Reversible Stabilization of Transition-Metal-Binding DNA G-Quadruplexes

Structure and Flexibility of Copper-Modified DNA G-Quadruplexes Investigated by 19 F ENDOR Experiments at 34 GHz

DNA G-quadruplexes (GQs) are of great interest due to their involvement in crucial biological processes such as telomerase maintenance and gene expression. Furthermore, they are reported as catalytically active DNAzymes and building blocks in bio-nanotechnology. GQs exhibit remarkable structural diversity and conformational heterogeneity, necessitating precise and reliable tools to unravel their structure-function relationships. Here, we present insights into the structure and conformational flexibility of a unimolecular GQ with high spatial resolution via electron-nuclear double resonance (ENDOR) experiments combined with Cu(II) and fluorine labeling. These findings showcase the successful application of the 19 F-ENDOR methodology at 34 GHz, overcoming the limitations posed by the complexity and scarcity of higher-frequency spectrometers. Importantly, our approach retains both sensitivity and orientational resolution. This integrated study not only enhances our understanding of GQs but also expands the methodological toolbox for studying other macromolecules.

Phenanthroline-modified DNA three-way junction structures stabilized by interstrand 3 : 1 metal complexation

Incorporation of interstrand metal complexes into DNA is a versatile strategy for metal-dependent stabilization and structural induction of DNA supramolecular structures. In this study, we have synthesized DNA three-way junction (3WJ) structures modified with phenanthroline (phen) ligands. The phen-modified 3WJ was found to be thermally stabilized (ΔTm = +16.9 °C) by the formation of an interstrand NiII(phen)3 complex. Furthermore, NiII-mediated structure induction of 3WJs was demonstrated with the phen-modified strands and their unmodified counterparts. This study suggests that ligand-modified 3WJs would be useful structural motifs for the construction of metal-responsive DNA molecular systems.

Determination of 5-formyluracil via oxime-based nucleotide-metal coordination

In this article, a small chemical molecule was synthesized, and its ability to regulate activities of DNA polymerase was tested. In addition, we also used isothermal amplification technology to detect the content of 5-formyluracil sites in irradiated genomic DNA, which confirmed its capability for the detection of 5-formyluracil content in general samples. This study presents the first example of the determination of 5fU based on coordination chemistry.

Modulating aptamer function by copper(II)-mediated base pair formation

Two aptamers, one for ATP and one for arginine, were modified using an artificial 2'-dexoyribonucleoside based on the nucleobase surrogate imidazole-4-carboxylate. This synthetic nucleoside substitute does not engage in hydrogen bonding but is capable of forming Cu(II)-mediated base pairs instead. Hence, the addition of Cu(II) can be used to influence the ability of the aptamer derivatives to adopt the correct fold necessary for binding their respective target molecule. As a result, aptamer function can be modulated via the addition of Cu(II). The extent of modulation ability depends on the identity of the aptamer and on the exact location of the artificial nucleosides within the oligonucleotide sequence.

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.

Bipyridine-Modified DNA Three-Way Junctions with Amide linkers: Metal-Dependent Structure Induction and Self-Sorting

DNA three-way junction (3WJ) structures are essential building blocks for the construction of DNA nanoarchitectures. We have synthesized a bipyridine (bpy)-modified DNA 3WJ by using a newly designed bpy-modified nucleoside, U_bpy -3, in which a bpy ligand is tethered via a stable amide linker. The thermal stability of the bpy-modified 3WJ was greatly enhanced by the formation of an interstrand Ni^II (bpy)₃ complex at the junction core (ΔT_m =+17.7 °C). Although the stereochemistry of the modification site differs from that of the previously reported bpy-modified nucleoside U_bpy -2, the degree of the Ni^II -mediated stabilization observed with U_bpy -3 was comparable to that of U_bpy -2. Structure induction of the 3WJs and the duplexes was carried out by the addition or removal of Ni^II ions. Furthermore, Ni^II -mediated self-sorting of 3WJs was performed by using the bpy-modified strands and their unmodified counterparts. Both transformations were driven by the formation of Ni^II (bpy)₃ complexes. The structural induction and self-sorting of bpy-modified 3WJs are expected to have many potential applications in the development of metal-responsive DNA materials.

