Impact of loop length and duplex extensions on the design of hybrid-type G-quadruplexes

A G-rich core sequence G3-TCA-G3-T1,2-G3-T1,2-G3 can be designed to fold into a parallel or into two different (3+1) hybrid-type G-quadruplexes, among them an elusive topology with one lateral followed by two propeller loops. Favored folds can be rationalized based on the number of intervening thymidines and on additional complementary flanking sequences.

Interference Reduction Biosensing Strategy for Highly Sensitive microRNA Detection

MicroRNAs are potential biomarkers for human cancers and other diseases due to their roles as post-transcriptional regulators for gene expression. However, the detection of miRNAs by conventional methods such as RT-qPCR, in situ hybridization, northern blot-based platforms, and next-generation sequencing is complicated by short length, low abundance, high sequence homology, and susceptibility to degradation of miRNAs. In this study, we developed a nicking endonuclease-mediated interference reduction rolling circle amplification (NEM-IR-RCA) strategy for the ultrasensitive and highly specific detection of miRNA-21. This method exploits the advantages of the optical properties of long-lived iridium(III) probes, in conjunction with time-resolved emission spectroscopy (TRES) and exponential rolling circle amplification (E-RCA). Under the NEM-IR-RCA-based signal enhancement processes, the limit of detection of miRNA-21 was down to 0.0095 fM with a linear range from 0.05 to 100 fM, which is comparable with the conventional RT-qPCR. Unlike RT-qPCR, the strategy was performed at a lower and constant temperature without heating/cooling cycles and reverse transcription. The strategy could clearly discriminate between matched and mismatched targets, demonstrating high specificity. Moreover, the potential application of this method was demonstrated in cancer cells and mouse serum samples, showing good agreement with RT-qPCR results. Apart from miRNA-21 detection, this platform could be also adapted for detecting other miRNAs, such as let-7a and miRNA-22, indicating its excellent potential for biomedical research and clinical diagnostics.

Label free detection of auramine O by G-quadruplex-based fluorescent turn-on strategy

Auramine o (AO) is a synthetic dye used in paper and textile industries. Although it has been an unauthorized food additive in many countries due to its toxic and carcinogenic possibility, its illegal uses have been detected in certain food products such as pasta, semolina and spices and also in pharmaceuticals. The presence of AO in food products should be monitored, therefore, to minimize the negative health effects on consumers. In this study, a simple, highly sensitive and selective label free detection method was investigated for AO by G-quadruplex-based fluorescent turn-on strategy. The optimum fluorescent detection assay was achieved with a specific G-quadruplex DNA sequence, c-myc, at 400 nM in Tris-HCl buffer at pH 7.4. The linearity of fluorescence intensity depending on AO concentration ranged from 0 to 0.07 µM and LOD and LOQ were 3 nM and 10 nM, respectively. The G-quadruplex-based detection assay was highly specific for AO as compared to other two synthetic food colorings and successfully applied to determine AO in pasta, bulgur and curry powder with recoveries in the range from 70.33% to 106.49%. This G-quadruplex-based label free detection assay has a significant potential to be used in the detection of AO in food products.

Zinc(ii), copper(ii) and cadmium(ii) complexes as fluorescent chemosensors for cations

The fluorescence chemosensing behavior of Zn(ii), Cu(ii), and Cd(ii) based complexes toward cations has been described. Cation detection via conventional mechanisms, metal-metal exchange and chemodosimetric approaches along with the importance of metal ions and the scope, significance, and challenges with regard to the detection of cations by metal complex based probes will be discussed in detail. The fundamentals of photophysical behavior and mechanisms involved in the fluorescence detection of analytes will also be described. This article provides a detailed overview of Zn(ii), Cu(ii), and Cd(ii) based complexes as fluorescent probes for cations, together with essential discussions pertaining to detection mechanisms.

