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

COVID-19 detection using AIE-active iridium complexes

The highly contagious COVID-19, caused by the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is commonly diagnosed using reverse transcription polymerase chain reaction (RT-PCR). However, despite being highly sensitive, RT-PCR is also time consuming and quite complex, which limits its use for point-of-care (POC) testing. We have developed a simple single-step fluorescence assay for SARS-CoV-2 RNA detection based on the principle of aggregation-induced emission (AIE) using iridium complexes. Our smartly designed iridium probes fluorescently "turn-on" in the presence of SARS-CoV-2 RNA and give specific results at room temperature within 10 min. The lower limit of detection (LOD) is 1.84 genome copies per reaction, and the sensitivity and specificity of the assay in 20 clinical samples are found to be 90% and 80%, respectively.

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.

Photodynamic therapy with mitochondria-targeted biscyclometallated Ir(III) complexes. Multi-action mechanism and strong influence of the cyclometallating ligand

Photodynamic therapy is an alternative to classical chemotherapy due to its potential to reduce side effects by a controlled activation of a photosensitizer through local irradiation with light. The photosensitizer then interacts with oxygen and generates reactive oxygen species. Iridium biscyclometallated complexes are very promising photosensitizers due to their exceptional photophysical properties and their ability to target mitochondria. Four Ir(III) biscyclometallated complexes of formula [Ir(C^N)₂(N^N')]Cl, where N^N' is a ligand containing a benzimidazolyl fragment, have been synthesized and characterized. The C^N ligands were 2-phenylpyridinate (ppy) and 2-(2,4-difluorophenyl)pyridinate (dfppy). The complexes exhibited high photostability. The electrochemical and photophysical properties were modulated by both the cyclometallating and the ancillary ligands. The dfppy derivatives yielded the highest emission energy values, quantum yields of phosphorescence and excited state lifetimes. All complexes generated ¹O₂ in aerated solutions upon irradiation. Biological studies revealed that these complexes have a moderate cytotoxicity in the dark against different human cancer cell lines: prostate (PC-3), colon (CACO-2) and melanoma (SK-MEL-28), and against non-malignant fibroblasts (CCD-18Co). However, derivatives with ppy ligands ([1a]Cl, [2a]Cl) yielded a relevant photodynamic activity upon light irradiation (450 nm, 24.1 J cm^-2), with phototoxicity indexes (EC_50,dark/EC_50,light) of 20.8 and 17.3, respectively, achieved in PC-3 cells. Mechanistic studies showed that these complexes are taken up by the cells through endocytosis and preferentially accumulate in mitochondria. Upon photoactivation, the complexes induced mitochondrial membrane depolarization and DNA damage, thus triggering cell death, mainly by apoptosis. Complex [1a]Cl is also able to oxidize NADH. This mitochondria-targeted photodynamic mechanism greatly inhibited the reproductive capacity of cancer cells and provides a valuable alternative to traditional chemotherapy for the controlled treatment of cancer.

Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4 by anticancer drug epirubicin

Anthracycline anticancer drugs show multiple strategies of action on gene functioning by regulation of telomerase enzyme by apoptotic factors, e.g. ceramide level, p53 activity, bcl-2 protein levels, besides inhibiting DNA/RNA synthesis and topoisomerase-II action. We report binding of epirubicin with G-quadruplex (G4) DNA, [d-(TTAGGGT)]₄, comprising human telomeric DNA sequence TTAGGG, using ¹H and ³¹P NMR spectroscopy. Diffusion ordered spectroscopy, sequence selective changes in chemical shift (~0.33 ppm) and line broadening in DNA signals suggest formation of a well-defined complex. Presence of sequential nuclear Overhauser enhancements at all base quartet steps and absence of large downfield shifts in ³¹P resonances preclude intercalative mode of interaction. Restrained molecular dynamics simulations using AMBER force field incorporating intermolecular drug to DNA interproton distances, involving ring D protons of epirubicin depict external binding close to T1-T2-A3 and G6pT7 sites. Binding induced thermal stabilization of G4 DNA (~36 °C), obtained from imino protons and differential scanning calorimetry, is likely to come in the way of telomerase association with telomeres. The findings pave the way for drug-designing with modifications at ring D and daunosamine sugar.

