Quantitative Detection of G-Quadruplex DNA in Live Cells Based on Photon Counts and Complex Structure Discrimination

G-quadruplex DNA show structural polymorphism, leading to challenges in the use of selective recognition probes for the accurate detection of G-quadruplexes in vivo. Herein, we present a tripodal cationic fluorescent probe, NBTE , which showed distinguishable fluorescence lifetime responses between G-quadruplexes and other DNA topologies, and fluorescence quantum yield (Φ_f) enhancement upon G-quadruplex binding. We determined two NBTE -G-quadruplex complex structures with high Φ_f values by NMR spectroscopy. The structures indicated NBTE interacted with G-quadruplexes using three arms through π–π stacking, differing from that with duplex DNA using two arms, which rationalized the higher Φ_f values and lifetime response of NBTE upon G-quadruplex binding. Based on photon counts of FLIM, we detected the percentage of G-quadruplex DNA in live cells with NBTE and found G-quadruplex DNA content in cancer cells is 4-fold that in normal cells, suggesting the potential applications of this probe in cancer cell detection.     

DNA G-四链体识别探针研究进展

G-四链体是一种由富含鸟嘌呤核酸序列形成的独特的二级结构,广泛分布于真核生物基因组,如端粒DNA、r DNA和一系列基因中的启动子区域。G-四链体结构对很多重要的生理过程如基因的转录、复制、重组以及保持染色体的稳定性方面具有重要作用。G-四链体的特异、高灵敏检测将为进一步了解G-四链体结构在人类细胞基因组中的分布、功能和机制奠定基础,也可能为靶向G-四链体的肿瘤治疗方法提供新的思路。因而过去几十年人们一直致力于开发设计具有高选择性和高灵敏度的G-四链体识别探针,这些探针已经广泛应用于溶液中G-四链体的识别,而且具有良好的选择性。目前也有少数探针能够直接用于检测活体G-四链体结构。本文综述了一些常见的靶向G-四链体的小分子配体,以及它们在染色体和活体细胞G-四链体检测中的应用。笔者希冀本文能为设计识别G-四链体的高性能探针,进一步实现活细胞内G-四链体的检测提供借鉴。     

Analytical potential of the quadruplex DNA-based FRET probes

DNA exhibits structural flexibility and may adopt also tetraplex structures known as guanine-quadruplexes or G-quadruplexes. These G-quadruplexes have recently received great attention because G-rich sequences are often found in genome and because of their potential links to mechanisms that relate to cancer, HIV, and other diseases. The unique structure of quadruplexes has also stimulated development of new analytical and bioanalytical assays based on fluorescence resonance energy transfer (FRET). Intramolecular folding of a flexible single-stranded DNA molecule into a compact G-quadruplex is a structural transition leading to closer proximity of its 5'- and 3'-ends. Thus, labeling both ends of a DNA strand with donor and acceptor fluorophores enables monitoring the quadruplex formation process by means of the FRET signal. This review shows how FRET technique contributes to G-quadruplex research and focuses mainly on analytical applications of FRET-labeled quadruplexes. Applications include studies of structural transitions of quadruplexes, FRET-based selection of ligands that bind to quadruplexes, design of molecular probes for protein recognition and development of sensors for detection of potassium ions in aqueous solution.     

A far-red fluorescent probe for selective G-quadruplex DNA targeting

The development of rapid and simple approaches for detection of G-quadruplex DNA structures has attracted significant attention to disclose their diverse physiological and pathological functions. Thiazole orange (TO) is a common fluorescence probe used for the detection of G-quadruplexes. However, it still suffers from some common problems like non-selective for G-quadruplex and emission in the lower wavelength region of spectrum, thus hampering its further applications. Probes with turn-on fluorescence in the far-red region are highly sought-after due to minimal auto-fluorescence and cellular damage. In this paper, we described a far-red fluorescent probe (L-1) by introducing an amine group into styrylquinolinium scaffold. The experimental results indicated that L-1 exhibited significant fluorescence enhancement when treated with G-quadruplexes but retained weak fluorescence in the presence of duplex DNAs. In addition, this probe also displayed higher binding affinity for parallel G-quadruplexes. The characteristics of L-1 were further investigated with UV–vis spectrophotometry, fluorescence, circular dichroism, KI quenching, FID assay and molecular docking to validate optical photophysical properties, as well as the selectivity, sensitivity and detailed binding mode toward G-quadruplex DNAs.     