DNA bioassays based on the fluorescence 'turn off' of silver nanocluster beacon

Recognition and quantification of oligonucleotide sequences play important roles in medical diagnosis. In this study, a new fluorescent oligonucleotide-stabilized silver nanocluster beacon (NCB) probe was designed for sensitive detection of oligonucleotide sequence targets. This probe contained two tailored DNA strands. One strand was a signal probe strand containing a cytosine-rich strand template for fluorescent silver nanocluster (Ag NC) synthesis and a detection sections at each end. The other strand was a fluorescence enhancing strand containing a guanine-rich section for signal enhancement at one end and a linker section complementary to one end of the signal probe strand. After synthesis of the Ag NCs and hybridization of the two strands, the fluorescence intensity of the as-prepared silver NCB was enhanced 200-fold compared with the Ag NCs. Two NCBs were designed to detect two disease-related oligonucleotide sequences, and results indicated that the two target oligonucleotide sequences in the range 50.0-600.0 and 50.0-200.0 nM could be linearly detected with detection limits of 20 and 25 nM, respectively. The developed fluorescence method using NCBs for oligonucleotide sequence detection was sensitive, facile and had potential for use in bioanalysis and diagnosis.

Detecting the long non‑coding RNA signature related to spinal cord ependymal tumor subtype using a genome‑wide methylome analysis approach

Ependymoma is a type of intramedullary tumor that tends to occur in the adult spinal cord. Ependymoma affects the nervous system and has significant impacts on the quality of life, and it may lead to mortality. Previous studies have performed molecular classification of spinal cord ependymal tumors at the DNA methylation level. However, the DNA methylation status of non-coding regions in spinal cord ependymal tumors remains unclear. In the present study, a genome-wide methylome method was used to characterize the DNA methylation landscape of long non-coding RNAs (lncRNAs) in spinal cord ependymal tumor samples. The present study identified lncRNA signatures associated with tumor subtypes based on the methylation status of lncRNA promoters. The present results suggested that the identified lncRNA signatures were associated with cancer- or nervous system-related protein-coding genes. The majority of the identified lncRNAs was hypomethylated, and may have a role in spinal cord development. The present findings suggested that detection of tumor subtype-specific lncRNAs may facilitate the identification of novel diagnostic and therapeutic strategies to treat patients with spinal cord ependymal tumor.

Cyclometalated rhodium and iridium complexes with imidazole containing Schiff bases: Synthesis, structure and cellular imaging

Cyclometalated rhodium(III) and iridium(III) complexes (1-4) of two Schiff base ligands L1 and L2 with the general formula [M(ppy)2(Ln)]Cl {M = Rh, Ir; ppy = 2-phenylpyridine; n = 1, 2; L = Schiff base ligand} have been synthesized. The new ligands and the complexes have been characterized with spectroscopic techniques. Electrochemistry of the complexes revealed anodic behavior, corresponding to an M(III) to M(IV) oxidation. The X-ray crystal structures of complexes 2 and 4 have also been determined to interpret the coordination behavior of the complexes. Photophysical study shows that all the complexes display fluorescence at room temperature with quantum yield of about 3 × 10-2 to 5 × 10-2. The electronic absorption spectra of all the complexes fit well with the computational studies. Cellular imaging studies were done with the newly synthesized complexes. To the best of our knowledge, this is the first report of organometallic complexes of rhodium(III) and iridium(III) with Schiff base ligands explored for cellular imaging. Emphasis of this work lies on the structural features, photophysical behavior, cellular uptake and imaging of the fluorescent transition metal complexes.

Fluorescent C-NanoDots for rapid detection of BRCA1, CFTR and MRP3 gene mutations

The authors report on a fluorometric method for the rapid detection of BRCA1, CFRT and MRP3 gene mutations. These are associated with breast cancer, cystic fibrosis and autoimmune hepatitis diseases, respectively. Carbon nanodots with blue fluorescence (with excitation/emission maxima at 340/440 nm) were synthesized and characterized, and their interactions with DNA were investigated. Changes in the fluorescence intensity following interaction with ssDNA and dsDNA were used for specific DNA sequence of BRCA1, CFRT and MRP3 genes detection. The response to DNAs is linear up to 200 nM and the detection limit is 270 pM. The assay selectivity allows the detection of single gene mutations. Under optimum conditions, the assay can rapidly discriminate between wild type and mutated samples. Graphical abstract Schematic representation of fluorescence assay for rapid detection of gene mutation based on fluorescent carbon nanodots.

