The noncovalent dimerization of a G-quadruplex/hemin DNAzyme improves its biocatalytic properties

While many protein enzymes exert their functions through multimerization, which improves both selectivity and activity, this has not yet been demonstrated for other naturally occurring catalysts. Here, we report a multimerization effect applied to catalytic DNAs (or DNAzymes) and demonstrate that the enzymatic efficiency of G-quadruplexes (GQs) in interaction with the hemin cofactor is remarkably enhanced by homodimerization. The resulting non-covalent dimeric GQ-DNAzyme system provides hemin with a structurally defined active site in which both the cofactor (hemin) and the oxidant (H2O2) are activated. This new biocatalytic system efficiently performs peroxidase- and peroxygenase-type biotransformations of a broad range of substrates, thus providing new perspectives for biotechnological application of GQs.

Loop permutation affects the topology and stability of G-quadruplexes

G-quadruplexes are unusual DNA and RNA secondary structures ubiquitous in a variety of organisms including vertebrates, plants, viruses and bacteria. The folding topology and stability of intramolecular G-quadruplexes are determined to a large extent by their loops. Loop permutation is defined as swapping two or three of these regions so that intramolecular G-quadruplexes only differ in the sequential order of their loops. Over the past two decades, both length and base composition of loops have been studied extensively, but a systematic study on the effect of loop permutation has been missing. In the present work, 99 sequences from 21 groups with different loop permutations were tested. To our surprise, both conformation and thermal stability are greatly dependent on loop permutation. Loop permutation actually matters as much as loop length and base composition on G-quadruplex folding, with effects on T_m as high as 17°C. Sequences containing a longer central loop have a high propensity to adopt a stable non-parallel topology. Conversely, sequences containing a short central loop tend to form a parallel topology of lower stability. In addition, over half of interrogated sequences were found in the genomes of diverse organisms, implicating their potential regulatory roles in the genome or as therapeutic targets. This study illustrates the structural roles of loops in G-quadruplex folding and should help to establish rules to predict the folding pattern and stability of G-quadruplexes.

G-quadruplexes as versatile scaffolds for catalysis

This review summarizes the beginning, progress, and prospects of non-canonical DNA-based hybrid catalysts focusing on G-quadruplexes as versatile scaffolds for catalysis.

Fluorescence Spectroscopic Insight into the Supramolecular Interactions in DNA-Based Enantioselective Sulfoxidation

Interactions of copper(II)-bipyridine cofactors and thioanisole substrate with human telomeric G-quadruplex DNA were studied by UV/Vis absorption, circular dichroism, and fluorescence quenching titration. Three copper(II)-bipyridine complexes are equivalently anchored to the G-quadruplex scaffold at all five fluorescently labeled sites. Thioanisole interacts with the DNA architecture at both the second loop and 3' terminus in the absence or presence of copper(II)-bipyridine complexes. These nonspecificities in the weak interactions of Cu^II complexes and thioanisole with G-quadruplex might explain why DNA only affords a modest enantioselectivity in the oxidation of thioanisole. These findings provide insights toward the construction of highly enantioselective DNA-based catalysts.

Catalytic Organic Reactions in Water toward Sustainable Society

Traditional organic synthesis relies heavily on organic solvents for a multitude of tasks, including dissolving the components and facilitating chemical reactions, because many reagents and reactive species are incompatible or immiscible with water. Given that they are used in vast quantities as compared to reactants, solvents have been the focus of environmental concerns. Along with reducing the environmental impact of organic synthesis, the use of water as a reaction medium also benefits chemical processes by simplifying operations, allowing mild reaction conditions, and sometimes delivering unforeseen reactivities and selectivities. After the "watershed" in organic synthesis revealed the importance of water, the development of water-compatible catalysts has flourished, triggering a quantum leap in water-centered organic synthesis. Given that organic compounds are typically practically insoluble in water, simple extractive workup can readily separate a water-soluble homogeneous catalyst as an aqueous solution from a product that is soluble in organic solvents. In contrast, the use of heterogeneous catalysts facilitates catalyst recycling by allowing simple centrifugation and filtration methods to be used. This Review addresses advances over the past decade in catalytic reactions using water as a reaction medium.