Metal-responsive reversible binding of triplex-forming oligonucleotides with 5-hydroxyuracil nucleobases

Metal-responsive triplex-forming oligonucleotides (TFOs) were synthesised by incorporating 5-hydroxyuracil (UOH) nucleobases as metal recognition sites. Binding of the UOH-containing TFO to the target natural DNA duplexes was reversibly regulated by the addition and removal of GdIII ions under isothermal conditions.

Modular Design of G-Quadruplex MetalloDNAzymes for Catalytic C-C Bond Formations with Switchable Enantioselectivity

Metal-binding DNA structures with catalytic function are receiving increasing interest. Although a number of metalloDNAzymes have been reported to be highly efficient, the exact coordination/position of their catalytic metal center is often unknown. Here, we present a new approach to rationally develop metalloDNAzymes for Lewis acid-catalyzed reactions such as enantioselective Michael additions. Our strategy relies on the predictable folding patterns of unimolecular DNA G-quadruplexes, combined with the concept of metal-mediated base-pairing. Transition-metal coordination environments were created in G-quadruplex loop regions, accessible by substrates. Therefore, protein-inspired imidazole ligandoside L was covalently incorporated into a series of G-rich DNA strands by solid-phase synthesis. Iterative rounds of DNA sequence design and catalytic assays allowed us to select tailored metalloDNAzymes giving high conversions and excellent enantioselectivities (≥99%). Based on their primary sequence, folding pattern, and metal coordination mode, valuable information on structure-activity relationships could be extracted. Variation of the number and position of ligand L within the sequence allowed us to control the formation of (S) and (R) enantiomeric reaction products, respectively.

Precise Distance Measurements in DNA G-Quadruplex Dimers and Sandwich Complexes by Pulsed Dipolar EPR Spectroscopy

DNA G-quadruplexes show a pronounced tendency to form higher-order structures, such as π-stacked dimers and aggregates with aromatic binding partners. Reliable methods for determining the structure of these non-covalent adducts are scarce. Here, we use artificial square-planar Cu(pyridine)4 complexes, covalently incorporated into tetramolecular G-quadruplexes, as rigid spin labels for detecting dimeric structures and measuring intermolecular Cu2+ -Cu2+ distances via pulsed dipolar EPR spectroscopy. A series of G-quadruplex dimers of different spatial dimensions, formed in tail-to-tail or head-to-head stacking mode, were unambiguously distinguished. Measured distances are in full agreement with results of molecular dynamics simulations. Furthermore, intercalation of two well-known G-quadruplex binders, PIPER and telomestatin, into G-quadruplex dimers resulting in sandwich complexes was investigated, and previously unknown binding modes were discovered. Additionally, we present evidence that free G-tetrads also intercalate into dimers. Our transition metal labeling approach, combined with pulsed EPR spectroscopy, opens new possibilities for examining structures of non-covalent DNA aggregates.

Metal-induced G-quadruplex polymorphism for ratiometric and label-free detection of lead pollution in tea

Lead pollution are critical concerns for food safety and human health. Herein, a ratiometric metal-induced G-quadruplex polymorphism was introduced to construct aptamer probes, enabling label-free and ratiometric detection of lead in tea, thus is promising for on-site detection of lead pollution. The key feature of the aptamer probe is the synergistic utilization of the dual-wavelength fluorescent signal outputs from a G-quadruplex specific dye and a DNA intercalation dye under a single-wavelength excitation, leading to a more stable and reliable recognition of Pb²⁺ than that of analyses based on single fluorescent reporter. The aptamer probe allowed to a mix-and-read, rapid, cost-effective detection of Pb²⁺ with high specificity and accuracy. Pb²⁺ analysis in tap water and tea exhibited good performance with recovery rates of 92.3%-109.0%. The adoption of ratiometric metal-induced G-quadruplex polymorphism would be a compelling design strategy for constructing robust aptasensor, facilitating the translation of aptamer for food safety control.