One Terminal Guanosine Flip of Intramolecular Parallel G-Quadruplex: Catalytic Enhancement of G-Quadruplex/Hemin DNAzymes

Numerous studies have shown compelling evidence that incorporation of an inversion of polarity site (IPS) in G-rich sequences can affect the topological and structural characteristics of G-quadruplexes (G4s). Herein, the influence of IPS on the formation of a previously studied intramolecular parallel G4 of d(G₃ TG₃ TG₃ TG₃ ) (TTT) and its stacked higher-order structures is explored. Insertion of 3'-3' or 5'-5' IPS did not change the parallel folding pattern of TTT. However, both the species and position of the IPS in TTT have a significant impact on the G4 stability and end-stacking through the alteration of G4-G4 interfaces properties. The data demonstrate that one base flip in each terminal G-tetrad can stabilize parallel G4s and facilitate intermolecular packing of monomeric G4s. Such modifications can also enhance the fluorescence and enzymatic performances by promoting interactions between parallel G4s with N-methyl mesoporphyrin IX (NMM) and hemin, respectively.

Structural basis for stabilization of human telomeric G-quadruplex [d-(TTAGGGT)]4 by anticancer drug adriamycin

Besides inhibiting DNA duplication, DNA dependent RNA synthesis and topoisomerase-II enzyme action, anticancer drug adriamycin is found to cause telomere dysfunction and shows multiple strategies of action on gene functioning. We present evidence of binding of adriamycin to parallel stranded intermolecular [d-(TTAGGGT)]₄ G-quadruplex DNA comprising human telomeric DNA by proton and phosphorus-31 nuclear magnetic resonance spectroscopy. Diffusion ordered spectroscopy shows formation of complex between the two molecules. Changes in chemical shift and line broadening of DNA and adriamycin protons suggest participation of specific chemical groups/moieties in interaction. Presence of sequential nuclear Overhauser enhancements at all base quartet steps and absence of large downfield shifts in ³¹P resonances give clear proof of absence of intercalation of adriamycin chromophore between base quartets. Restrained molecular dynamics simulations using observed 15 short intermolecular inter proton distance contacts depict stacking of ring D of adriamycin with terminal G6 quartet by displacing T7 base and external groove binding close to T1-T2-A3 bases. The disappearance of imino protons monitored as a function of temperature and differential scanning calorimetry experiments yield thermal stabilization of 24 °C, which is likely to come in the way of telomerase association with telomeres. The findings pave the way for design of alternate anthracycline based drugs with specific modifications at ring D to enhance induced thermal stabilization and use alternate mechanism of binding to G-quadruplex DNA for interference in functional pathway of telomere maintenance by telomerase enzyme besides their well known action on duplex DNA. Communicated by Ramaswamy H. Sarma.

Luminescent detection of Ochratoxin A using terbium chelated mesoporous silica nanoparticles

This work represents the time-resolved fluorescence detection of Ochratoxin A (OTA), a highly toxic and commonly found toxin in food stuffs, by a terbium (Tb³⁺) chelated nanoparticle sensor with high sensitivity and remarkable selectivity. The coordination of OTA to Tb³⁺ center on nanoparticle surface resulted in the significant enhancement of the fluorescence signal in nanomolar concentrations with a detection limit of 20 ppb. In contrast, no enhancements were observed in the presence of other common mycotoxins such as Aflatoxin B1, Zearalenone, Citrinin and Patulin. The results indicate that the Tb³⁺ chelated nanoparticle sensor has great potential for applications in food analysis and safety.

