Ion‐Selective Formation of a Guanine Quadruplex on DNA Origami Structures

DNA origami nanostructures are a versatile tool that can be used to arrange functionalities with high local control to study molecular processes at a single‐molecule level. Here, we demonstrate that DNA origami substrates can be used to suppress the formation of specific guanine (G) quadruplex structures from telomeric DNA. The folding of telomeres into G‐quadruplex structures in the presence of monovalent cations (e.g. Na⁺ and K⁺) is currently used for the detection of K⁺ ions, however, with insufficient selectivity towards Na⁺. By means of FRET between two suitable dyes attached to the 3′‐ and 5′‐ends of telomeric DNA we demonstrate that the formation of G‐quadruplexes on DNA origami templates in the presence of sodium ions is suppressed due to steric hindrance. Hence, telomeric DNA attached to DNA origami structures represents a highly sensitive and selective detection tool for potassium ions even in the presence of high concentrations of sodium ions.     

Multitasking Water‐Soluble Synthetic G‐Quartets: From Preferential RNA–Quadruplex Interaction to Biocatalytic Activity

Natural G‐quartets, a cyclic and coplanar array of four guanine residues held together through a Watson–Crick/Hoogsteen hydrogen‐bond network, have received recently much attention due to their involvement in G‐quadruplex DNA, an alternative higher‐order DNA structure strongly suspected to play important roles in key cellular events. Besides this, synthetic G‐quartets (SQ), which artificially mimic native G‐quartets, have also been widely studied for their involvement in nanotechnological applications (i.e., nanowires, artificial ion channels, etc.). In contrast, intramolecular synthetic G‐quartets (iSQ), also named template‐assembled synthetic G‐quartets (TASQ), have been more sparingly investigated, despite a technological potential just as interesting. Herein, we report on a particular iSQ named ^PNADOTASQ, which demonstrates very interesting properties in terms of DNA and RNA interaction (notably its selective recognition of quadruplexes according to a bioinspired process) and catalytic activities, through its ability to perform peroxidase‐like hemin‐mediated oxidations either in an autonomous fashion (i.e., as pre‐catalyst for TASQzyme reactions) or in conjunction with quadruplex DNA (i.e., as enhancing agents for DNAzyme processes). These results provide a solid scientific basis for TASQ to be used as multitasking tools for bionanotechnological applications.     

Methyl Substitution Regulates the Enantioselectivity of Supramolecular Complex Binding to Human Telomeric G‐Quadruplex DNA

Chiral supramolecular compounds with substituents at different positions show different binding properties with human telomeric G‐quadruplex DNA. These different positions of methyl substitution in chiral supramolecular compounds can modulate their enantioselectivity and structural preference when binding with human telomeric G‐quadruplex DNA.     

Stabilization of Human Telomeric G‐Quadruplex and Inhibition of Telomerase Activity by Propeller‐Shaped Trinuclear PtII Complexes

Two novel propeller‐shaped, trigeminal‐ligand‐containing, flexible trinuclear Pt^II complexes, {[Pt(dien)]₃(ptp)}(NO₃)₆ ( 1 ) and {[Pt(dpa)]₃(ptp)}(NO₃)₆ ( 2 ) (dien: diethylenetriamine; dpa: bis‐(2‐pyridylmethyl)amine; ptp: 6′‐(pyridin‐3‐yl)‐3,2′:4′,3′′‐terpyridine), have been designed and synthesized, and their interactions with G‐quadruplex (G4) sequences are characterized. A combination of biophysical and biochemical assays reveals that both Pt^II complexes exhibit higher affinity for human telomeric (hTel) and c‐myc promoter G4 sequences than duplex DNA. Complex 1 binds and stabilizes hTel G4 sequence more effectively than complex 2 . Both complexes are found to induce and stabilize either antiparallel or parallel conformation of G4 structures. Molecular docking studies indicate that complex 1 binds into the large groove of the antiparallel hTel G4 structure (PDB ID: 143D) and complex 2 stacks onto the exposed G‐quartet of the parallel hTel G4 structure (PDB ID: 1KF1). Telomeric repeat amplification protocol assays demonstrate that both complexes are good telomerase inhibitors, with IC₅₀ values of (16.0±0.4) μM and (4.20±0.25) μM for 1 and 2 , respectively. Collectively, the results suggest that these propeller‐shaped flexible trinuclear Pt^II complexes are effective and selective G4 binders and good telomerase inhibitors. This work provides valuable information for the interaction between multinuclear metal complexes with G4 DNA.     

