Roland K. O. Sigel

Solution structure of a DNA double helix with consecutive metal-mediated base pairs

Metal-mediated base pairs represent a powerful tool for the site-specific functionalization of nucleic acids with metal ions. The development of applications of the metal-modified nucleic acids will depend on the availability of structural information on these double helices. We present here the NMR solution structure of a self-complementary DNA oligonucleotide with three consecutive imidazole nucleotides in its centre. In the absence of transition-metal ions, a hairpin structure is adopted with the artificial nucleotides forming the loop. In the presence of Ag(i) ions, a duplex comprising three imidazole-Ag(+)-imidazole base pairs is formed. Direct proof for the formation of metal-mediated base pairs was obtained from ¹J(¹⁵N,¹⁰⁷/¹⁰⁹Ag) couplings upon incorporation of ¹⁵N-labelled imidazole. The duplex adopts a B-type conformation with only minor deviations in the region of the artificial bases. This work represents the first structural characterization of a metal-modified nucleic acid with a continuous stretch of metal-mediated base pairs.

Metal ion binding sites in a group II intron core

Group II introns are catalytic RNA molecules that require divalent metal ions for folding, substrate binding, and chemical catalysis. Metal ion binding sites in the group II core have now been elucidated by monitoring the site-specific RNA hydrolysis patterns of bound ions such as Tb3+ and Mg2+. Major sites are localized near active site elements such as domain 5 and its surrounding tertiary interaction partners. Numerous sites are also observed at intron substructures that are involved in binding and potentially activating the splice sites. These results highlight the locations of specific metal ions that are likely to play a role in ribozyme catalysis.

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

The three-dimensional architecture and function of nucleic acids strongly depend on the presence of metal ions, among other factors. Given the negative charge of the phosphate-sugar backbone, positively charged species, mostly metal ions, are necessary for compensation. However, these ions also allow and induce folding of complicated RNA structures. Furthermore, metal ions bind to specific sites, stabilizing local motifs and positioning themselves correctly to aid (or even enable) a catalytic mechanism, as, for example, in ribozymes. Many nucleic acids thereby exhibit large differences in folding and activity depending not only on the concentration but also on the kind of metal ion involved. As a consequence, understanding the role of metal ions in nucleic acids requires knowing not only the exact positioning and coordination sphere of each specifically bound metal ion but also its intrinsic site affinity. However, the quantification of metal ion affinities toward certain sites in a single-stranded (though folded) nucleic acid is a demanding task, and few experimental data exist. In this Account, we present a new tool for estimating the binding affinity of a given metal ion, based on its ligating sites within the nucleic acid. To this end, we have summarized the available affinity constants of Mg(2+), Ca(2+), Mn(2+), Cu(2+), Zn(2+), Cd(2+), and Pb(2+) for binding to nucleobase residues, as well as to mono- and dinucleotides. We have also estimated for these ions the stability constants for coordinating the phosphodiester bridge. In this way, stability increments for each ligand site are obtained, and a clear selectivity of the ligating atoms, as well as their discrimination by different metal ions, can thus be recognized. On the basis of these data, we propose a concept that allows one to estimate the intrinsic stabilities of nucleic acid-binding pockets for these metal ions. For example, the presence of a phosphate group has a much larger influence on the overall affinity of Mg(2+), Ca(2+), or Mn(2+) compared with, for example, that of Cd(2+) or Zn(2+). In the case of Cd(2+) and Zn(2+), the guanine N7 position is the strongest intrinsic binding site. By adding up the individual increments like building blocks, one derives an estimate not only for the overall stability of a given coordination sphere but also for the most stable complex if an excess of ligating atoms is available in a binding pocket saturating the coordination sphere of the metal ion. Hence, this empirical concept of adding up known intrinsic stabilities, like building blocks, to an estimated overall stability will help in understanding the accelerating or inhibiting effects of different metal ions in ribozymes and DNAzymes.