Heteroleptic Coordination Environments in Metal-Mediated DNA G-Quadruplexes

The presence of metal centers with often highly conserved coordination environments is crucial for roughly half of all proteins, having structural, regulatory, or enzymatic function. To understand and mimic the function of metallo-enzymes, bioinorganic chemists pursue the challenge of synthesizing model compounds with well-defined, often heteroleptic metal sites. Recently, we reported the design of tailored homoleptic coordination environments for various transition metal cations based on unimolecular DNA G-quadruplex structures, templating the regioselective positioning of imidazole ligandosides L^I. Here, we expand this modular system to more complex, heteroleptic coordination environments by combining L^I with a new benzoate ligandoside L^B within the same oligonucleotide. The modifications still allow the correct folding of parallel tetramolecular and antiparallel unimolecular G-quadruplexes. Interestingly, the incorporation of L^B results in strong destabilization expressed in lower thermal denaturation temperatures T_m. While no transition metal cations could be bound by G-quadruplexes containing only L^B, heteroleptic derivatives containing both L^I and L^B were found to complex Cu^II, Ni^II, and Zn^II. Especially in case of Cu^II we found strong stabilizations of up to ΔT_m = +34°C. The here shown system represents an important step toward the design of more complex coordination environments inside DNA scaffolds, promising to culminate in the preparation of functional metallo-DNAzymes.

Supramolecular DNA Three-Way Junction Motifs With a Bridging Metal Center

Various nano-sized supramolecular architectures have been constructed from DNA molecules via sequence-dependent self-assembly. A DNA three-way junction (3WJ), consisting of three oligonucleotides that are partially complementary to each other, is one of the simplest DNA supramolecular structures. This minireview covers studies on DNA 3WJ motifs bridged by an interstrand metal complex with some related works. The incorporation of interstrand metal complexes into DNA has attracted increasing attention because it potentially allows for metal-dependent regulation of the thermal stability and the structure of DNA supramolecules. Metal-bridged DNA 3WJs were synthesized from three DNA strands containing a bipyridine (bpy)-modified nucleotide in the presence of appropriate metal ions. The bpy-modified DNA strands were crosslinked by an interstrand 3:1 metal complex [Ni^II(bpy)₃ etc.] at the junction core. As a result, the thermal stability of the 3WJs was significantly enhanced upon metal complexation. Furthermore, metal-mediated structural transformation between DNA duplexes and 3WJs was demonstrated by using the same bpy-modified DNA strands. A mixture of bpy-modified strands and their natural complementary strands were self-assembled exclusively into duplexes in the absence of any transition metal ions. In contrast, addition of Ni^II ions induced the formation of 3WJs through the formation of an interstrand Ni^II(bpy)₃ complex, which served as a template for the 3WJ assembly. Because DNA 3WJ structures are essential structural motifs for DNA-based nanoarchitectures, the metal-mediated stabilization and structural induction of metal-locked 3WJs would lead to many potential applications to artificial DNA architectures.

Tailored Transition-Metal Coordination Environments in Imidazole-Modified DNA G-Quadruplexes

Two types of imidazole ligands were introduced both at the end of tetramolecular and into the loop region of unimolecular DNA G‐quadruplexes. The modified oligonucleotides were shown to complex a range of different transition‐metal cations including Ni^II, Cu^II, Zn^II and Co^II, as indicated by UV/Vis absorption spectroscopy and ion mobility mass spectrometry. Molecular dynamics simulations were performed to obtain structural insight into the investigated systems. Variation of ligand number and position in the loop region of unimolecular sequences derived from the human telomer region (htel) allows for a controlled design of distinct coordination environments with fine‐tuned metal affinities. It is shown that Cu^II, which is typically square‐planar coordinated, has a higher affinity for systems offering four ligands, whereas Ni^II prefers G‐quadruplexes with six ligands. Likewise, the positioning of ligands in a square‐planar versus tetrahedral fashion affects binding affinities of Cu^II and Zn^II cations, respectively. Gaining control over ligand arrangement patterns will spur the rational development of transition‐metal‐modified DNAzymes. Furthermore, this method is suited to combine different types of ligands, for example, those typically found in metalloenzymes, inside a single DNA architecture.