An ultrasensitive electrochemical DNA sensing strategy free from pre-immobilization via G-quadruplex based homogenous proximity hybridization

Motivated by the desire for simple, rapid and highly sensitive DNA detection, we presented a signal-on electrochemical DNA (E-DNA) sensing strategy utilizing cooperative proximity hybridization based on a G-quadruplex (G4) probe labeled with the SH, which could specifically hybridize with its target DNA in homogenous solution. In the presence of target DNA, proximity hybridization was triggered to form a Y-shaped complex and the SH was released from G4 probe stem, companied by chemisorption on the electrode surface through Au-S binding when applied a positive potential, which brought Fc labeled on the signal probe close to the electrode surface. Thus, electrochemical signal dramatically increased, ensuring the highly sensitive "signal-on" assay. Such an E-DNA sensing strategy allows for ultrasensitive DNA detection with a detection limit as low as 2.82 × 10^-15 M and a wide linear response from 1.0 × 10^-9 to 1.0 × 10^-15 M. In addition, the powerful discriminating ability of the mismatched DNA from the perfect matched target DNA was also demonstrated. More importantly, this homogenous proximity hybridization strategy could expand to colorimetric assay by incorporating G4 probe with hemin to form DNAzyme, which could effectively catalyze ABTS to generate a visual color change. Taking the joint advantages of G4 stem-loop probe and homogenous proximity hybridization, this sensing strategy exhibits greatly enhanced sensitivity and excellent specificity, making it a promising strategy for point-of-care testing.

Dual mode of binding of anti cancer drug epirubicin to G-quadruplex [d-(TTAGGGT)]4 containing human telomeric DNA sequence induces thermal stabilization

Epirubicin exerts its anti cancer action by blocking DNA/RNA synthesis and inhibition of topoisomerase-II enzyme. Recent reports on its influence on telomere maintenance, suggest interaction with G-quadruplex DNA leading to multiple strategies of action. The binding of epirubicin with parallel stranded inter molecular G-quadruplex DNA [d-(TTAGGGT)]₄ comprising human telomeric DNA sequence TTAGGG was investigated by absorption, fluorescence, circular dichroism and nuclear magnetic resonance spectroscopy. The epirubicin binds as monomer to G-quadruplex DNA with affinity, K_b1 = 3.8 × 10⁶ M^-1 and K_b2 = 2.7 × 10⁶ M^-1, at two independent sites externally. The specific interactions induce thermal stabilization of DNA by 13.2-26.3 °C, which is likely to come in the way of telomere association with telomerase enzyme and contribute to epirubicin-induced apoptosis in cancer cell lines. The findings pave the way for drug designing in view of the possibility of altering substituent groups on anthracyclines to enhance efficacy using alternate mechanism of its interaction with G4 DNA, causing interference in telomere maintenance pathway by inducing telomere dysfunction.

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.

An iridium(III) complex/G-quadruplex ensemble for detection of ochratoxin A based on long-lifetime luminescent

A G-quadruplex-based platform has been developed for the time-resolved monitoring of ochratoxin A (OTA). The simple platform displays good sensitivity for OTA with a detection limit of 40 nM via steady-state emission spectroscopy. Notably, the platform showed a detection limit of 10.8 nM via time-resolved emission spectroscopy (TRES), which is about 4 times more sensitive than steady-state mode. Moreover, the probe showed excellent selectivity for OTA over other mycotoxins. Furthermore, OTA was successfully detected in actual herbal plant extracts samples. Our platform is the first to detect OTA using TRES to distinguish between the target signals versus the auto-fluorescence of real samples. This platform shows improved detection speed, accuracy and sensitivity with simple operation, low cost, and no requirement for complicated pre-processing.

Luminescent carbon nanodots based aptasensors for rapid detection of kanamycin residue

Despite the success in long-term storage of food and dietary products using antibiotics as supplements, enormous levels of their residues have remained as a significant health concern, leading to severe toxicity issues on consumption. Herein, we report an ultrasensitive and highly selective aptasensor based on carbon nanoparticles (CNPs) through a fluorescence-based aptamer-linked immunosorbent assay (FALIA) for rapid detection of kanamycin (KAA) residue. The fabricated CNP-aptasensor exhibited superior selectivity with exceptional photoluminescence properties. Under the optimal conditions, the linear equation of standard KAA solution was Y = -0.2279LogX+1.3648 (R = -0.9893) ranged from 10^-4 to 10^-7 ppb with excellent relative standard deviations (RSD) between 3.12 and 5.59 % (n = 3). Moreover, the limit of detection (LOD) was lower than 5.0 × 10^-8 ppb. Together, the excellent recovery and significant efficacy in the rapid detection of antibiotics at a low level in milk indicate that this fabricated CNP-aptasensor has a great potential in the establishment of an efficient antibiotic detector system in food and other nutraceutical industries.