Impact of Small Molecules on Intermolecular G-Quadruplex Formation

We performed single molecule studies to investigate the impact of several prominent small molecules (the oxazole telomestatin derivative L2H2-6OTD, pyridostatin, and Phen-DC₃) on intermolecular G-quadruplex (i-GQ) formation between two guanine-rich DNA strands that had 3-GGG repeats in one strand and 1-GGG repeat in the other (3+1 GGG), or 2-GGG repeats in each strand (2+2 GGG). Such structures are not only physiologically significant but have recently found use in various biotechnology applications, ranging from DNA-based wires to chemical sensors. Understanding the extent of stability imparted by small molecules on i-GQ structures, has implications for these applications. The small molecules resulted in different levels of enhancement in i-GQ formation, depending on the small molecule and arrangement of GGG repeats. The largest enhancement we observed was in the 3+1 GGG arrangement, where i-GQ formation increased by an order of magnitude, in the presence of L2H2-6OTD. On the other hand, the enhancement was limited to three-fold with Pyridostatin (PDS) or less for the other small molecules in the 2+2 GGG repeat case. By demonstrating detection of i-GQ formation at the single molecule level, our studies illustrate the feasibility to develop more sensitive sensors that could operate with limited quantities of materials.

The presence of a single-nucleotide mismatch in linker increases the fluorescence of guanine-enhanced DNA-templated Ag nanoclusters and their application for highly sensitive detection of cyanide

Fluorescence of DNA-templated silver nanoclusters can be enhanced by more than 100-fold by placing the nanoclusters in proximity to guanine-rich DNA sequences after hybridization. We found that the fluorescence of the guanine-enhanced silver nanoclusters is not increased with the guanine-rich DNA sequence closer to the silver nanoclusters. By studying the different numbers of mismatches in the linker sequences, we found that the presence of a single-nucleotide mismatch in the linker increases fluorescence more than the complementary nucleotide. Further study indicated the mismatch position of the linker sequence also affects the fluorescence of the hybridized DNA-Ag NCs. The evidence reported here indicated that the mismatch of the linker sequence affects the fluorescence enhancement of guanine-enhanced silver nanoclusters. We also found that DNA-Ag NCs is an excellent fluorescence sensor for cyanide, as cyanide effectively quenches the fluorescence of NCs at a very low concentration with high selectivity. Cyanide in the range from 0.10 μM to 0.35 μM could be linearly detected, with a detection limit of 25.6 nM.

Label-free molecular probe based on G-quadruplex and strand displacement for sensitive and selective detection and naked eye discrimination of exon 2 deletion of AIMP2

Exon 2 deletion of aminoacyl tRNA synthetase complex-interacting multifunctional protein 2 (AIMP2) is a genetic deletion related to various cancers, for instance ovarian and lung cancers. It can be worked as an indicator of cancer for diagnosis of diseases. Here, we developed a label-free method based on the formation of split G-quadruplex in the presence of target DNA combined with strand displacement to detect exon 2 deletion of AIMP2 (DE2) sensitively and selectively. This method is easy-operating and cost-saving. Moreover, it has observed discrimination of gene deletion from wild-types by naked eyes. The results demonstrate that this strategy can be further used for the detection of different gene deletions to achieve early diagnosis of diseases and allow better prognosis.

Characterizations of distinct parallel and antiparallel G-quadruplexes formed by two-repeat ALS and FTD related GGGGCC sequence

The large expansion of GGGGCC (G4C2) repeats of the C9orf72 gene have been found to lead to the pathogenesis of devastating neurological diseases, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The structural polymorphisms of C9orf72 HRE DNA and RNA may cause aberrant transcription and contribute to the development of ALS and FTD. Here we showed that the two-repeat G4C2 DNA, d(G4C2)₂, simultaneously formed parallel and antiparallel G-quadruplex conformations in the potassium solution. We separated different folds of d(G4C2)₂ by anion exchange chromatography, followed with characterizations by circular dichroism and nuclear magnetic resonance spectroscopy. The parallel d(G4C2)₂ G-quadruplex folded as a symmetric tetramer, while the antiparallel d(G4C2)₂ adopted the topology of an asymmetric dimer. These folds are distinct from the antiparallel chair-type conformation we previously identified for the d(G4C2)₄ G-quadruplex. Our findings have demonstrated the conformational heterogeneity of the C9orf72 HRE DNA, and provided new insights into the d(G4C2)_n folding. Meanwhile, the purified d(G4C2)₂ G-quadruplex samples are suitable for further three-dimensional structure characterizations, which are required for the structure-based design of small molecules targeting ALS and FTD related C9orf72 HRE.