Nickel and its surprising impact in nature

Volume 2 focuses on the vibrant research area concerning nickel as well as its complexes and their role in Nature. With more than 2800 references and over 130 illustrations, it is an essential resource for scientists working in the wide range from inorganic biochemistry all the way through to medicine. In 17 stimulating chapters, written by 47 internationally recognized experts, Nickel and Its Surprising Impact in Nature highlights critically the biogeochemistry of nickel, its role in the environment, in plants and cyanobacteria, as well as for the gastric pathogen Helicobacter pylori, for gene expression and carcinogenensis. In addition, it covers the complex-forming properties of nickel with amino acids, peptides, phosphates, nucleotides, and nucleic acids. The volume also provides sophisticated insights in the recent progress made in understanding the role of nickel in enzymes such as ureases, hydrogenases, superoxide dismutases, acireductone dioxygenases, acetyl-coenzyme A synthases, carbon monoxide dehydrogenases, methyl-coenzyme M reductases ... and it reveals the chaperones of nickel metabolism. The book opens with the biogeochemistry of this element and its release into the environment, which occurs from both natural and anthropogenic sources, whereby atmospheric distribution plays an important role. In the second chapter the impact of nickel on the metabolism of cyanobacteria and eukaryotic plants including deficiency and toxicity is considered, as is the application of nickel hyperaccumulator plants for phytomining and phytoremediation. Complex formation of nickel(II/III) with amino acids and peptides as well as of nickel(II) with sugar residues, nucleobases, phosphates, nucleosides, and nucleic acids is summarized in Chapters 3 and 4, respectively, by also taking into account intramolecular equilibria and comparisons with related metal ions. Bioinspired nickel coordination chemistry has flourished in recent years and the resulting synthetic models for the active sites of nickel-containing enzymes are reviewed in Chapter 5. In fact, each of the well established biological nickel sites is rather unique with respect to its structure and function. Hence, the following eight chapters are individually devoted to the various nickel enzymes which catalyze rather diverse reactions. For example, urease reduces the half life of urea in water from about 3.6 years to a few microseconds, whereas nickel-iron hydrogenases catalyze the heterolytic conversion of dihydrogen into protons and electrons and vice versa. Next, methyl-coenzyme M reductase and its nickel corphin coenzyme F430 in methanogenic archaea are described in detail as are acetyl-coenzyme A synthases and nickel-containing carbon monoxide dehydrogenases. These critical reviews are followed by in depth considerations on nickel superoxide dismutase, and the nickel-dependent glyoxalase I enzymes. The role of nickel in acireductone dioxygenase and the properties of the nickel-regulated peptidyl-prolyl cis/trans isomerase SlyD are discussed next. Nickel is toxic to cells and therefore the synthesis of nickel enzymes requires carefully controlled nickel-processing mechanisms that range from selective transport of nickel into the cells to productive insertion of nickel into the correct apoproteins. This demanding task is in the focus of Chapter 14 devoted to the chaperones of nickel metabolism. The primary colonization and long-term survival of Helicobacter pylori in the hostile gastric niche and the role of nickel in this environmental adaptation is covered in detail in Chapter 15. Nickel is widely employed in modern industry in conjunction with other metals for the production of alloys for coins, jewellery, and stainless steel; it is also used for plating, battery production, as a catalyst, etc. Workers are exposed to nickel at all stages of the processing of nickel-containing products through air, water or skin contacts. For example, the exposure to airborne nickel-containing particles has long been known to cause acute respiratory symptoms ranging from mild irritation and inflammation of the respiratory system to bronchitis, asthma, and pulmonary fibrosis and edema. Another well known adverse effect is allergic contact dermatitis. The indicated health problems caused by nickel exposure are mediated by an active change in the expression of genes that control inflammation, the response to stress, cell proliferation or cell death. All this and more is covered in Chapter 16. However, the most serious health effects beyond nickel toxicity relate to carcinogenesis; these concerns represent an area of considerable research activity today as is evident from the terminating chapter of Nickel and Its Surprising Impact in Nature.

Single-molecule studies of group II intron ribozymes

Group II intron ribozymes fold into their native structure by a unique stepwise process that involves an initial slow compaction followed by fast formation of the native state in a Mg2+-dependent manner. Single-molecule fluorescence reveals three distinct on-pathway conformations in dynamic equilibrium connected by relatively small activation barriers. From a most stable near-native state, the unobserved catalytically active conformer is reached. This most compact conformer occurs only transiently above 20 mM Mg2+ and is stabilized by substrate binding, which together explain the slow cleavage of the ribozyme. Structural dynamics increase with increasing Mg2+ concentrations, enabling the enzyme to reach its active state.

Solution structure of domain 5 of a group II intron ribozyme reveals a new RNA motif

Domain 5 (D5) is the central core of group II intron ribozymes. Many base and backbone substituents of this highly conserved hairpin participate in catalysis and are crucial for binding to other intron domains. We report the solution structures of the 34-nucleotide D5 hairpin from the group II intron ai5γ in the absence and presence of divalent metal ions. The bulge region of D5 adopts a novel fold, where G26 adopts a syn conformation and flips down into the major groove of helix 1, close to the major groove face of the catalytic AGC triad. The backbone near G26 is kinked, exposing the base plane of the adjacent A-U pair to the solvent and causing bases of the bulge to stack intercalatively. Metal ion titrations reveal strong Mg2+ binding to a minor groove shelf in the D5 bulge. Another distinct metal ion–binding site is observed along the minor groove side of the catalytic triad, in a manner consistent with metal ion binding in the ribozyme active site.

Controlling ribozyme activity by metal ions

The observed rates of ribozyme cleavage reactions are strongly dependent on the nature of the metal ion present. Metal ions can thereby exhibit a stronger inhibiting or accelerating effect compared to Mg(2+), which is usually considered the natural cofactor. Alkaline, alkaline earth, transition, d(10), and other metal ions are applied either to gain a spectroscopic handle on the metal center, and/or to elucidate the catalytic mechanism. Here we shortly review some of the most recent publications on the influence of different metal ions on catalysis of the hammerhead, hepatitis delta virus, and group II intron ribozymes. Comparison of the observed cleavage rates of hammerhead ribozymes with the metal ion affinities of different ligands reveals that these rates correlate perfectly with the intrinsic phosphate affinities of the metal ions involved.

