A Minimal Sequence for Left‐Handed G‐Quadruplex Formation

Recently, we observed the first example of a left‐handed G‐quadruplex structure formed by natural DNA, named Z‐G4. We analysed the Z‐G4 structure and inspected its primary 28‐nt sequence in order to identify motifs that convey the unique left‐handed twist. Using circular dichroism spectroscopy, NMR spectroscopy, and X‐ray crystallography, we revealed a minimal sequence motif of 12 nt (GTGGTGGTGGTG) for formation of the left‐handed DNA G‐quadruplex, which is found to be highly abundant in the human genome. A systematic analysis of thymine loop mutations revealed a moderate sequence tolerance, which would further broaden the space of sequences prone to left‐handed G‐quadruplex formation.     

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.     

An Unprecedented Knot‐like G‐Quadruplex Peripheral Motif

A knot‐like G‐quadruplex peripheral structure is formed by a 7‐nt DNA sequence DL7 (TGTTGGT), in which six out of its seven nucleobases participate in compact base‐pairing interactions. Here, the solution NMR structure of a 24‐nt DNA oligonucleotide containing the DL7 sequence shows the interaction between a two‐layer anti‐parallel G‐quadruplex core and the peripheral knot‐like structure, including the construction of two sharp turns in the DNA backbone. The formation of this novel structural element highlights the intricate properties of single‐stranded DNA folding in presence of G‐quadruplex‐forming motifs. We demonstrated the compatibility of the DL7 knot‐like structure with various G‐quadruplexes, which could have implications in drug design and DNA engineering.     

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.     

Photocrosslinking of G‐Quadruplex‐Forming Sequences found in Human Promoters

While is it well known that human telomeric DNA sequences can adopt G‐quadruplex structures, some promoters sequences have also been found to form G‐quadruplexes, and over 40% of promoters contain putative G‐quadruplex‐forming sequences. Because UV light has been shown to crosslink human telomeric G‐quadruplexes by cyclobutane pyrimidine dimer (CPD) formation between T's on adjacent loops, UV light might also be able to photocrosslink G‐quadruplexes in promoters. To investigate this possibility, 15 potentially UV‐crosslinkable G‐quadruplex‐forming sequences found in a search of human DNA promoters were UVB irradiated in vitro, and three were confirmed to have formed nonadjacent CPDs by mass spectrometry. In addition to nonadjacent T=T CPDs found in human telomeric DNA, a nonadjacent T=U CPD was discovered that presumably arose from deamination of a nonadjacent T=C CPD. Analysis of the three sequences by circular dichroism, melting temperature analysis and chemical footprinting confirmed the presence of G‐quadruplexes that could explain the formation of the nonadjacent CPDs. The formation of nonadjacent CPDs from the sequences in vitro suggests that they might be useful probes for the presence of non‐B DNA structures, such as G‐quadruplexes, in vivo, and if they were to form in vivo, might also have significant biological consequences.     

Base‐Pairing Directed Folding of a Bimolecular G‐Quadruplex: New Insights into G‐Quadruplex‐Based DNAzymes

Base pairs, magic hands : An additional base‐pairing duplex is utilized to control the folding topologies of a bimolecular G‐quadruplex formed by two G‐rich single‐stranded DNAs (see picture), which is dependent on the position of base pairs. This study clearly reveals an important intrinsic role of additional base pairs in the G‐quadruplex structure, and also provides a clue to the formation mechanism of the G‐quadruplex‐based DNAzyme.

     

Ruthenium Complex “Light Switches” that are Selective for Different G‐Quadruplex Structures

Recognition and regulation of G‐quadruplex nucleic acid structures is an important goal for the development of chemical tools and medicinal agents. The addition of a bromo‐substituent to the dipyridylphenazine (dppz) ligands in the photophysical “light switch”, [Ru(bpy)₂dppz]²⁺, and the photochemical “light switch”, [Ru(bpy)₂dmdppz]²⁺, creates compounds with increased selectivity for an intermolecular parallel G‐quadruplex and the mixed‐hybrid G‐quadruplex, respectively. When [Ru(bpy)₂dppz‐Br]²⁺ and [Ru(bpy)₂dmdppz‐Br]²⁺ are incubated with the G‐quadruplexes, they have a stabilizing effect on the DNA structures. Activation of [Ru(bpy)₂dmdppz‐Br]²⁺ with light results in covalent adduct formation with the DNA. These complexes demonstrate that subtle chemical modifications of Ru^II complexes can alter G‐quadruplex selectivity, and could be useful for the rational design of in vivo G‐quadruplex probes.     