A molecular beacon based on DNA-templated silver nanoclusters for the highly sensitive and selective multiplexed detection of virulence genes

In this work, we develop a fluorescent molecular beacon based on the DNA-templated silver nanoclusters (DNA-Ag NCs). The skillfully designed molecular beacon can be conveniently used for detection of diverse virulence genes as long as the corresponding recognition sequences are embedded. Importantly, the constructed detection system allows simultaneous detection of multiple nucleic acids, which is attributed to non-overlapping emission spectra of the as-synthesized silver nanoclusters. Based on the target-induced fluorescence enhancement, three infectious disease-related genes HIV, H1N1, and H5N1 are detected, and the corresponding detection limits are 3.53, 0.12 and 3.95nM, respectively. This design allows specific, versatile and simultaneous detection of diverse targets with easy operation and low cost.

Detection of large deletion in human BRCA1 gene in human breast carcinoma MCF-7 cells by using DNA-Silver Nanoclusters

Here we describe a label-free detection strategy for large deletion mutation in breast cancer (BC) related gene BRCA1 based on a DNA-silver nanocluster (NC) fluorescence upon recognition-induced hybridization. The specific hybridization of DNA templated silver NCs fluorescent probe to target DNAs can act as effective templates for enhancement of AgNCs fluorescence, which can be used to distinguish the deletion of BRCA1 due to different fluorescence intensities. Under the optimal conditions, the fluorescence intensity of the DNA-AgNCs at emission peaks around 440 nm (upon excitation at 350 nm) increased with the increasing deletion type within a dynamic range from 1.0 × 10^-10 to 2.4 × 10^-6 M with a detection limit (LOD) of 6.4 × 10^-11 M. In this sensing system, the normal type shows no significant fluorescence; on the other hand, the deletion type emits higher fluorescence than normal type. Using this nanobiosensor, we successfully determined mutation using the non-amplified genomic DNAs that were isolated from the BC cell line.

Luminescent Strategies for Label-Free G-Quadruplex-Based Enzyme Activity Sensing

By catalyzing highly specific and tightly controlled chemical reactions, enzymes are essential to maintaining normal cellular physiology. However, aberrant enzymatic activity can be linked to the pathogenesis of various diseases. Therefore, the unusual activity of particular enzymes can represent testable biomarkers for the diagnosis or screening of certain diseases. In recent years, G-quadruplex-based platforms have attracted wide attention for the monitoring of enzymatic activities. In this Personal Account, we discuss our group's works on the development of G-quadruplex-based sensing system for enzyme activities by using mainly iridium(III) complexes as luminescent label-free probes. These studies showcase the versatility of the G-quadruplex for developing assays for a variety of different enzymes.

Interaction of an Iridium(III) Complex with G-Quadruplex DNA and Its Application in Luminescent Switch-On Detection of Siglec-5

Sialic acid (Sia) binding immunoglobulin (Ig)-like lectin-5 (Siglec-5) is a type-I transmembrane protein, and it has been demonstrated as a biomarker of granulocytic maturation and acute myeloid leukemia phenotype. Herein we aimed to construct a method that could sensitively detect Siglec-5 by taking advantage of the high affinity and selectivity of the K19 aptamer for its cognate target, and the selective interaction of luminescent iridium(III) transition metal complexes with G-quadruplex DNA. The iridium(III) complex 1 [Ir(tpyd)₂(2,9-dmphen)]PF₆ (where tpyd =2-(m-tolyl)pyridine; 2,9-dmphen =2,9-dimethyl-1,10-phenanthroline) was synthesized, and it displayed high luminescence for G-quadruplex DNA compared to dsDNA and ssDNA. Additionally, complex 1 exhibited a blue shift luminescence response to c-kit2 G-quadruplex, and the interaction between 1 and G-quadruplexes was discussed based on the results of G-tetrad assay, loop effect assay, and other assays. Then complex 1 was utilized to develop a G-quadruplex-based sensing platform for Siglec-5 in aqueous solution. Upon the addition of Siglec-5, the specific binding of the K19 aptamer sequence results in a conformational change that generates a split G-quadruplex structure, which is then recognized by the G-quadruplex-specific iridium(III) complex with an enhanced luminescent response. Futhermore, the use of the assay for detecting Siglec-5 in cellular debris was demonstrated.