Effects of N7-methylation, N7-platination, and C8-hydroxylation of guanine on H-bond formation with cytosine: platinum coordination strengthens the Watson-Crick pair

The hydrogen bonding properties of 1-methylcytosine (1-MeC) with the following guanine base derivatives have been studied in DMSO-d6, applying concentration-dependent 1H NMR spectroscopy: 9-ethylguanine, 7,9-dimethylguanine (7,9-DimeGH+), and 7,8-dihydro-8-oxo-9-methylguanine (8-O-9-MeGH), as well as three 9-ethylguanine complexes carrying different Pt(II) moieties at the N7 position. The association constants K for the Watson-Crick pairing schemes are by a factor 2–3 higher in the cases of platinated guanine complexes compared to the Watson-Crick pair between 9-ethylguanine and 1-methylcytosine (K= 6.9 ± 1.3 M−1). Similar enhanced stabilities are observed for the pairs formed between 1-MeC and 7,9-DimeGH+ or 8-O-9-MeGH. The increase in N1H acidity of the guanine derivative upon modification at the N7 or C8 positions can be correlated with the association constants K; the result is a bell-shaped curve meaning that acidification initially stabilizes hydrogen bond formation up to a certain maximum; further acidification then leads to a destabilization. For two of the examples studied in solution, hydrogen bonding according to Watson-Crick between N7-platinated 9-ethylguanine and 1-methylcytosine has also been established by X-ray crystallography.

Using in vitro transcription to construct scaffolds for one-dimensional arrays of mercuric ions.

In vitro transcription by T7 RNA polymerase can be used to construct scaffolds for the one-dimensional arrangement of mercury(II) ions. In these constructs, the metal ions are located inside of RNA double helices. By replacing the amide protons of two oppositely located uracil residues of complementary strands, mercury(II) becomes coordinated in a linear fashion to form metal-ion mediated base pairs, analogous to the well-known thymine-Hg-thymine base pair in DNA. This is shown here by a combination of various experimental techniques, including NMR spectroscopy, dynamic light scattering, as well as UV and CD spectroscopy. A total of five different double helices, including both palindromic and non-palindromic RNA sequences and between two and twenty consecutive uracil residues, have been synthesized and shown to be able to incorporate mercury(II). The synthesis of r(GGAGU 20CUCC) demonstrates that T7 polymerase is capable of handling long continuous stretches of identical nucleotides, albeit at the cost of an increasing number of abortion products and longer oligonucleotide strands that need to be separated by polyacrylamide gel electrophoresis. This work introduces RNA into the group of nucleic acids that can form metal ion mediated base pairs. The use of such metal-modified nucleic acids has been envisaged in various fields of research, including the generation of molecular wires.

Photo-induced uncaging of a specific Re(I) organometallic complex in living cells

In the last decades, a large number of organometallic complexes have shown promising anti-proliferative activity towards different cancer cell lines. However, these compounds generally had low cellular uptake and low selectivity towards cancer cells over healthy cells. The use of external triggers (e.g. light, ultra-sound, temperature, etc.) to modify the cytotoxic effect of a prodrug and the coupling of a targeting vector (e.g. peptides, antibodies, etc.) to a drug were found to be very successful techniques to tackle these drawbacks. Here, we envisioned combining these two methods, namely an external trigger (i.e. light activation) and a targeting vector, in an organometallic compound. More specifically, a Re(I) tricarbonyl N,N-bis(quinolinoyl) complex (Re-NH2) was derivatised with a photo-labile protecting group (PLPG) to cage Re-NH2 by formation of Re-PLPG. For organelle/cellular specificity, Re-PLPG was then further coupled to a nuclear localization sequence (NLS) or a bombesin peptide derivative to give Re-PLPG-NLS or Re-PLPG-Bombesin, respectively. Photolysis experiments in PBS buffer (pH 7.4) demonstrated that Re-NH2 was completely photo-released from Re-PLPG-NLS and Re-PLPG-Bombesin using a very low irradiation dose (1.2 J cm−2). To the best of our knowledge, these are the first two examples of the selective photo-release of an intact organometallic compound from a bioconjugate. Of high interest, both derivatives showed toxicity comparable to that of cisplatin towards cervical cancer cells (HeLa) upon light irradiation, although the phototoxic index (PTI) varied greatly with the targeting peptide. The cell death mechanism of Re-PLPG-NLS was explored using different techniques, including fluorescence microscopy, ICP-MS, gel electrophoresis, flow cytometry and transmission electron microscopy (TEM). It could be demonstrated that HeLa cells treated with Re-PLPG-NLS in the dark and upon irradiation showed severe cell stress (nucleolar segregation, pyknosis and vacuolation). The data obtained from an Annexin V/propidium iodide (PI) assay indicated that, after an early apoptotic stage, the onset induced by Re-PLPG-NLS led to cell death, with features ascribable to late apoptosis and necrosis, which were more marked for the treatment involving irradiation.