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.     

Copper‐Induced Topology Switching and Thrombin Inhibition with Telomeric DNA G‐Quadruplexes

The topological diversity of DNA G‐quadruplexes may play a crucial role in its biological function. Reversible control over a specific folding topology was achieved by the synthesis of a chiral, glycol‐based pyridine ligand and its fourfold incorporation into human telomeric DNA by solid‐phase synthesis. Square‐planar coordination to a Cu^II ion led to the formation of a highly stabilizing intramolecular metal–base tetrad, substituting one G‐tetrad in the parent unimolecular G‐quadruplex. For the Tetrahymena telomeric repeat, Cu^II‐triggered switching from a hybrid‐dominated conformer mixture to an antiparallel topology was observed. Cu^II‐dependent control over a protein–G‐quadruplex interaction was shown for the thrombin–tba pair (tba=thrombin‐binding aptamer).     

Orienting Tetramolecular G‐Quadruplex Formation: The Quest for the Elusive RNA Antiparallel Quadruplex

DNA and RNA G‐quadruplexes (G4) are unusual nucleic acid structures involved in a number of key biological processes. RNA G‐quadruplexes are less studied although recent evidence demonstrates that they are biologically relevant. Compared to DNA quadruplexes, RNA G4 are generally more stable and less polymorphic. Duplexes and quadruplexes may be combined to obtain pure tetrameric species. Here, we investigated whether classical antiparallel duplexes can drive the formation of antiparallel tetramolecular quadruplexes. This concept was first successfully applied to DNA G4. In contrast, RNA G4 were found to be much more unwilling to adopt the forced antiparallel orientation, highlighting that the reason RNA adopts a different structure must not be sought in the loops but in the G‐stem structure itself. RNA antiparallel G4 formation is likely to be restricted to a very small set of peculiar sequences, in which other structural features overcome the formidable intrinsic barrier preventing its formation.     

Photoresponsive Formation of an Intermolecular Minimal G‐Quadruplex Motif

The ability of three different bifunctional azobenzene linkers to enable the photoreversible formation of a defined intermolecular two‐tetrad G‐quadruplex upon UV/Vis irradiation was investigated. Circular dichroism and NMR spectroscopic data showed the formation of G‐quadruplexes with K⁺ ions at room temperature in all three cases with the corresponding azobenzene linker in an E conformation. However, only the para–para‐substituted azobenzene derivative enables photoswitching between a nonpolymorphic, stacked, tetramolecular G‐quadruplex and an unstructured state after E–Z isomerization.     

Direct and Single‐Molecule Visualization of the Solution‐State Structures of G‐Hairpin and G‐Triplex Intermediates

We present the direct and single‐molecule visualization of the in‐pathway intermediates of the G‐quadruplex folding that have been inaccessible by any experimental method employed to date. Using DNA origami as a novel tool for the structural control and high‐speed atomic force microscopy (HS‐AFM) for direct visualization, we captured images of the unprecedented solution‐state structures of a tetramolecular antiparallel and (3+1)‐type G‐quadruplex intermediates, such as G‐hairpin and G‐triplex, with nanometer precision. No such structural information was reported previously with any direct or indirect technique, solution or solid‐state, single‐molecule or bulk studies, and at any resolution. Based on our results, we proposed a folding mechanism of these G‐quadruplexes.     

Tetraphenylethene Derivatives with Different Numbers of Positively Charged Side Arms have Different Multimeric G‐Quadruplex Recognition Specificity