Sequence-Specific Biosensing of DNA Target through Relay PCR with Small-Molecule Fluorophore

Polymerase chain reaction coupled with signal generation offers sensitive recognition of target DNA sequence; however, these procedures require fluorophore-labeled oligonucleotide probes and high-tech equipment to achieve high specificity. Therefore, intensive research has been conducted to develop reliable, convenient, and economical DNA detection methods. The relay PCR described here is the first sequence-specific detection method using a small-molecule fluorophore as a sensor and combines the classic 5'-3' exonuclease activity of Taq polymerase with an RNA mimic of GFP to build a label-free DNA detection platform. Primarily, Taq polymerase cleaves the 5' noncomplementary overhang of the target specific probe during extension of the leading primer to release a relay oligo to initiate tandem PCR of the reporting template, which encodes the sequence of RNA aptamer. Afterward, the PCR product is transcribed to mRNA, which could generate a fluorescent signal in the presence of corresponding fluorophore. In addition to high sensitivity and specificity, the flexibility of choosing different fluorescent reporting signals makes this method versatile in either single or multiple target detection.

A luminescent G-quadruplex-selective iridium(iii) complex for the label-free detection of lysozyme

A novel Ir(iii) complex 1 displays high selectivity for the G-quadruplex, and was used to establish a label-free G-quadruplex-based detection platform for lysozyme in buffer.

A Luminescent Cocaine Detection Platform Using a Split G-Quadruplex-Selective Iridium(III) Complex and a Three-Way DNA Junction Architecture

In this study, a series of 10 in-house cyclometalated iridium(III) complexes bearing different auxiliary ligands were tested for their selectivity toward split G-quadruplex in order to construct a label-free switch-on cocaine detection platform employing a three-way junction architecture and a G-quadruplex motif as a signal output unit. Through two rounds of screening, we discovered that the iridium(III) complex 7 exhibited excellent selectivity toward the intermolecular G-quadruplex motif. A detection limit as low as 30 nM for cocaine can be achieved by this sensing approach with a linear relationship between luminescence intensity and cocaine concentration established from 30 to 300 nM. Furthermore, this sensing approach could detect cocaine in diluted oral fluid. We hope that our simple, signal-on, label-free oligonucleotide-based sensing method for cocaine using a three-way DNA junction architecture could act as a useful platform in bioanalytical research.

Label-free nucleic acids detection based on DNA templated silver nanoclusters fluorescent probe

Based on DNA templated Ag NCs (DNA/Ag NCs) fluorescent probe, a label-free fluorescent method was developed for the detection of clinical significant DNA fragments from human immunodeficiency virus type 1 (HIV-1) DNA. Firstly, a hairpin probe, containing target DNA recognition sequence and guanine-rich sequence, was designed to hybridize with the target DNA and form a blunt 3'-terminus DNA duplex. Then, exonuclease III (Exo III) was employed to stepwise hydrolyze the mononucleotides from formed blunt 3'-terminus DNA duplex, releasing the target DNA and guanine-rich sequence. Finally, DNA/Ag NCs fluorescent probe was introduced to hybridize with the guanine-rich sequence, leading to an enhanced fluorescence signal for detection. The proposed method could detect as low as 2.9×10(-10) mol L(-1) HIV-1 DNA and exhibited excellent selectivity against mismatched target DNA. Furthermore, the method possessed perfect recoveries in cells lysate and human serum, showing potential to be used in biological samples.