Metal-Modified Nucleic Acids: Metal-Mediated Base Pairs, Triples, and Tetrads

The incorporation of metal ions into nucleic acids by means of metal-mediated base pairs represents a promising and prominent strategy for the site-specific decoration of these self-assembling supramolecules with metal-based functionality. Over the past 20 years, numerous nucleoside surrogates have been introduced in this respect, broadening the metal scope by providing perfectly tailored metal-binding sites. More recently, artificial nucleosides derived from natural purine or pyrimidine bases have moved into the focus of Ag^I -mediated base pairing, due to their expected compatibility with regular Watson-Crick base pairs. This minireview summarizes these advances in metal-mediated base pairing but also includes further recent progress in the field. Moreover, it addresses other aspects of metal-modified nucleic acids, highlighting an expansion of the concept to metal-mediated base triples (in triple helices and three-way junctions) and metal-mediated base tetrads (in quadruplexes). For all types of metal-modified nucleic acids, proposed or accomplished applications are briefly mentioned, too.

Imidazole-modified G-quadruplex DNA as metal-triggered peroxidase

Four imidazoles, serving as metalloprotein-inspired ligands for complexing a range of transition metal cations, were incorporated into tetramolecular G-quadruplex DNA structures. Modified quadruplexes were found to complex Cu(ii), Ni(ii), Zn(ii) and Co(ii) in a 1 : 1 ratio with unprecedented strong thermal stabilizations of up to ΔT _1/2 = +51 °C. Furthermore, addition of Cu(ii) was found to lead to extraordinarily fast G-quadruplex association rates with k _on values being ∼100 times higher compared to unmodified G-quadruplexes. This is ascribed to a template effect of Cu(ii), preorganizing the four single strands via coordination, followed by rapid formation of hydrogen-bonded G-quartets. Native electrospray ionization mass spectrometry (ESI), coupled with trapped ion-mobility spectrometry (timsTOF), supports the proposed 1 : 1 G-quadruplex-metal complexes and could further disclose their ability to bind the iron-porphyrin complex hemin in a 1 : 1 stoichiometry. DNA sequence design allowed us to equip this G-quadruplex-hemin complex, known to function as a horseradish peroxidase mimic, with a metal-dependent trigger. A competitive screen of transition metals revealed a high selectivity for Cu(ii), even in mixtures of several divalent metal cations. Once formed, the Cu(ii)-carrying DNAzyme was shown to be preserved in the presence of EDTA, attributed to its remarkable kinetic stability. Stimuli-responsive G-quadruplexes promise application in DNAzymes with switchable activity, adaptive sensors and dynamic DNA origami constructs.

Controlling anticancer drug mediated G-quadruplex formation and stabilization by a molecular container

Controlling of ligand mediated G-quadruplex DNA (GQ-DNA) formation and stabilization is an important and challenging aspect due to its active involvement in many biologically important processes such as DNA replication, transcription, etc. Here, we have demonstrated that topotecan (TPT), a potential anticancer drug, can instigate the formation and stabilization of GQ-DNA (H24 → GQ-DNA) in the absence of Na⁺/K⁺ ions via circular dichroism, fluorescence, NMR, UV melting and molecular dynamics (MD) simulation studies. The primary binding mode of TPT to GQ was found to be stacking at the terminal rather than binding to the groove. We have also reverted this conformational transition (GQ-DNA → H24) using a molecular container, cucurbit[7]uril (CB7), by means of the translocation of the drug (TPT) from GQ-DNA to its nanocavity. Importantly, we have carried out the detection of these conformational transitions using the fluorescence color switch of the drug, which is more direct and simple than some of the other methods that involve sophisticated and complex detection techniques.

DNA metallization: principles, methods, structures, and applications

This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.

Di-copper(ii) DNA G-quadruplexes as EPR distance rulers

Paramagnetic Cu(ii) complexes, immobilized via four-point-attachment to both ends of G-quadruplexes, serve as EPR-based distance rulers for studying DNA structure.