G-quadruplex DNA and ligand interaction in living cells using NMR spectroscopy

Gathering structural information from biologically relevant molecules inside living cells has always been a challenging task. In this work, we have used multidimensional NMR spectroscopy to probe DNA G-quadruplexes inside living Xenopus laevis oocytes. Some of these structures can be found in key regions of chromosomes. G-quadruplexes are considered potential anticancer therapeutic targets and several lines of evidence indirectly point out roles in key biological processes, such as cell proliferation, genomic instability or replication initiation. However, direct demonstrations of the existence of G-quadruplexes in vivo are scarce. Using SOFAST-HMQC type spectra, we probed a tetramolecular G-quadruplex model made of d(TG₄T)₄ inside living Xenopus laevis oocytes. Our observations lead us to conclude that the quadruplex structure is formed within the cell and that the intracellular environment preferentially selects a conformation that most resembles the one found in vitro under KCl conditions. We also show for the first time that specific ligands targeting G-quadruplexes can be studied using high resolution NMR directly inside living cells, opening new avenues to study ligand binding discrimination under physiologically relevant conditions with atomic detail.     

Triphenylmethane dyes as fluorescent probes for G-quadruplex recognition

Triphenylmethane (TPM) dyes normally render rather weak fluorescence due to easy vibrational deexcitation. However, when they stack onto the two external G-quartets of a G-quadruplex (especially intramolecular G-quadruplex), such vibrations will be restricted, resulting in greatly enhanced fluorescence intensities. Thus, TPM dyes may be developed as sensitive G-quadruplex fluorescent probes. Here, fluorescence spectra and energy transfer spectra of five TPM dyes in the presence of G-quadruplexes, single- or double-stranded DNAs were compared. The results show that the fluorescence spectra of four TPM dyes can be used to discriminate intramolecular G-quadruplexes from intermolecular G-quadruplexes, single- and double-stranded DNAs. The energy transfer fluorescence spectra and energy transfer fluorescence titration can be used to distinguish G-quadruplexes (including intramolecular and intermolecular G-quadruplexes) from single- and double-stranded DNAs. Positive charges and substituent size in TPM dyes may be two important factors in influencing the binding stability of the dyes and G-quadruplexes.     

Chiral metallo-supramolecular complexes selectively induce human telomeric G-quadruplex formation under salt-deficient conditions

Chiral molecular recognition of human telomeric DNA is important for rational drug design and developing structural probes of G-quadruplexes. Here we report that a chiral supramolecular complex can selectively induce human telomeric G-quadruplex formation and discriminate different G-quadruplex sequences under salt-deficient conditions studied by circular dichroism (CD), UV meltings, stopped-flow spectroscopy, fluorescence resonance energy transfer, enzyme cleavage, and gel electrophoresis. P-enantiomer induced G-quadruplex formation is fast and does not require a large excess of P enantiomer. More importantly, this chiral compound induces loop sequence-dependent G-quadruplex formation.     

Specific Binding of Anionic Porphyrin and Phthalocyanine to the G-Quadruplex with a Variety of <em>i</em><em>n Vitro</em> and<em> </em><em>i</em><em>n Vivo</em> Applications