Enzyme-mediated single-nucleotide variation detection at room temperature with high discrimination factor

We demonstrate a new powerful tool to detect single-nucleotide variation in DNA at room temperature with high selectivity, based on predetermined specific interactions between Lambda exonuclease and a chemically modified DNA substrate structure which comprises two purposefully introduced mismatches and a covalently attached fluorophore. The fluorophore not only acts as a signal reporter in the detection system, but also plays a notable role in the specific molecular recognition between the enzyme and the probe/target hybrid substrate. The method is single-step, rapid, and can be easily adapted to different high-throughput micro-devices without the need for temperature control.

Versatile G-quadruplex-mediated strategies in label-free biosensors and logic systems

This review addresses how G-quadruplex (G4)-mediated biosensors convert the events of target recognition into a measurable physical signal. The application of label-free G4-strategies in the construction of logic systems is also discussed.

A label-free fluorescent molecular switch for a DNA hybridization assay utilizing a G-quadruplex-selective auramine O

A G-quadruplex molecular switch (G4-MS) assembled using auramine O and the G-rich single stranded DNA is developed for a DNA assay.

Miniaturized paper-based gene sensor for rapid and sensitive identification of contagious plant virus

Plant viruses cause significant production and economic losses in the agricultural industry worldwide. Rapid and early identification of contagious plant viruses is an essential prerequisite for the effective control of further spreading of infection. In this work, we describe a miniaturized paper-based gene sensor for the rapid and sensitive identification of a contagious plant virus. Our approach makes use of hybridization-mediated target capture based on a miniaturized lateral flow platform and gold nanoparticle colorimetric probes. The captured colorimetric probes on the test line and control line of the gene sensor produce characteristic red bands, enabling visual detection of the amplified products within minutes without the need for sophisticated instruments or the multiple incubation and washing steps performed in most other assays. Quantitative analysis is realized by recording the optical intensity of the test line. The sensor was used successfully for the identification of banana bunchy top virus (BBTV). The detection limit was 0.13 aM of gene segment, which is 10 times higher than that of electrophoresis and provides confirmation of the amplified products. We believe that this simple, rapid, and sensitive bioactive platform has great promise for warning against plant diseases in agricultural production.

Group 9 organometallic compounds for therapeutic and bioanalytical applications

CONSPECTUS: Compared with organic small molecules, metal complexes offer several distinct advantages as therapeutic agents or biomolecular probes. Carbon atoms are typically limited to linear, trigonal planar, or tetrahedral geometries, with a maximum of two enantiomers being formed if four different substituents are attached to a single carbon. In contrast, an octahedral metal center with six different substituents can display up to 30 different stereoisomers. While platinum- and ruthenium-based anticancer agents have attracted significant attention in the realm of inorganic medicinal chemistry over the past few decades, group 9 complexes (i.e., iridium and rhodium) have garnered increased attention in therapeutic and bioanalytical applications due to their adjustable reactivity (from kinetically liable to substitutionally inert), high water solubility, stability to air and moisture, and relative ease of synthesis. In this Account, we describe our efforts in the development of group 9 organometallic compounds of general form [M(C(∧)N)2(N(∧)N)] (where M = Ir, Rh) as therapeutic agents against distinct biomolecular targets and as luminescent probes for the construction of oligonucleotide-based assays for a diverse range of analytes. Earlier studies by researchers had focused on organometallic iridium(III) and rhodium(III) half-sandwich complexes that show promising anticancer activity, although their precise mechanisms of action still remain unknown. More recently, kinetically-inert group 9 complexes have arisen as fascinating alternatives to organic small molecules for the specific targeting of enzyme activity. Research in our laboratory has shown that cyclometalated octahedral rhodium(III) complexes were active against Janus kinase 2 (JAK2) or NEDD8-activating enzyme (NAE) activity, or against NO production leading to antivasculogenic activity in cellulo. At the same time, recent interest in the development of small molecules as modulators of protein-protein interactions has stimulated our research group to investigate whether kinetically-inert metal complexes could also be used to target protein-protein interfaces relevant to the pathogenesis of certain diseases. We have recently discovered that cyclometalated octahedral iridium(III) and rhodium(III) complexes bearing C(∧)N ligands based on 2-phenylpyridine could function as modulators of protein-protein interactions, such as TNF-α, STAT3, and mTOR. One rhodium(III) complex antagonized STAT3 activity in vitro and in vivo and displayed potent antitumor activity in a mouse xenograft model of melanoma. Notably, these studies were among the first to demonstrate the direct inhibition of protein-protein interfaces by kinetically-inert group 9 metal complexes. Additionally, we have discovered that group 9 solvato complexes carrying 2-phenylpyridine coligands could function as inhibitors and probes of β-amyloid fibrillogenesis. Meanwhile, the rich photophysical properties of iridium complexes have made them popular tools for the design of luminescent labels and probes. Luminescent iridium(III) complexes benefit from a high quantum yield, responsive emissive properties, long-lived phosphorescence lifetimes, and large Stokes shift values. Over the past few years, our group has developed a number of kinetically-inert, organometallic iridium(III) complexes bearing various C(∧)N and N(∧)N ligands that are selective for G-quadruplex DNA, which is a DNA secondary structure formed from planar stacks of guanine tetrads stabilized by Hoogsteen hydrogen bonding. These complexes were then employed to develop G-quadruplex-based, label-free luminescence switch-on assays for nucleic acids, enzyme activity, small molecules, and metal ions.

