PyBox-La(OTf)3-Catalyzed Enantioselective Diels-Alder Cycloadditions of 2-Alkenoylpyridines with Cyclopentadiene

The PyBox-La(OTf)3-catalyzed enantioselective Diels-Alder cycloaddition of 2-alk-2-enoylpyridines with cyclopentadiene is realized, producing enantiopure disubstituted norbornenes, which possess four contiguous stereocenters and are biologically relevant structures in up to 92:8 dr and 99:1 er.

Dopamine oxidation promoted by human telomeric DNA models in the presence of a Cu(II) terpyridine chelate

We found that under oxidative stress conditions, the coexistence of human telomeric DNA (HT-DNA) and a copper-terpyridine metallodrug can accelerate dopamine oxidation. The unwinding of HT-DNA from a duplex to cytosine-rich (C-rich) and guanine-rich (G-rich) single strands promotes dopamine oxidation in a general order of C-rich > G-rich > duplex. Along with dopamine oxidation, HT-DNA also undergoes severe damage.

Cyclic Dinucleotide-Based Enantioselective Fluorination in Water

The diverse structures of DNA serve as potent chiral scaffolds for DNA-based asymmetric catalysis, yet in most cases tens to hundreds of nucleotides in DNA hybrid catalysts hinder the deep insight into their structure-activity relationship. Owing to the structural simplicity and design flexibility of nucleotides, nucleotide-based catalysts have been emerging as a promising way to obtain fine structural information and understand the catalytic mechanisms. Herein, we found that a cyclic dinucleotide of cyclic di-AMP (c-di-AMP) and 1,10-phenanthroline copper(II) nitrate (Cu(phen)(NO₃)₂) are assembled to a c-di-AMP-based catalyst (c-di-AMP/Cu(phen)(NO₃)₂), which could fast achieve enantioselective fluorination in water with 90-99% yields and up to 90% enantiomeric excess (ee). The host-guest interaction between c-di-AMP and Cu(phen)(NO₃)₂ has been proposed mainly in a supramolecular interaction mode as evidenced by spectroscopic techniques of ultraviolet-visible, fluorescence, circular dichroism, and nuclear magnetic resonance. Cu(phen)(NO₃)₂ tightly binds to c-di-AMP with a binding constant of 1.7 ± 0.3 × 10⁵ M^-1, and the assembly of c-di-AMP/Cu(phen)(NO₃)₂ shows a modest rate enhancement to carbon-fluorine bond formations as supported by kinetic studies.

Recent Developments in G-Quadruplex Binding Ligands and Specific Beacons on Smart Fluorescent Sensor for Targeting Metal Ions and Biological Analytes

The G-quadruplex structure is crucial in several biological processes, including DNA replication, transcription, and genomic maintenance. G-quadruplex-based fluorescent probes have recently gained popularity because of their ease of use, low cost, excellent selectivity, and sensitivity. This review summarizes the latest applications of G-quadruplex structures as detectors of genome-wide, enantioselective catalysts, disease therapeutics, promising drug targets, and smart fluorescence probes. In every section, sensing of G-quadruplex and employing G4 for the detection of other analytes were introduced, respectively. Since the discovery of the G-quadruplex structure, several studies have been conducted to investigate its conformations, biological potential, stability, reactivity, selectivity for chemical modification, and optical properties. The formation mechanism and advancements for detecting different metal ions (Na⁺, K⁺, Ag⁺, Tl⁺, Cu⁺/Cu²⁺, Hg²⁺, and Pb²⁺) and biomolecules (AMP, ATP, DNA/RNA, microRNA, thrombin, T4 PNK, RNase H, ALP, CEA, lipocalin 1, and UDG) using fluorescent sensors based on G-quadruplex modification, such as dye labels, artificial nucleobase moieties, dye complexes, intercalating dyes, and bioconjugated nanomaterials (AgNCs, GO, QDs, CDs, and MOF) is described herein. To investigate these extremely efficient responsive agents for diagnostic and therapeutic applications in medicine, fluorescence sensors based on G-quadruplexes have also been employed as a quantitative visualization technique.

Harnessing DNA as a Designable Scaffold for Asymmetric Catalysis: Recent Advances and Future Perspectives

Since the first report of DNAzyme by in vitro selection in 1994, catalytic DNA has investigated extensively, and their application has expanded continually in virtue of rapid advances in molecular biology and biotechnology. Nowadays, DNA is in the second prime time by way of DNA-based hybrid catalysts and DNA metalloenzymes in which helical chirality of DNA serves to asymmetric catalysis. DNA-based hybrid catalysts are attractive system to respond the demand of the times to pursuit green and sustainable society beyond traditional catalytic systems that value reaction efficiency. Herein, we highlight the recent advances and perspective of DNA-based hybrid catalysts with various aspects of DNA as a versatile scaffold for asymmetric synthesis. We hope that scientists in a variety of fields will be encouraged to join and promote remarkable evolution of this interesting research.

