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Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes
(2020)
This review aims at juxtaposing common versus distinct structural and functional strategies that are applied by aptamers, riboswitches, and ribozymes/DNAzymes. Focusing on recently discovered systems, we begin our analysis with small-molecule binding aptamers, with emphasis on in vitro-selected fluorogenic RNA aptamers and their different modes of ligand binding and fluorescence activation. Fundamental insights are much needed to advance RNA imaging probes for detection of exo- and endogenous RNA and for RNA process tracking. Secondly, we discuss the latest gene expression–regulating mRNA riboswitches that respond to the alarmone ppGpp, to PRPP, to NAD+, to adenosine and cytidine diphosphates, and to precursors of thiamine biosynthesis (HMP-PP), and we outline new subclasses of SAM and tetrahydrofolate-binding RNA regulators. Many riboswitches bind protein enzyme cofactors that, in principle, can catalyse a chemical reaction. For RNA, however, only one system (glmS ribozyme) has been identified in Nature thus far that utilizes a small molecule – glucosamine-6-phosphate – to participate directly in reaction catalysis (phosphodiester cleavage). We wonder why that is the case and what is to be done to reveal such likely existing cellular activities that could be more diverse than currently imagined. Thirdly, this brings us to the four latest small nucleolytic ribozymes termed twister, twister-sister, pistol, and hatchet as well as to in vitro selected DNA and RNA enzymes that promote new chemistry, mainly by exploiting their ability for RNA labelling and nucleoside modification recognition. Enormous progress in understanding the strategies of nucleic acids catalysts has been made by providing thorough structural fundaments (e.g. first structure of a DNAzyme, structures of ribozyme transition state mimics) in combination with functional assays and atomic mutagenesis.
The initial goal was the conversion of Bifidobacterium adolescentis Sucrose Phosphorylase (BaSP) into a polyphenol glucosidase by structure based enzyme engineering. BaSP was chosen because of its ability to utilize sucrose, an economically viable and sustainable donor substrate, and transfer the glucosyl moiety to various acceptor substrates. The introduction of aromatic residues into the active site was considered a viable way to render it more suitable for aromatic acceptor compounds by reducing its polarity and potentially introducing π-π-interactions with the polyphenols. An investigation of the active site revealed Gln345 as a suitable mutagenesis target. As a proof of concept BaSP Q345F was employed in the glycosylation of (+)-catechin, (-)-epicatechin and resveratrol. The variant was selective for the aromatic acceptor substrates and the glucose disaccharide side reaction was only observed after almost quantitative conversion of the aromatic substrates. A crystal structure of BaSP Q345F in complex with glucose was obtained and it displayed an unexpected shift of an entire domain by 3.3 Å. A crystal structure of BaSP D192N-Q345F, an inactive variant in complex with resveratrol-3-α-D-glucosid, the glucosylation product of resveratrol, synthesized by BaSP Q345F was solved. It proved that the domain shift is in fact responsible for the ability of the variant to glycosylate aromatic compounds. Simultaneously a ligand free crystal structure of BaSP Q345F disproved an induced fit effect as the cause of the domain shift. The missing link, a crystal structure of BaSP Q345F in the F-conformation is obtained. This does not feature the domain shift, but is in outstanding agreement with the wildtype structure. The domain shift is therefore not static but rather a step in a dynamic process. It is further conceivable that the domain shifted conformation of BaSP Q345F resembles the open conformation of the wild type and that an adjustment of a conformational equilibrium as a result of the Q345F point mutation is observed. An investigation into the background reaction, the formation of glucose-glucose disaccharides of BaSP Q345F and three further variants that addressed the same region (L341C, D316C-L341C and D316C-N340C) revealed the formation of nigerose by BaSP Q345F.
The aim of the thesis was to develop water soluble poly(2-oxazoline) (POx) copolymers with new side group functionalities, which can be used for the formation of hydrogels in biomedical applications and for the development of peptide-polymer conjugates.
First, random copolymers of the monomer MeOx or EtOx with ButEnOx and EtOx with DecEnOx were synthesized and characterized. The vinyl functionality brought into the copolymer by the monomers ButEnOx and DecEnOx would later serve for post-polymerization functionalization. The synthesized copolymers were further functionalized with thiols via post-polymerization functionalization using a newly developed synthesis protocol or with a protected catechol molecule for hydrogel formation. For the formation of peptide-polymer conjugates, a cyclic thioester, namely thiolactone acrylamide and an azlactone precursor, whose synthesis was newly developed, were attached to the side chain of P(EtOx-co-ButEnOx) copolymers.