The G-quadruplex, a four-stranded DNA structure with stacked guanine tetrads (G-quartets), has recently been attracting attention because of its critical roles in vitro and in vivo. In particular, the G-quadruplex functions as ligands for metal ions and aptamers for various molecules. Interestingly, the G-quadruplex can show peroxidase-like activity with an anionic porphyrin, iron (III) protoporphyrin IX (hemin). Importantly, hemin binds to G-quadruplexes with high selectivity over single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA), which is attributable to an electrostatic repulsion of phosphate groups in ssDNA and dsDNA. The G-quadruplex and hemin-G-quadruplex complex allow development of sensing techniques to detect DNA, metal ions and proteins. In addition to hemin, anionic phthalocyanines also bind to the G-quadruplex formed by human telomere DNA, specifically over ssDNA and dsDNA. Since the binding of anionic phthalocyanines to the G-quadruplex causes an inhibition of telomerase activity, which plays a role in the immortal growth of cancer cells, anionic phthalocyanines are promising as novel anticancer drug candidates. This review focuses on the specific binding of hemin and anionic phthalocyanines to G-quadruplexes and the applications in vitro and in vivo of this binding property.     

Cascaded strand displacement for non-enzymatic target recycling amplification and label-free electronic detection of microRNA from tumor cells

The monitoring of microRNA (miRNA) expression levels is of great importance in cancer diagnosis. In the present work, based on two cascaded toehold-mediated strand displacement reactions (TSDRs), we have developed a label- and enzyme-free target recycling signal amplification approach for sensitive electronic detection of miRNA-21 from human breast cancer cells. The junction probes containing the locked G-quadruplex forming sequences are self-assembled on the senor surface. The presence of the target miRNA-21 initiates the first TSDR and results in the disassembly of the junction probes and the release of the active G-quadruplex forming sequences. Subsequently, the DNA fuel strand triggers the second TSDR and leads to cyclic reuse of the target miRNA-21. The cascaded TSDRs thus generate many active G-quadruplex forming sequences on the sensor surface, which associate with hemin to produce significantly amplified current response for sensitive detection of miRNA-21 at 1.15 fM. The sensor is also selective and can be employed to monitor miRNA-21 from human breast cancer cells.     

Sequence-specific detection of nucleic acids utilizing isothermal enrichment of G-quadruplex DNAzymes

G-quadruplex DNAzymes are peroxidase-like complexes formed by nucleic acid G-quadruplexes and hemin. Various chemical sensors and biosensors have been developed, based on such DNAzymes. Here we report a novel, specific nucleic acid detection method utilizing the isothermal amplification strategy of G-quadruplex DNAzymes. In this method, an unlabeled oligonucleotide probe was used. The probing sequence of the oligonucleotide was in the form of a stem-loop structure. A G-rich sequence, containing three GGG repeats, was linked to the 5′-end of the stem-loop structure. In the presence of target, the probing sequence hybridized to the target, and a G_n (n ≥ 2) repeat was extended from its 3′-end. This G_n repeat, together with the three GGG repeats at the 5′-end, folded into a G-quadruplex, and displayed enhanced peroxidase acitivity upon hemin binding. Utilizing the dynamic binding interaction between the probe and its target, the enrichment of G-quadruplex DNAzymes was achieved. Using this method, simple, rapid and cost-effective nucleic acid detection could be achieved. This method displayed high target-length tolerance and good detection specificity; one-base mismatch could be judged easily, even by visual inspection. This method may be used as an auxiliary tool for amplified detection of specific DNA targets in some situations, in which isothermal detection is desirable.     

钾离子浓度依赖的铅离子稳定G-四链体构型转化

已有研究普遍认为铅离子(Pb²⁺)诱导富G适体链形成的G-四链体(Pb²⁺-G4)比钾离子(K⁺)诱导富G适体链形成的G-四链体(K⁺-G4)更为稳定,因而Pb²⁺可以置换K⁺-G4中的K⁺,而且K⁺的存在不影响Pb²⁺-G4的稳定性。有趣的是本研究发现K⁺ (20 μmol∙L⁻¹–1 mmol∙L⁻¹)不仅可以诱导10 µmol∙L⁻¹ Pb²⁺稳定的T2TT(Pb²⁺-T2TT,杂合G4结构)发生构型转换,甚至还可取代Pb²⁺-T2TT中的Pb²⁺,形成K⁺稳定的T2TT (K⁺-T2TT,平行G4结构),最终转化形成的K⁺-G4结构与单独K⁺诱导富G适体链形成K⁺-G4的构型基本一致。随后,进一步考察了另外7条富G适体链,发现这一转化过程具有一定的普适性。该研究结果为理解G4构型转化以及内嵌离子交换提供了新的视角,也为拓展G4在生化分析和生物领域的应用提供了新的理论基础。     