Characterizing the Diastereoisomeric Distribution of Phosphorothioate Oligonucleotides by Metal Ion Complexation Chromatography, In-Series Reversed Phase-Strong Anion Exchange Chromatography, and 31P NMR

Replacement of a non-bridging oxygen atom of the phosphate diester linkage of an oligonucleotide by sulfur conveys pharmacokinetic benefits, such as increased nuclease resistance and enhanced protein binding. Substitution renders the internucleotide linkages chiral, and so phosphorothioate diester (PS) oligonucleotides comprise complex mixtures of diastereoisomers. Currently, chromatographic separation of individual diastereoisomers is limited to oligonucleotides that contain no more than about four or five PS linkages. The development of therapeutic PS oligonucleotides, which often contain >15 PS linkages, would be greatly aided by methods useful for assessing batch-to-batch stereo-reproducibility. To this effect, the relative sensitivities of metal ion complexation chromatography (MICC), in-series reversed phase-strong anion exchange chromatography (RP-SAX), and ³¹P NMR toward changes in the diastereoisomeric distributions of therapeutic PS oligonucleotides were compared. Model oligonucleotides synthesized under conditions known to impact PS stereochemistry were used to evaluate the method performance, and all three methods showed excellent sensitivity toward changes in the diastereoisomeric composition. Interactions via the solvent-accessible areas and a combination of hydrophobic and electrostatic forces may be responsible for the selectivity demonstrated by MICC and in-series RP-SAX, respectively.

A stable uncompleted tetramolecular G-quadruplex formed by d(AGnA) under acidic condition

In this work, the effects of terminal adenines on the formation and stability of tetramolecular G-quadruplexes (G4s) have been studied by electrospray ionization mass spectrometry (ESI-MS), UV, CD and NMR spectroscopy. Several evidences suggested that the sequences d(AG_nA) (n = 4 or 5) form stable uncompleted tetramolecular G4 at acidic condition which is different from the canonical one in the neutral condition. In addition, hydrolysis of guanine has also been observed in acidic condition that may occur for unpaired strands rather than in complete G4. Thus, a new G4 topology containing incomplete G-quartet is proposed that is very stable and particularly presents in acidic ammonium ions solution. The information presented in this study provides the new insight on the polymorphism of G4s in acidic environment, which may help understand of the special role of adenines on the formation of G4s.

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.

Covalently Functionalized DNA Duplexes and Quadruplexes as Hybrid Catalysts in an Enantioselective Friedel-Crafts Reaction

The precise site-specific positioning of metal-ligand complexes on various DNA structures through covalent linkages has gained importance in the development of hybrid catalysts for aqueous-phase homogeneous catalysis. Covalently modified double-stranded and G-quadruplex DNA-based hybrid catalysts have been investigated separately. To understand the role of different DNA secondary structures in enantioselective Friedel-Crafts alkylation, a well-known G-quadruplex-forming sequence was covalently modified at different positions. The catalytic performance of this modified DNA strand was studied in the presence and absence of a complementary DNA sequence, resulting in the formation of two different secondary structures, namely duplex and G-quadruplex. Indeed, the secondary structures had a tremendous effect on both the yield and stereoselectivity of the catalyzed reaction. In addition, the position of the modification, the topology of the DNA, the nature of the ligand, and the length of the linker between ligand and DNA were found to modulate the catalytic performance of the hybrid catalysts. Using the optimal linker length, the quadruplexes formed the (-)-enantiomer with up to 65% ee, while the duplex yielded the (+)-enantiomer with up to 62% ee. This study unveils a new and simple way to control the stereochemical outcome of a Friedel-Crafts reaction.

Recyclable iron(ii) caffeine-derived ionic salt catalyst in the Diels–Alder reaction of cyclopentadiene and α,β-unsaturated N-acyl-oxazolidinones in dimethyl carbonate

Iron(ii) triflate was used in combination with caffeine-derived salts as recyclable catalysts for the Diels–Alder reaction run in dimethyl carbonate (DMC) as a green solvent.

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.

Stereodivergent Catalysis

This review covers diastereo- and enantiodivergent catalyzed reactions in acyclic and cyclic systems using metal complexes or organocatalysts. Among them, nucleophilic addition to carbon-carbon and carbon-nitrogen double bonds, α-functionalization of carbonyl compounds, allylic substitutions, and ring opening of oxiranes and aziridines are considered. The diastereodivergent synthesis of alkenes from alkynes is also included. Finally, stereodivergent intramolecular and intermolecular cycloadditions and other cyclizations are also reported.

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.

Relations between the loop transposition of DNA G-quadruplex and the catalytic function of DNAzyme

The structures of DNA G-quadruplexes are essential for their functions in vivo and in vitro. Our present study revealed that sequential order of the three G-quadruplex loops, that is, loop transposition, could be a critical factor to determinate the G-quadruplex conformation and consequently improved the catalytic function of G-quadruplex based DNAzyme. In the presence of 100mM K⁺, loop transposition induced one of the G-quadruplex isomers which shared identical loops but differed in the sequential order of loops into a hybrid topology while the others into predominately parallel topologies. ¹D NMR spectroscopy and mutation analysis suggested that the hydrogen bonding from loops residues with nucleotides in flanking sequences may be responsible for the stabilization of the different conformations. A well-known DNAzyme consisting of G-quadruplex and hemin (Ferriprotoporphyrin IX chloride) was chosen to test the catalytic function. We found that the loop transposition could enhance the reaction rate obviously by increasing the hemin binding affinity to G-quadruplex. These findings disclose the relations between the loop transposition, G-quadruplex conformation and catalytic function of DNAzyme.

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.

Hot off the press

A personal selection of 32 recent papers is presented covering various aspects of current developments in bioorganic chemistry and novel natural products such as sigillin A from Ceratophysella sigillata.