The application of the functionalized thiol copolymers as hydrogels using thiol-ene chemistry for cross-linking was demonstrated. The swelling behavior and mechanical properties were characterized. The hydrophilicity of the network as well as the cross-linking density strongly influenced the swelling behavior and the mechanical strength of the hydrogels. All hydrogels showed good cell viability results.
The hydrogel networks based on MeOx and EtOx were loaded with two dyes, fluorescein and methylene blue. It was observed that the uptake of the more hydrophilic dye fluorescein depended more on the ability of the hydrogel to swell. In contrast, the uptake of the more hydrophobic dye methylene blue was less dependent on the swelling degree, but much more on the hydrophilicity of the network.
For the potential application as cartilage glue, (biohybrid) hydrogels were synthesized based on the catechol-functionalized copolymers, with and without additional fibrinogen, using sodium periodate as the oxidizing agent. The system allowed for degradation due to the incorporated ester linkages at the cross-linking points. The swelling behavior as well as the mechanical properties were characterized. As expected, hydrogels with higher degrees of cross-linking showed less swelling and higher elastic modulus. The addition of fibrinogen however increased the elasticity of the network, which can be favorable for the intended application as a cartilage glue. Biological evaluation clearly demonstrated the advantage of degradable ester links in the hydrogel network, where chondrocytes were able to bridge the artificial gap in contrast to hydrogels without any ester motifs.
Lastly, different ways to form peptide-polymer conjugates were presented. Peptides were attached with the thiol of the terminal cysteine group to the vinyl side chain of P(EtOx-co-ButEnOx) copolymers by radical thiol-ene chemistry. Another approach was to use a cyclic thioester, thiolactone, or an azlactone functionality to bind a model peptide via native chemical ligation. The two latter named strategies to bind peptides to POx side chains are especially interesting as one and in the case of thiolactone two free thiols are still present at the binding site after the reaction, which can, for example, be used for further thiol-ene cross-linking to form POx hydrogels.
In summary, side functional poly(oxazoline) copolymers show great potential for numerous biomedical applications. The various side chain functionalities can be introduced by an appropriate monomer or by post-polymerization functionalization, as demonstrated. By their multi-functionality, hydrogel characteristics, such as cross-linking degree and mechanical strength, can be fine-tuned and adjusted depending on the application in the human body. In addition, the presented chemoselective and orthogonal reaction strategies can be used in the future to synthesize polymer conjugates, which can, for example, be used in drug delivery or in tissue regeneration.
Herein we report a broad series of new trinuclear supramolecular Ru(bda) macrocycles bearing different substituents at the axial or equatorial ligands which enabled investigation of substituent effects on the catalytic activities in chemical and photocatalytic water oxidation. Our detailed investigations revealed that the activities of these functionalized macrocycles in water oxidation are significantly affected by the position at which the substituents were introduced. Interestingly, this effect could not be explained based on the redox properties of the catalysts since these are not markedly influenced by the functionalization of the ligands. Instead, detailed investigations by X-ray crystal structure analysis and theoretical simulations showed that conformational changes imparted by the substituents are responsible for the variation of catalytic activities of the Ru macrocycles. For the first time, macrocyclic structure of this class of water oxidation catalysts is unequivocally confirmed and experimental indication for a hydrogen-bonded water network present in the cavity of the macrocycles is provided by crystal structure analysis. We ascribe the high catalytic efficiency of our Ru(bda) macrocycles to cooperative proton abstractions facilitated by such a network of preorganized water molecules in their cavity, which is reminiscent of catalytic activities of enzymes at active sites.
Nearly all classes of coding and non-coding RNA undergo post-transcriptional modification including RNA methylation. Methylated nucleotides belong to the evolutionarily most conserved features of tRNA and rRNA.1,2 Many contemporary methyltransferases use the universal cofactor S-adenosylmethionine (SAM) as methyl group donor. This and other nucleotide-derived cofactors are considered as evolutionary leftovers from an RNA World, in which ribozymes may have catalysed essential metabolic reactions beyond self-replication.3 Chemically diverse ribozymes seem to have been lost in Nature, but may be reconstructed in the laboratory by in vitro selection. Here, we report a methyltransferase ribozyme that catalyses the site-specific installation of 1-methyladenosine (m1A) in a substrate RNA, utilizing O6-methylguanine (m6G) as a small-molecule cofactor. The ribozyme shows a broad RNA sequence scope, as exemplified by site-specific adenosine methylation in tRNAs. This finding provides fundamental insights into RNA’s catalytic abilities, serves a synthetic tool to install m1A in RNA, and may pave the way to in vitro evolution of other methyltransferase and demethylase ribozymes.