Switchable Optical Probes for Simultaneous Targeting of Multiple Anions

Traditional optical probes primarily work on the concept of one‐to‐one recognition strategy. Therefore, simultaneous detection of multiple anions is difficult using this kind of sensory systems. Similarly, designing of multi‐responsive array‐based materials is synthetically challenging as well as difficult to optimize. Thus, researchers across the globe became interested in developing single molecular probes, capable of detecting multiple anions (or anionic biomolecules) by simultaneously activating optically distinguishable output channels. Here, the modes of interaction largely depend on the structural features of the binding sites (cleft size, number of available coordination sites etc.), characteristics of the anions (ionic radius, hydration enthalpy, basicity, coordination number, pk_a of corresponding acids etc.) and the microenvironment around the probe molecules (micropolarity, viscosity, dielectric constant etc.) in the host matrix. In this review, we are mostly focusing on the structure‐activity relationships of such multiple anions sensing optical probes and their stimuli‐responsive properties.     

Target recycling amplification for label-free and sensitive colorimetric detection of adenosine triphosphate based on un-modified aptamers and DNAzymes

Based on target recycling amplification, the development of a new label-free, simple and sensitive colorimetric detection method for ATP by using un-modified aptamers and DNAzymes is described. The association of the model target molecules (ATP) with the corresponding aptamers of the dsDNA probes leads to the release of the G-quadruplex sequences. The ATP-bound aptamers can be further degraded by Exonuclease III to release ATP, which can again bind the aptamers of the dsDNA probes to initiate the target recycling amplification process. Due to this target recycling amplification, the amount of the released G-quadruplex sequences is significantly enhanced. Subsequently, these G-quadruplex sequences bind hemin to form numerous peroxidase mimicking DNAzymes, which cause substantially intensified color change of the probe solution for highly sensitive colorimetric detection of ATP down to the sub-nanomolar (0.33 nM) level. Our method is highly selective toward ATP against other control molecules and can be performed in one single homogeneous solution, which makes our sensing approach hold great potential for sensitive colorimetric detection of other small molecules and proteins.     

Selective probes targeting c-MYC Pu22 G-quadruplex and their application in live mice imaging

Several probes containing benzothiazole-guided conjugated systems(BGCS) were designed and synthesized, and two molecules(BGCS5 and BGCS6) of which were discovered as selective probes targeting c-MYC Pu22 G-quadruplex DNA. The fluorescence intensity of BGCS5 and BGCS6 in the presence of c-MYC Pu22 far exceeds that of the typical G4 probe TO1. Especially, the fluorescence of BGCS6 increased almost193-fold in the presence of c-MYC Pu22 G4 compared to that alone in aqueous buffer condition with almo...     

Label-Free and Simple G-quadruplex-based Turn-Off Fluorescence Assay for the Detection of Kanamycin

We have developed a label-free and turn-off fluorescence assay for the determination of kanamycin. The detection system consists of an aptamer for specifically recognizing kanamycin and two auxiliary probes functionalized with two GGG repeats at the 3′ or 5′ ends for signal reporting. Two probes both hybridize with the aptamer and then their G-rich sequences combine to form a G-quadruplex. When thioflavin T, a fluorophore, is bound to the G-quadruplex, the fluorescence intensity of the solution dramatically increases. Upon the addition of the kanamycin, the aptamer–kanamycin binding inhibits the hybridization of two probes and aptamer, and restrains the GGG repeats from getting closer to form the G-quadruplex structure, resulting a significant decrease in the fluorescence intensity. The proposed aptamer-based fluorescent sensing platform showed a linear relationship with the concentration of kanamycin from 0.6 to 20.0?nM. The detection limit was determined to be 0.33?nM. The sensing platform provides resistance to interferences from other antibiotics and can be used to efficiently recognize kanamycin in real samples.     