Photo‐Cross‐Linking Probes for Trapping G‐Quadruplex DNA

We have developed a straightforward synthetic pathway to a set of six photoactivatable G‐quadruplex ligands with a validated G4‐binding motif (the bisquinolinium pyridodicarboxamide PDC‐360A) tethered through various spacers to two different photo‐cross‐linking groups: benzophenone and an aryl azide. The high quadruplex‐versus‐duplex selectivity of the PDC core was retained in the new derivatives and resulted in selective alkylation of two well‐known G‐quadruplexes (human telomeric G4 and oncogene promoter c‐myc G4) under conditions of harsh competition. The presence of two structurally different photoactivatable functions allowed the selective alkylation of G‐quadruplex structures at specific nucleobases and irreversible G4 binding. The topology and sequence of the quadruplex matrix appear to influence strongly the alkylation profile, which differs for the telomeric and c‐myc quadruplexes. The new compounds are photoactive in cells and thus provide new tools for studying G4 biology.     

Label‐Free Logic Modules and Two‐Layer Cascade Based on Stem‐Loop Probes Containing a G‐Quadruplex Domain

A simple, versatile, and label‐free DNA computing strategy was designed by using toehold‐mediated strand displacement and stem‐loop probes. A full set of logic gates (YES, NOT, OR, NAND, AND, INHIBIT, NOR, XOR, XNOR) and a two‐layer logic cascade were constructed. The probes contain a G‐quadruplex domain, which was blocked or unfolded through inputs initiating strand displacement and the obviously distinguishable light‐up fluorescent signal of G‐quadruplex/NMM complex was used as the output readout. The inputs are the disease‐specific nucleotide sequences with potential for clinic diagnosis. The developed versatile computing system based on our label‐free and modular strategy might be adapted in multi‐target diagnosis through DNA hybridization and aptamer‐target interaction.     

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.

     

Involvement of Long‐Lived Intermediate States in the Complex Folding Pathway of the Human Telomeric G‐Quadruplex

The energy landscapes of human telomeric G‐quadruplexes are complex, and their folding pathways have remained largely unexplored. By using real‐time NMR spectroscopy, we investigated the K⁺‐induced folding of the human telomeric DNA sequence 5′‐TTGGG(TTAGGG)₃A‐3′. Three long‐lived states were detected during folding: a major conformation (hybrid‐1), a previously structurally uncharacterized minor conformation (hybrid‐2), and a partially unfolded state. The minor hybrid‐2 conformation is formed faster than the more stable hybrid‐1 conformation. Equilibration of the two states is slow and proceeds via a partially unfolded intermediate state, which can be described as an ensemble of hairpin‐like structures.     

A Platinum(II) Phenylphenanthroimidazole with an Extended Side‐Chain Exhibits Slow Dissociation from a c‐Kit G‐Quadruplex Motif

A series of three platinum(II) phenanthroimidazoles each containing a protonable side‐chain appended from the phenyl moiety through copper(I)‐catalyzed azide–alkyne cycloaddition (CuAAC) were evaluated for their capacities to bind to human telomere, c‐Myc, and c‐Kit derived G‐quadruplexes. The side‐chain has been optimized to enable a multivalent binding mode to G‐quadruplex motifs, which would potentially result in selective targeting. Molecular modeling, high‐throughput fluorescence intercalator displacement (HT‐FID) assays, and surface plasmon resonance (SPR) studies demonstrate that complex 2 exhibits significantly slower dissociation rates compared to platinum phenanthroimidazoles without side‐chains and other reported G‐quadruplex binders. Complex 2 showed little cytotoxicity in HeLa and A172 cancer cell lines, consistent with the fact that it does not follow a telomere‐targeting pathway. Preliminary mRNA analysis shows that 2 specifically interacts with the ckit promoter region. Overall, this study validates 2 as a useful molecular probe for c‐Kit related cancer pathways.     