A new perylene bisimide (PBI), with a fluorescence quantum yield up to unity, self‐assembles into two polymorphic supramolecular polymers. This PBI bears four solubilizing acyloxy substituents at the bay positions and is unsubstituted at the imide position, thereby allowing hydrogen‐bond‐directed self‐assembly in nonpolar solvents. The formation of the polymorphs is controlled by the cooling rate of hot monomer solutions. They show distinctive absorption profiles and morphologies and can be isolated in different polymorphic liquid‐crystalline states. The interchromophoric arrangement causing the spectral features was elucidated, revealing the formation of columnar and lamellar phases, which are formed by either homo‐ or heterochiral self‐assembly, respectively, of the atropoenantiomeric PBIs. Kinetic studies reveal a narcissistic self‐sorting process upon fast cooling, and that the transformation into the heterochiral (racemic) sheetlike self‐assemblies proceeds by dissociation via the monomeric state.
Thalassodendron ciliatum (Forssk.) Den Hartog is a seagrass belonging to the plant family Cymodoceaceae with ubiquitous phytoconstituents and important pharmacological potential, including antioxidant, antiviral, and cytotoxic activities. In this work, a new ergosterol derivative named thalassosterol (1) was isolated from the methanolic extract of T. ciliatum growing in the Red Sea, along with two known first-reported sterols, namely ergosterol (2) and stigmasterol (3), using different chromatographic techniques. The structure of the new compound was established based on 1D and 2D NMR spectroscopy and high-resolution mass spectrometry (HR-MS) and by comparison with the literature data. The new ergosterol derivative showed significant in vitro antiproliferative potential against the human cervical cancer cell line (HeLa) and human breast cancer (MCF-7) cell lines, with IC\(_{50}\) values of 8.12 and 14.24 µM, respectively. In addition, docking studies on the new sterol 1 explained the possible binding interactions with an aromatase enzyme; this inhibition is beneficial in both cervical and breast cancer therapy. A metabolic analysis of the crude extract of T. ciliatum using liquid chromatography combined with high-resolution electrospray ionization mass spectrometry (LC-ESI-HR-MS) revealed the presence of an array of phenolic compounds, sterols and ceramides, as well as di- and triglycerides.
In this work the catalytic activity of nanodiamond particles with different dopants and surface terminations and of diamond nanomaterials funtionalized with ruthenium-based photocatalysts was investigated, illustrating materials application in photoredox chemistry and the photo(electro)catalytic reduction of CO2. Regarding the application of diamond nanomaterials in photocatalysis, methods to fabricate and characterize several (un)doped nanoparticles with different surface termination were successfully developed. Various photocatalysts, attached to nanodiamond particles via linker systems, were tested in photoredox catalysis and the photo(electro)catalytic reduction of CO2.
Tristriazolotriazines (TTTs) with a threefold alkoxyphenyl substitution were prepared and studied by DSC, polarized optical microscopy (POM) and X-ray scattering. Six pentyloxy chains are sufficient to induce liquid-crystalline behavior in these star-shaped compounds. Thermotropic properties of TTTs with varying substitution patterns and a periphery of linear chains of different lengths, branching in the chain and swallow-tails, are compared. Generally, these disks display broad and stable thermotropic mesophases, with the tangential TTT being superior to the radial isomer. The structure–property relationships of the number of alkyl chains, their position, length and structure were studied.
We synthesized new pyrene derivatives with strong bis(para ‐methoxyphenyl)amine donors at the 2,7‐positions and n ‐azaacene acceptors at the K‐region of pyrene. The compounds possess a strong intramolecular charge transfer, leading to unusual properties such as emission in the red to NIR region (700 nm), which has not been reported before for monomeric pyrenes. Detailed photophysical studies reveal very long intrinsic lifetimes of >100 ns for the new compounds, which is typical for 2,7‐substituted pyrenes but not for K‐region substituted pyrenes. The incorporation of strong donors and acceptors leads to very low reduction and oxidation potentials, and spectroelectrochemical studies show that the compounds are on the borderline between localized Robin‐Day class‐II and delocalized Robin‐Day class‐III species.