Recognize three different human telomeric G-quadruplex conformations by quinacrine

Recognition of different human telomeric G-quadruplex structures has been a very important task for developing anti-cancer drug design. However, it also is a very challenging question since multiple conformational isomers of telomeric G-quadruplexes coexist under some conditions. Here, three different conformations including parallel, antiparallel, and mixed-type telomeric G-quadruplex structures have been well recognized by quinacrine (QNA) through monitoring its absorption, fluorescence, and fluorescence lifetime spectra. The multiple structures of H22 G-quadruplexes under physiological K(+) conditions could also be easily determined to coexist as mixed-type and antiparallel G-quadruplexes. The recognition mechanism based on the different binding affinity and binding sites has been further elucidated by association with the nuclear magnetic resonance (NMR) results.     

Study on the recognition of G-quadruplexes by two stereoisomers of alkaloids

G-quadruplexes have been widely researched as new targets for cancer treatment owing to their non-canonical structure and crucial role in biological processes. Although attention has been paid to the development of selective G-quadruplex ligands, few studies have focused on the binding affinity of stereoisomers towards G-quadruplex, which will be conducive to support the optimal design of G-quadruplex ligands in future studies. Here, tetrandrine and isotetrandrine were used to study the binding affinity and difference of stereoisomers towards G-quadruplex structures. The results showed that tetrandrine had a high possibility of binding to the N-myc and Bcl-2 G-quadruplexes through hydrogen bonding, whereas the possibility of binding of isotetrandrine was low and it seemed to have no possibility of forming hydrogen bonds. Our study shows that optical isomerism of ligand molecules has an important effect on G-quadruplex recognition, which is helpful for the design of G-quadruplex ligands in future studies.

Graphical abstract

     

Solution NMR Structure of a Ligand/Hybrid-2-G-Quadruplex Complex Reveals Rearrangements that Affect Ligand Binding

Telomeric G-quadruplexes have recently emerged as drug targets in cancer research. Herein, we present the first NMR structure of a telomeric DNA G-quadruplex that adopts the biologically relevant hybrid-2 conformation in a ligand-bound state. We solved the complex with a metalorganic gold(III) ligand that stabilizes G-quadruplexes. Analysis of the free and bound structures reveals structural changes in the capping region of the G-quadruplex. The ligand is sandwiched between one terminal G-tetrad and a flanking nucleotide. This complex structure involves a major structural rearrangement compared to the free G-quadruplex structure as observed for other G-quadruplexes in different conformations, invalidating simple docking approaches to ligand–G-quadruplex structure determination.     

Parallel G-quadruplex Structures Increase Cellular Uptake and Cytotoxicity of 5-Fluoro-2′-deoxyuridine Oligomers in 5-Fluorouracil Resistant Cells

Fluoropyrimidines, such as 5-fluorouracil (5-FU) and related prodrugs have been considered first-line chemotherapy agents for the treatment of colorectal cancer. However, poor specificity and tumor cell resistance remain major limiting bottlenecks. G-quadruplexes, have been suggested as preferred nanostructures for enhancing cellular uptake mediated by G-quadruplex binding proteins which are abundant at the membranes of some tumor cells. In the current study, we propose a new strategy to deliver 5-fluoro-2′-deoxyuridine (5-FdU) monophosphate, the main active drug from 5-FU derivatives that may circumvent the cellular mechanisms of FU-resistant cancer cells. Two G-quadruplexes delivery systems containing four and six G-tetrads ((TG₄T) and (TG₆T)) linked to a FdU oligonucleotide were synthesized. Biophysical studies show that the G-quadruplex parallel structures are not affected by the incorporation of the 5 units of FdU at the 5’-end. Internalization studies confirmed the ability of such G-quadruplex nanostructures to facilitate the transport of the FdU pentamer and increase its cytotoxic effect relative to conventional FU drug in FU-resistant colorectal cancer cells. These results suggest that FdU oligomers linked to G-quadruplex parallel sequences may be a promising strategy to deliver fluoropyrimidines to cancer cells.