Benzodifurans for biomedical applications: BZ4, a selective anti-proliferative and anti-amyloid lead compound

AIM

Our goal is to evaluate benzodifuran-based scaffolds for biomedical applications.

METHODOLOGY

We here explored the anticancer and anti-amyloid activities of a novel compound (BZ4) in comparison with other known benzodifuran analogs, previously studied in our group, and we have explored its ability to interact with different DNA model systems.

RESULTS

BZ4 shows antiproliferative activity on different cancer cells; does not affect noncancerous control cells and alters the aggregation properties of β-amyloid, as ascertained by circular dichroism, fluorescence spectroscopy and scanning electron microscopy analysis. An overall, qualitative picture on the mechanistic aspects related to the biological activities is discussed in light of the dynamic light scattering, UV, circular dichroism and fluorescence data, as well as of the metal ion-binding properties of BZ4.

Telomerase and poly(ADP-ribose) polymerase-1 activity sensing based on the high fluorescence selectivity and sensitivity of TOTO-1 towards G bases in single-stranded DNA and poly(ADP-ribose)

Telomerase and poly(ADP-ribose) polymerase-1 (PARP-1) are two potential cancer biomarkers and are closely related to tumor initiation and malignant progression. TOTO-1 is well-known for differentiating ss-DNA from ds-DNA because it is virtually non-fluorescent without DNA and exhibits very low fluorescence with ss-DNA, while it emits strong fluorescence with ds-DNA. In this paper, for the first time, it was found that TOTO-1 has high fluorescence selectivity and sensitivity towards the G bases in single-stranded DNA and poly(ADP-ribose) (PAR). Poly(dG) was used as the model target to explore its possible mechanism. Molecular dynamics (MD) simulation proved that intramolecular π-π stacking existed in TOTO-1 (in an aqueous solution), while intermolecular π-π stacking formed between TOTO-1 and poly(dG) in a similar way as that observed for dsDNA. Interestingly, telomerase and PARP-1 catalyzed the formation of G-rich DNA and PAR in vivo, respectively. Therefore, TOTO-1 was explored in detecting both of them, obtaining satisfactory results. To the best of our knowledge, no probe has been reported to recognize PAR. It is also the first time where telomerase is detected based on the specific recognition of G bases. Importantly, integrating multiple functions into one probe that can detect not only telomerase but also PARP-1 will significantly raise the specificity of screening cancer and decrease false positive proportion, which make TOTO-1 a promising candidate probe for clinical diagnosis and pharmaceutical screening.

Luminescent conjugates between dinuclear rhenium complexes and 17α-ethynylestradiol: synthesis, photophysical characterization, and cell imaging

New luminescent conjugates between dinuclear rhenium complexes and an estradiol moiety.

A novel iridium(iii) complex for sensitive HSA phosphorescence staining in proteome research

A novel iridium(iii) complex (Ir1) for sensitive HSA staining is reported. It is simpler and less time-consuming than Coomassie blue.

On-site detection of stacked genetically modified soybean based on event-specific TM-LAMP and a DNAzyme-lateral flow biosensor

Stacked genetically modified organisms (GMO) are becoming popular for their enhanced production efficiency and improved functional properties, and on-site detection of stacked GMO is an urgent challenge to be solved. In this study, we developed a cascade system combining event-specific tag-labeled multiplex LAMP with a DNAzyme-lateral flow biosensor for reliable detection of stacked events (DP305423× GTS 40-3-2). Three primer sets, both event-specific and soybean species-specific, were newly designed for the tag-labeled multiplex LAMP system. A trident-like lateral flow biosensor displayed amplified products simultaneously without cross contamination, and DNAzyme enhancement improved the sensitivity effectively. After optimization, the limit of detection was approximately 0.1% (w/w) for stacked GM soybean, which is sensitive enough to detect genetically modified content up to a threshold value established by several countries for regulatory compliance. The entire detection process could be shortened to 120min without any large-scale instrumentation. This method may be useful for the in-field detection of DP305423× GTS 40-3-2 soybean on a single kernel basis and on-site screening tests of stacked GM soybean lines and individual parent GM soybean lines in highly processed foods.

