (19).…”