Structure-Property Relationships in CuII -Binding Tetramolecular G-Quadruplex DNA

A series of artificial metal-base tetrads composed of a Cu^II cation coordinating to four pyridines, covalently attached to the ends of tetramolecular G-quadruplex DNA strands [L^A-D d(G₄ )]₄ (L^A-D =ligand derivatives), was systematically studied. Structurally, the square-planar [Cu(pyridine)₄ ] complex behaves analogously to the canonical guanine quartet. Copper coordination to all studied ligand derivatives was found to increase G-quadruplex thermodynamic stability, tolerating a great variety of ligand linker lengths (1-5 atoms) and thus demonstrating the robustness of the chosen ligand design. Only at long linker lengths, the stabilizing effect of copper binding is compensated by the loss of conformational freedom. A previously reported ligand L^E with chiral backbone enables incorporation at any oligonucleotide position. We show that ligand chirality distinctly steers Cu^II -induced G-quadruplex stabilization. 5'-End formation of two metal-base tetrads by tetramolecular G-quadruplex [L^E₂ d(G)₄ ]₄ shows that stabilization in the presence of Cu^II is not additive. All results are based on UV/Vis thermal denaturation, thermal difference, circular dichroism experiments and molecular dynamics simulations.

Metal-mediated base pairs in parallel-stranded DNA

In nucleic acid chemistry, metal-mediated base pairs represent a versatile method for the site-specific introduction of metal-based functionality. In metal-mediated base pairs, the hydrogen bonds between complementary nucleobases are replaced by coordinate bonds to one or two transition metal ions located in the helical core. In recent years, the concept of metal-mediated base pairing has found a significant extension by applying it to parallel-stranded DNA duplexes. The antiparallel-stranded orientation of the complementary strands as found in natural B-DNA double helices enforces a cisoid orientation of the glycosidic bonds. To enable the formation of metal-mediated base pairs preferring a transoid orientation of the glycosidic bonds, parallel-stranded duplexes have been investigated. In many cases, such as the well-established cytosine-Ag(I)-cytosine base pair, metal complex formation is more stabilizing in parallel-stranded DNA than in antiparallel-stranded DNA. This review presents an overview of all metal-mediated base pairs reported as yet in parallel-stranded DNA, compares them with their counterparts in regular DNA (where available), and explains the experimental conditions used to stabilize the respective parallel-stranded duplexes.

Metal-Mediated Base Pairs: From Characterization to Application

The investigation of metal-mediated base pairs and the development of their applications represent a prominent area of research at the border of bioinorganic chemistry and supramolecular coordination chemistry. In metal-mediated base pairs, the complementary nucleobases in a nucleic acid duplex are connected by coordinate bonds to an embedded metal ion rather than by hydrogen bonds. Because metal-mediated base pairs facilitate a site-specific introduction of metal-based functionality into nucleic acids, they are ideally suited for use in DNA nanotechnology. This minireview gives an overview of the general requirements that need to be considered when devising a new metal-mediated base pair, both from a conceptual and from an experimental point of view. In addition, it presents selected recent applications of metal-modified nucleic acids to indicate the scope of metal-mediated base pairing.

Peripheral Templation Generates an M(II) 6 L4 Guest-Binding Capsule

Pseudo‐octahedral M^II₆L₄ capsules result from the subcomponent self‐assembly of 2‐formylphenanthroline, threefold‐symmetric triamines, and octahedral metal ions. Whereas neutral tetrahedral guests and most of the anions investigated were observed to bind within the central cavity, tetraphenylborate anions bound on the outside, with one phenyl ring pointing into the cavity. This binding configuration is promoted by the complementary arrangement of the phenyl rings of the intercalated guest between the phenanthroline units of the host. The peripherally bound, rapidly exchanging tetraphenylborate anions were found to template an otherwise inaccessible capsular structure in a manner usually associated with slow‐exchanging, centrally bound agents. Once formed, this cage was able to bind guests in its central cavity.

Metal-responsive structural transformation between artificial DNA duplexes and three-way junctions

Metal-responsive structural transformation between DNA duplexes and three-way junction structures was demonstrated utilizing artificial oligonucleotides modified with a 2,2’-bipyridine ligand.

