Trianguleniums as Optical Probes for G‐Quadruplexes: A Photophysical,Electrochemical, and Computational Study

Nucleic acids can adopt non‐duplex topologies, such as G‐quadruplexes in vitro. Yet it has been challenging to establish their existence and function in vivo due to a lack of suitable tools. Recently, we identified the triangulenium compound DAOTA‐M2 as a unique fluorescence probe for such studies. This probe's emission lifetime is highly dependent on the topology of the DNA it interacts with opening up the possibility of carrying out live‐cell imaging studies. Herein, we describe the origin of its fluorescence selectivity for G‐quadruplexes. Cyclic voltammetry predicts that the appended morpholino groups can act as intra‐ molecular photo‐induced electron transfer (PET) quenchers. Photophysical studies show that a delicate balance between this effect and inter‐molecular PET with nucleobases is key to the overall fluorescence enhancement observed upon nucleic acid binding. We utilised computational modelling to demonstrate a conformational dependence of intra‐molecular PET. Finally, we performed orthogonal studies with a triangulenium compound, in which the morpholino groups were removed, and demonstrated that this change inverts triangulenium fluorescence selectivity from G‐quadruplex to duplex DNA, thus highlighting the importance of fine tuning the molecular structure not only for target affinity, but also for fluorescence response.     

A Photoreactive G‐Quadruplex Ligand Triggered by Green Light

A photoreactive molecular dye targeting the G‐quadruplex nucleic acid (G4) of the human telomeric sequence Tel22, and several mutated analogues, was activated by green light (λ=532 nm). Highly selective covalent modification of G4 versus single‐stranded and double‐stranded DNA was achieved with efficiency up to 64 %. The phenoxyl radical was generated and detected by laser‐flash photolysis as a reactive intermediate that targeted loop thymine residues. These insights may suggest a non‐invasive tool for selective nucleic acid tagging and “pull‐down” cellular applications.     

Inverting the G‐Tetrad Polarity of a G‐Quadruplex by Using Xanthine and 8‐Oxoguanine

G‐quadruplexes are four‐stranded nucleic acid structures that are built from consecutively stacked guanine tetrad (G‐tetrad) assemblies. The simultaneous incorporation of two guanine base lesions, xanthine (X) and 8‐oxoguanine (O), within a single G‐tetrad of a G‐quadruplex was recently shown to lead to the formation of a stable G?G?X?O tetrad. Herein, a judicious introduction of X and O into a human telomeric G‐quadruplex‐forming sequence is shown to reverse the hydrogen‐bond polarity of the modified G‐tetrad while preserving the original folding topology. The control exerted over G‐tetrad polarity by joint X?O modification will be valuable for the design and programming of G‐quadruplex structures and their properties.     

Click Chemistry for the Identification of G‐Quadruplex Structures: Discovery of a DNA–RNA G‐Quadruplex

A trap that closes with a “click” : The copper‐catalyzed azide–alkyne cycloaddition can occur in different G‐quadruplex structures (see scheme). The species trapped by the click reaction can then be separated and analyzed. By using this approach, a DNA–RNA hybrid‐type G‐quadruplex structure formed by human telomeric DNA and RNA sequences was detected.

     

Hierarchical Self‐Assembly of a Biomimetic Light‐Harvesting Antenna Based on DNA G‐Quadruplexes

A new modular approach to an artificial light‐harvesting antenna system is presented. The approach involves the hierarchical self‐assembly of porphyrin acceptor molecules to G‐quadruplexes tethered to coumarin donor moieties.     

Macrocyclic Polyoxazoles as G‐Quadruplex Ligands

This review deals with recent progress in the synthesis and evaluation of our telomestatin‐inspired macrocyclic polyoxazoles as G‐quadruplex (G4) ligands. The hexaoxazole derivatives (6OTDs) interact with and stabilize G4‐forming oligonucleotides, depending upon the character of the side chain functional groups. Cationic functional groups are particularly effective due to their secondary interaction with phosphate in the DNA backbone. On the other hand, heptaoxazole derivatives (7OTDs) showed potent G4‐binding and stabilization activity regardless of the functional groups on the side chain. A caged G4 ligand, Y2Nv2‐6OTD ( 7 ), and a fluorescent G4 ligand, L1BOD‐7OTD ( 13 ), have been synthesized.     

Carbohydrate–DNA Interactions at G‐Quadruplexes: Folding and Stability Changes by Attaching Sugars at the 5′‐End

Quadruplex DNA structures are attracting an enormous interest in many areas of chemistry, ranging from chemical biology, supramolecular chemistry to nanoscience. We have prepared carbohydrate–DNA conjugates containing the oligonucleotide sequences of G‐quadruplexes (thrombin binding aptamer (TBA) and human telomere (TEL)), measured their thermal stability and studied their structure in solution by using NMR and molecular dynamics. The solution structure of a fucose–TBA conjugate shows stacking interactions between the carbohydrate and the DNA G‐tetrad in addition to hydrogen bonding and hydrophobic contacts. We have also shown that attaching carbohydrates at the 5′‐end of a quadruplex telomeric sequence can alter its folding topology. These results suggest the possibility of modulating the folding of the G‐quadruplex by linking carbohydrates and have clear implications in molecular recognition and the design of new G‐quadruplex ligands.