Photoluminescence properties of a novel cyclometalated iridium(III) complex with coumarin-boronate and its recognition of hydrogen peroxide

A novel neutral iridium(III) complex-based phosphorescent probe (Ir-2) for hydrogen peroxide (H2O2) has been designed and synthesized by incorporating a benzeneboronic acid pinacol ester (bpe) moiety into 3-(benzothiazol-2-yl)-7-hydroxy-coumarin (Bthc) as a cyclometalated ligand (Bthc-bpe). The photophysical behavior of Ir-2 was investigated by UV-Vis absorption spectroscopy, photoluminescence spectroscopy, and quantum mechanical calculations. The absorption spectra of the complex Ir-2 are dominated by the cyclometalated ligand; thus it shows an intense absorption band in the visible region at 460 nm with a molar extinction coefficient (ε) of about 3 × 10(4) M(-1) cm(-1), which is rarely found for typical polypyridine iridium(III) complexes. The complex Ir-2 displays efficient phosphorescent emission at 560 nm at room temperature originating from a mixed triplet metal-to-ligand charge-transfer ((3)MLCT, dπ(Ir) → π* (Bthc-bpe)) and triplet intraligand ((3)ILCT, π-π* (Bthc-bpe)) excited states as suggested by the DFT computational studies. Upon reaction with H2O2, the complex displays an emission decrease induced by an intense intermolecular aggregation due to the cleavage of the bulky benzeneboronic acid pinacol ester substituent, indicating that Ir-2 could act as an ON-OFF-type phosphorescent probe for H2O2. Additionally, selectivity studies reveal that the complex Ir-2 possesses high selectivity toward H2O2 over other reactive oxygen species (ROS).

A colorimetric chemosensor for Cu²⁺ ion detection based on an iridium(III) complex

We report herein the synthesis and application of a series of novel cyclometalated iridium(III) complexes 1-3 bearing a rhodamine-linked NˆN ligand for the detection of Cu(2+) ions. Under the optimised conditions, the complexes exhibited high sensitivity and selectivity for Cu(2+) ions over a panel of other metal ions, and showed consistent performance in a pH value range of 6 to 8. Furthermore, the potential application of this system for the monitoring of Cu(2+) ions in tap water or natural river water samples was demonstrated.

A fluorescent aptasensor for potassium ion detection-based triple-helix molecular switch

Here, a biosensor based on a quadruplex-forming aptamer for the determination of potassium ion (K(+)) is presented. The aptamer was used as a molecular recognition element; it was adjacent to two arm fragments and a dual-labeled oligonucleotide serving as a signal transduction probe (STP) that is complementary of the arm fragment sequence. In the presence of K(+), the aptamer was displaced from the STP, which was accompanied by decreased signal. The quenching percentage of fluorescence intensity was proportional to the concentration of K(+) in the range of 0.05 to 1.4mM. A detection limit of 0.014 mM was achieved. Furthermore, other metal ions, such as Na(+), Li(+), NH4(+), Mg(2+), and Ca(2+), caused no notable interference on the detection of K(+).