DNA three-way junctions (3WJs) are essential structural motifs for DNA nanoarchitectures and DNA-based materials. We report herein a metal-responsive structural transformation between DNA duplexes and 3WJs using artificial oligonucleotides modified with a 2,2′-bipyridine (bpy) ligand. A mixture of bpy-modified DNA strands and natural complementary strands were self-assembled exclusively into duplexes without any transition metal ions, while they formed 3WJs in the presence of Ni^II ions. This transformation was induced by the formation of an interstrand Ni^II(bpy)₃ complex, which served as a template for the 3WJ assembly. Altering the amount and identity of the metal ion regulated the 3WJ induction efficiency. Removal of the metal using EDTA quantitatively regenerated the duplexes. The metal-dependent structural conversion shown here has many potential applications in the development of stimuli-responsive DNA materials.

Towards metal-mediated g-quartet analogues: 1,2,4-triazole nucleotides

We proposed that metal-coordinating nucleotides could be used to control the assembly of G-quadruplexes through the formation of an artificial metal-centered quartet. Several guanine-rich DNA sequences containing 1,2,4-triazole-functionalized nucleotides were investigated. These oligonucleotides were designed to form quartets mediated by metal-triazole bonding both on the surface of and within the G-quadruplex core. In contrast to duplex studies in which 1,2,4-triazole nucleosides serve as a mimic of Watson-Crick base-pairs, our results show that these nucleosides are not suitable components of an artificial metal-centered quartet.

Formation of a G-quartet-Fe complex and modulation of electronic and magnetic properties of the Fe center

Although the G-quartet structure has been extensively investigated due to its biological importance, the formation mechanism, in particular, the necessity of metal centers, of an isolated G-quartet on solid surfaces remains ambiguous. Here, by using scanning tunneling microscopy under well-controlled ultra-high-vacuum conditions and density functional theory calculations we have been able to clarify that besides the intraquartet hydrogen bonding a metal center is mandatory for the formation of an isolated G-quartet. Furthermore, by subtly perturbing the local coordination bonding schemes within the formed G-quartet complex via local nanoscale scanning tunneling microscopy manipulations, we succeed in modulating the d orbitals and the accompanying magnetic properties of the metal center. Our results demonstrate the feasibility of forming an isolated G-quartet complex on a solid surface and that the strategy of modulating electronic and magnetic properties of the metal center can be extended to other related systems such as molecular spintronics.

"Signal-on" photoelectrochemical sensing strategy based on target-dependent aptamer conformational conversion for selective detection of lead(II) ion

A "signal-on" photoelectrochemical sensing strategy for selective determination of Pb(2+) is designed on the basis of the combination of Pb(2+)-induced conformational conversion, the amplified effect of reduced graphene oxide (RGO) and resonance energy transfer between CdS quantum dots (QDs) and gold nanoparticles (AuNPs). The RGO/CdS/aptamer platform is constructed via a stepwise modification method, and characterized by electrochemical impedance spectroscopy. In the absence of Pb(2+), the AuNP-labeled DNA, as a signal quenching element, can be introduced by hybridization with aptamer on the surface of sensing platform, which quenches the photocurrent of QDs via an energy transfer process. Upon addition of Pb(2+), the aptamer is induced into a G-quadruplex structure, which can greatly hinder the hybridization between aptamer and AuNP-labeled DNA due to the competitive occupation of binding sites and steric effect, leading to the recovery of photocurrent. Under optimized conditions, this "signal-on" photoelectrochemical biosensor shows a linear relationship between photocurrent variation and the logarithm of Pb(2+) concentration in the range of 0.1-50 nM with a detection limit of 0.05 nM. Meanwhile, it also exhibits good selectivity for Pb(2+) over other interfering ions, and is successfully applied to the detection of Pb(2+) in environmental water samples. By substituting the aptamers with other sequences, this proposed strategy could be conveniently extended to detect different targets as versatile photoelectrochemical devices.

EPR based distance measurement in Cu-porphyrin–DNA

Measurement of EPR spectra of Cu-porphyrin–DNA reveals intermolecular interactions between the DNA strands with average distances of 6.5–8.9 Å.