Some G‐rich sequences in the human genome have the potential to fold into a multimeric G‐quadruplex (G4) structure and the formation of telomeric multimeric G4 has been demonstrated. Searching for highly specific multimeric G4 ligands is important for structure probing and for study of the function of G‐rich gene sequences, as well as for the design of novel anticancer drugs. We found different numbers of positively charged side‐arm substituents confer tetraphenylethene (TPE) derivatives with different multimeric G4 recognition specificity. 1,2‐Bis{4‐[(trimethylammonium)butoxy]phenyl}‐1,2‐tetraphenylethene dibromide (DATPE), which contains two side arms and gives a fluorescence response to only multimeric G4, has a low level of cytotoxicity and little or no effect on multimeric G4 conformation or stability. These features make DATPE a promising fluorescent probe for detection of multimeric G4 specifically in biological samples or in vivo. 1,1,2,2‐Tetrakis{4‐[(trimethylammonium)butoxy]phenyl}tetraphenylethene tetrabromide (QATPE), which contains four side arms, has a lower level of specificity for multimeric G4 recognition compared to DATPE but its binding affinity to multimeric G4 is higher compared to other structural DNAs. Its high multimeric G4‐binding affinity, excellent multimeric G4‐stabilizing ability, and the promotion of parallel G4 formation make QATPE a good candidate for novel anticancer drugs targeting multimeric G4 specifically, especially telomeric multimeric G4. This work provides information that might aid the design of specific multimeric G4 probes and the development of novel anticancer drugs.     

Generation of 8‐oxo‐7,8‐dihydroguanine in G‐Quadruplexes Models of Human Telomere Sequences by One‐electron Oxidation

The mechanistic aspects of one‐electron oxidation of G‐quadruplexes in the basket (Na⁺ ions) and hybrid (K⁺ ions) conformations were investigated by transient absorption laser kinetic spectroscopy and HPLC detection of the 8‐oxo‐7,8‐dihydroguanine (8‐oxoG) oxidation product. The photo‐induced one‐electron abstraction from G‐quadruplexes was initiated by sulfate radical anions (SO₄˙^?) derived from the photolysis of persulfate ions by 308 nm excimer laser pulses. In neutral aqueous solutions (pH 7.0), the transient absorbance of neutral guanine radicals, G(‐H)˙, is observed following the complete decay of SO₄˙^? radicals (~10 μs after the actinic laser flash). In both basket and hybrid conformations, the G(‐H)˙ decay is biphasic with one component decaying with a lifetime of ~0.1 ms, and the other with a lifetime of 20–30 ms. The fast decay component (~0.1 ms) in G‐quadruplexes is correlated with the formation of 8‐oxoG lesions. We propose that in G‐quadruplexes, G(‐H)˙ radicals retain radical cation character by sharing the N1‐proton with the O⁶‐atom of G in the [G˙⁺: G] Hoogsteen base pair; this [G(‐H)˙: H⁺G G˙⁺: G] leads to the hydration of G˙⁺ radical cation within the millisecond time domain, and is followed by the formation of the 8‐oxoG lesions.     

Ion‐Responsive Hemin–G‐Quadruplexes for Switchable DNAzyme and Enzyme Functions

Programmed nucleic acid sequences undergo K⁺ ion‐induced self‐assembly into G‐quadruplexes and separation of the supramolecular structures by the elimination of K⁺ ions by crown ether or cryptand ion‐receptors. This process allows the switchable formation and dissociation of the respective G‐quadruplexes. The different G‐quadruplex structures bind hemin, and the resulting hemin–G‐quadruplex structures reveal horseradish peroxidase DNAzyme catalytic activities. The following K⁺ ion/receptor switchable systems are described: 1) The K⁺‐induced self‐assembly of the Mg²⁺‐dependent DNAzyme subunits into a catalytic nanostructure using the assembly of G‐quadruplexes as bridging unit. 2) The K⁺‐induced stabilization of the anti‐thrombin G‐quadruplex nanostructure that inhibits the hydrolytic functions of thrombin. 3) The K⁺‐induced opening of DNA tweezers through the stabilization of G‐quadruplexes on the “tweezers’ arms" and the release of a strand bridging the tweezers into a closed structure. In all of the systems reversible, switchable, functions are demonstrated. For all systems two different signals are used to follow the switchable functions (fluorescence and the catalytic functions of the derived hemin–G‐quadruplex DNAzyme).     

A Light‐up Logic Platform for Selective Recognition of Parallel G‐Quadruplex Structures via Disaggregation‐Induced Emission

The design of turn‐on dyes with optical signals sensitive to the formation of supramolecular structures provides fascinating and underexplored opportunities for G‐quadruplex (G4) DNA detection and characterization. Here, we show a new switching mechanism that relies on the recognition‐driven disaggregation (on‐signal) of an ultrabright coumarin‐quinazoline conjugate. The synthesized probe selectively lights‐up parallel G4 DNA structures via the disassembly of its supramolecular state, demonstrating outputs that are easily integrable into a label‐free molecular logic system. Finally, our molecule preferentially stains the G4‐rich nucleoli of cancer cells.