Visualization of Zn²⁺ ions in live zebrafish using a luminescent iridium(III) chemosensor

A novel luminescent cyclometalated iridium(III) complex-based chemosensor (1) bearing a zinc-specific receptor, tris(2-pyridylmethyl)amine, and the 3-phenyl-1H-pyrazole ligand has been designed and synthesized. Upon the addition of Zn(2+) ions to a solution of iridium(III) complex 1, a pronounced luminescence color change from blue to green can be observed, which may be attributed to the suppression of photoinduced electron transfer upon complexation of complex 1 with Zn(2+) ions. The interaction of iridium(III) complex 1 with Zn(2+) ions was investigated by UV-vis absorption titration, emission titration, and (1)H NMR titration. Furthermore, the iridium(III) complex 1 exhibited good selectivity for Zn(2+) over 13 other common metal ions, including K(+), Ag(+), Na(+), Ni(2+), Fe(3+), Hg(2+), Cd(2+), Mg(2+), Ca(2+), Cu(2+), Mn(2+), Co(2+), and Pb(2+) ions. The practical application of the iridium(III) complex 1 in visualizing intracellular Zn(2+) distribution in live zebrafish was also demonstrated.

Targeting unimolecular G-quadruplex nucleic acids: a new paradigm for the drug discovery?

INTRODUCTION

G-quadruplexes (G4s) are targets of great interest because of their roles in crucial biological processes, such as aging and cancer. G4s are based on the formation of G-quartets, stabilised by Hoogsteen-type hydrogen bonds and by interaction with cations between the tetrads. These biologically relevant conformations were first discovered in eukaryotic chromosomal telomeric DNA, but have also been found in the proximal location of promoters in a number of human genes. Therefore, the extensive analysis of an intriguing target could move towards the rational drug design of new selective anticancer agents.

AREAS COVERED

The authors review G4 structural characterisation, with detailed insight related to the polymorphism issue. The authors describe the topologically distinct G4 structural forms and the factors involved in their interconversion mechanisms, such as the sequence of the oligonucleotides, the strand stoichiometry and orientation, the syn-anti conformation of the guanine glycosidic bonds and the G4 loop types and the environmental factors. Furthermore, the authors report several studies related to folding and unfolding kinetic profiles in order to understand the conformational view of monomolecular G4 formations.

EXPERT OPINION

G4 unimolecular nucleic acids can be considered as valid targets for the rational drug development of novel anticancer agents. Structural biology represents an essential link between the biology and medicinal chemistry knowledge in this field. In silico methods have already been demonstrated to be useful, especially if well integrated with biophysical tests. If this proves successful, the G4-targeting paradigm could also be extended to drug discovery beyond neoplastic pathologies.

An oligonucleotide-based label-free luminescent switch-on probe for RNA detection utilizing a G-quadruplex-selective iridium(III) complex

We report herein the synthesis and application of a novel G-quadruplex-selective luminescent iridium(iii) complex for the construction of an oligonucleotide-based, label-free, rapid and convenient luminescent RNA detection platform.

Yolk-shell upconversion nanocomposites for LRET sensing of cysteine/homocysteine

The fabrication of lanthanide upconversion nanocomposites as probes has become a new research hotspot due to its special advantages via utilizing upconversion luminescence (UCL) as a detection signal. Herein, a hybrid organic dye modified upconversion nanophosphor is successfully developed as a nanoprobe for cysteine/homocysteine. Yolk-shell structured upconversion nanoparticles (YSUCNP) with lanthanide upconversion nanophosphor as moveable core and silica as mesoporous shell are synthesized, and a colorimetric chemodosimeter for cysteine/homocysteine is accommodated in the hollow cavities. Thus, cysteine/homocysteine can be quantitatively detected on the basis of luminescent resonance energy transfer (LRET) in a UCL turn-off pattern. The dye-loaded YSUCNP possess good dispersibility in aqueous solution; thus detection of the targeted molecule can be achieved in pure water. Cellular experiments carried out with laser-scanning upconversion luminescence microscopy further demonstrate that the dye-loaded YSUCNP can serve as an intracellular nanoprobe to detect cysteine/homocysteine. Moreover, this dye-loading protocol can be developed as a common approach to construct other chemodosimeter-modified UCNP hybrid nanoprobes, as proved by a UCL turn-on style sensor for cyanide.