Exploring Metal Ion Coordination to Nucleic Acids by NMR

Abstract

Metal ions play a crucial role in charge compensation, folding and stabilization of tertiary structures of large nucleic acids. In addition, they may be directly involved in the catalytic mechanism of ribozymes. Most metal ions applied in the context of nucleic acids in vivo and in vitro bind in a kinetically labile fashion. Hence, the detection of metal ion binding sites, not to mention the elucidation of the specific coordination sphere, still poses largely unresolved problems. Here we describe the different strategies applied and the progress made over the last years to characterize metal ion coordination to large nucleic acids by NMR. Metal ions play a crucial role in charge compensation, folding and stabilization of tertiary structures of large nucleic acids. In addition, they may be directly involved in the catalytic mechanism of ribozymes. Most metal ions applied in the context of nucleic acids in vivo and in vitro bind in a kinetically labile fashion. Hence, the detection of metal ion binding sites, not to mention the elucidation of the specific coordination sphere, still poses largely unresolved problems. Here we describe the different strategies applied and the progress made over the last years to characterize metal ion coordination to large nucleic acids by NMR.

NMR Spectroscopy in Bioinorganic Chemistry

“…[11,18] 2.1. . [12] Aside from the above described changes of the RNA chemical shifts, the observation of NOE cross peaks between its NH 3 protons and the protons of the RNA (Fig. 3) allows a direct localization of the metal ion binding site.…”

“…However, they are modular in nature, and hence offer an optimal platform for the study of metal ion-RNA binding properties. [12,13,32] The single parts can be transcribed in large amounts, [33] studied independently, and their properties translated to the whole intron. For this reason we largely focus on single parts or domains of the yeast mitochondrial group II intron Sc.ai5γ being one the best investigated introns.…”

“…[34] As these metal ions are also not observable with most other spectroscopic techniques, they are considered spectroscopically silent, and hence often other metal ions are used to mimic their binding and function. [12] . The assignment refers to the respective intranucleotide cross peaks H1'-H8.…”

“…Nuclear magnetic resonance (NMR) spectroscopy is a crucial technique that we use not only to obtain structural information on our molecules at an atomic level [6][7][8][9][10][11] but, even more important, to elucidate in detail their metal ion binding. [2,9,10,[12][13][14][15][16][17][18] Fig. 1 shows three examples of recently solved structures, belonging to the three families of biomolecules we are working with: the exon/intron binding site 1 (EBS1/IBS1; PDB ID 2K65) [19] of the yeast mitochondrial group II intron Sc.ai5γ, a silver modified duplex DNA (PDB ID 2KE8), [8] and the C-terminal domain of the seed-specific wheat MT Zn 6 E c -1, denoted as Zn 4 β E -E c -1 (PDB ID 2KAK).…”

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

“…Line broadening indicates direct Mg 2+ coordination. The panel is adapted from [7] and [252]. the experimental data from H6 of U21 in a group II intron domain 6 after the first and the fifth iteration [7].…”