Bifunctional Diaminoterephthalate Scaffolds as Fluorescence Turn‐On Probes for Thiols

The fluorescent diaminoterephthalate scaffold was equipped by amidation with three types of reactive functions: thiols for metal‐surface binding, alkynes for click reactions, and maleimides for ligation with proteins. Starting from a succinyl succinate derivative with two orthogonally cleavable ester functions, three monoamides (38–57 % yield over three steps) and two bisamides (19 and 25 % yield over five steps) were prepared. Although alkyne and thiol derivatized compounds showed reasonable luminescence behavior (Φ≈1–4 %), the fluorescence was quenched by the maleimide moiety. It was turned on (10‐ to 20‐fold increase of fluorescence quantum yield) by conjugate addition of thiols.     

Key Structural Elements of Unsymmetrical Cyanine Dyes for Highly Sensitive Fluorescence Turn‐On DNA Probes

Unsymmetrical cyanine dyes, such as thiazole orange, are useful for the detection of nucleic acids with fluorescence because they dramatically enhance the fluorescence upon binding to nucleic acids. Herein, we synthesized a series of unsymmetrical cyanine dyes and evaluated their fluorescence properties. A systematic structure–property relationship study has revealed that the dialkylamino group at the 2‐position of quinoline in a series of unsymmetrical cyanine dyes plays a critical role in the fluorescence enhancement. Four newly designed unsymmetrical cyanine dyes showed negligible intrinsic fluorescence in the free state and strong fluorescence upon binding to double‐stranded DNA (dsDNA) with a quantum yield of 0.53 to 0.90, which is 2 to 3 times higher than previous unsymmetrical cyanine dyes. A detailed analysis of the fluorescence lifetime revealed that the dialkylamino group at the 2‐position of quinoline suppressed nonradiative decay in favor of increased fluorescence quantum yield. Moreover, these newly developed dyes were able to stain the nucleus specifically in fixed HeLa cells examined by using a confocal laser‐scanning microscope.     

Programmed Self‐Assembly of a Quadruplex DNA Nanowire

The ability to produce, reproducibly and systematically, well‐defined quadruplex DNA nanowires through controlled rational design is poorly understood despite potential utility in structural nanotechnology. The programmed hierarchical self‐assembly of a long four‐stranded DNA nanowire through cohesive self‐assembly of GpC and CpG “sticky” ends is reported. The encoding of bases within the quadruplex stem allows for an uninterrupted π‐stacking system with rectilinear propagation for hundreds of nanometers in length. The wire is mechanically stable and features superior nuclease resistance to double‐stranded DNA. The study indicates the feasibility for programmed assembly of uninterrupted quadruplex DNA nanowires. This is fundamental to the systematic investigation of well‐defined DNA nanostructures for uses in optoelectronic and electronic devices as well as other structural nanotechnology applications.     

Determination Limit of Fluorescence Turn‐On Probes for the Acetate Anion

Three fluorescent turn‐on probes containing 3,6‐dichloro‐9H‐carbazole as carbazyl part have been designed and synthesized. Among studied anions F^?, AcO^?, H₂PO , Cl^?, Br^? and I^?, AcO^? showed the strongest binding ability with all probes. The strong basic anions, such as AcO^?, H₂PO , and F^?, induced a significant red‐shift in absorption and a concomitant increase in fluorescent emission of the probes caused by photoinduced electron transfer (PET). The determination limit of probe 3 (Scheme 1) toward AcO^? is 3.0×10^?7 M . ¹H‐NMR Titration experiments shed light on the nature of the interaction between the probes and the anions. Theoretical investigation further illustrated the possible binding mode in these host? guest interactions and the roles of molecular frontier orbitals in molecular interplay.     

Dynamics of Fluorescent Dyes Attached to G‐Quadruplex DNA and their Effect on FRET Experiments

FRET spectroscopy is a promising approach for investigating the dynamics of G‐quadruplex DNA folds and improving the targeting of G‐quadruplexes by potential anticancer compounds. To better interpret such experiments, classical and replica‐exchange molecular dynamics simulations and fluorescence‐lifetime measurements are used to understand the behavior of a range of Cy3‐based dyes attached to the 3′ end of G‐quadruplex DNA. The simulations revealed that the dyes interact extensively with the G‐quadruplex. Identification of preferred dye positions relative to the G‐quadruplex in the simulations allows the impact of dye–DNA interactions on FRET results to be determined. All the dyes show significant deviations from the common approximation of being freely rotating and not interacting with the host, but one of the Cy3 dye analogues is slightly closer to this case.     

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.