Specifically targeting mixed-type dimeric G-quadruplexes using berberine dimers

Berberine dimer (1a) with the shortest polyether linker demonstrates highest binding affinity, selectivity and thermal stabilization towards mixed-type dimeric quadruplexes.

A decade of DNA-hybrid catalysis: from innovation to comprehension

Since the pioneering work of Roelfes and Feringa in the field of DNA-based asymmetric catalysis, the unique chirality of oligonucleotides has allowed the development of a variety of asymmetric synthetic transformations. This review offers a complete overview of the field.

Expanding biohybrid-mediated asymmetric catalysis into the realm of RNA

We report here the first example of an RNA-based catalyst involving a catalytically active metal complex interacting in a non-covalent fashion with short RNA sequences.

Enantioselective sulfoxidation reaction catalyzed by a G-quadruplex DNA metalloenzyme

Enantioselective sulfoxidation reaction is achieved for the first time by a human telomeric G-quadruplex DNA based biocatalyst.

Tuning the stereoselectivity of a DNA-catalyzed michael addition through covalent modification

Complexes of G-quadruplex DNA and Cu(II) ions have previously been applied as catalysts in asymmetric reactions, but the largely unspecific and noncovalent nature of the interaction has impeded understanding of the structural basis of catalysis. To better control the formation of a catalytically competent species, DNA quadruplexes were derivatized with linker-bpy-Cu(II) complexes in a site-specific manner and applied in asymmetric aqueous Michael additions. These modified quadruplexes exhibited high rate acceleration and stereoselectivity. Different factors were found to be important for the catalytic performance of the modified G-quadruplexes, among them, the position of modification, the topology of the quadruplex, the nature of the ligand, and the length of the linker between the ligand and DNA. Moving the same ligand by just two nucleotides inverted the stereochemical outcome: quadruplexes modified at position 10 formed the (-)-enantiomer with up to 92 % ee, while DNA derivatized at position 12 formed the (+)-enantiomer with up to 75 % ee. This stereopreference was maintained when applied to structurally different Michael acceptors. This work demonstrates a new and simple way to tune the stereoselectivity in DNA-based asymmetric catalysis.

Terpyridine-Cu(ii) targeting human telomeric DNA to produce highly stereospecific G-quadruplex DNA metalloenzyme

The cofactors commonly involved in natural enzymes have provided the inspiration for numerous advances in the creation of artificial metalloenzymes. Nevertheless, to design an appropriate cofactor for a given biomolecular scaffold or vice versa remains a challenge in developing efficient catalysts in biochemistry. Herein, we extend the idea of G-quadruplex-targeting anticancer drug design to construct a G-quadruplex DNA metalloenzyme. We found that a series of terpyridine-Cu(ii) complexes (CuLn) can serve as excellent cofactors to dock with human telemetric G-quadruplex DNA. The resulting G-quadruplex DNA metalloenzyme utilising CuL1 catalyzes an enantioselective Diels-Alder reaction with enantioselectivity of >99% enantiomeric excess and about 73-fold rate acceleration compared to CuL1 alone. The terpyridine-Cu(ii) complex cofactors demonstrate dual functions, both as an active site to perform catalysis and as a structural regulator to promote the folding of human telemetric G-quadruplex DNA towards excellent catalysts.

Higher-order human telomeric G-quadruplex DNA metalloenzyme catalyzed Diels–Alder reaction: an unexpected inversion of enantioselectivity modulated by K+ and NH4+ ions

K⁺ and NH₄⁺, bearing approximately equal ionic radius, present different allosteric activation for higher-order human telomeric G-quadruplex DNA metalloenzyme.