A MnO2 nanosheet-assisted GSH detection platform using an iridium(iii) complex as a switch-on luminescent probe

A rapid and sensitive detection platform for GSH has been constructed by combining a MnO₂ nanosheet with a luminescent iridium(iii) complex [Ir(Cl-phq)₂(Cl-phen)]⁺. The MnO₂ nanosheet was prepared by using a facile one-step approach and was characterized by TEM. The luminescence intensity of the detection platform responded linearly with the GSH concentration from 1 to 200 μM (R² = 0.9951), and the detection limit for GSH was 0.13 μM. More importantly, practical application of the detection platform for visualizing the intracellular GSH distribution in living zebrafish has also been demonstrated.

A NIR phosphorescent osmium(ii) complex as a lysosome tracking reagent and photodynamic therapeutic agent

In comparison to a ruthenium(ii) complex, an osmium(ii) complex has great advantages of NIR phosphorescence imaging and NIR photodynamic therapy.

The application of a G-quadruplex based assay with an iridium(iii) complex to arsenic ion detection and its utilization in a microfluidic chip

In this work, the iridium(iii) complex 1 was synthesized and employed in constructing an assay which is based on a G-quadruplex for detecting arsenic ions in aqueous solution.

Invading stacking primer: A trigger for high-efficiency isothermal amplification reaction with superior selectivity for detecting microRNA variants

Searching for a strategy to enhance the efficiency of nucleic acid amplification and achieve exquisite discrimination of nucleic acids at the single-base level for biological detection has become an exciting research direction in recent years. Here, we have developed a simple and universal primer design strategy which produces a fascinating effect on isothermal strand displacement amplification (iSDA). We refer to the resultant primer as "invading stacking primer (IS-Primer)" which is based on contiguous stacking hybridization and toehold-mediated exchange reaction and function by merely changing the hybridization location of the primer. Using the IS-Primer, the sensitivity in detecting the target miR-21 is improved approximately five fold compared with the traditional iSDA reaction. It was further demonstrated that the IS-Primer acts as an invading strand to initiate branch migration which can increase the efficiency of the untwisting of the hairpin probe. This effect is equivalent to reducing the free energy of the stem, and the technique shows superior selectivity for single-base mismatches. By demonstrating the enhanced effect of the IS-Primer in the iSDA reaction, this work may provide a potentially new avenue for developing more sensitive and selective nucleic acids assays.

Activity Enhancement of G-Quadruplex/Hemin DNAzyme by Flanking d(CCC)

G-quadruplex (G4)/hemin DNAzymes have been extensively applied in bioanalysis and molecular devices. However, their catalytic activity is still much lower than that of proteinous enzymes. The G4/hemin DNAzyme activity is correlated with the G4 conformations and the solution conditions. However, little is known about the effect of the flanking sequences on the activity, though they are important parts of G4s. Here, we report sequences containing d(CCC), flanked on both ends of the G4-core sequences remarkably enhance their DNAzyme activity. By using circular dichroism and UV-visible spectroscopy, the d(CCC) flanking sequences were demonstrated to improve the hemin binding affinity to G4s instead of increasing the parallel G4 formation, which might explain the enhanced DNAzyme activity. Meanwhile, the increased hemin binding ability promoted the degradation of hemin within the DNAzyme by H2O2. Furthermore, the DNAzyme with d(CCC) flanking sequences showed strong tolerance to pH value changes, which makes it more suitable for applications requiring wide pH conditions. The results highlight the influence of the flanking sequences on the DNAzyme activity and provide insightful information for the design of highly active DNAzymes.

Development of a luminescent G-quadruplex-selective iridium(III) complex for the label-free detection of adenosine

A panel of six luminescent iridium(III) complexes were synthesized and evaluated for their ability to act as G-quadruplex-selective probes. The novel iridium(III) complex 1 was found to be highly selective for G-quadruplex DNA, and was employed for the construction of a label-free G-quadruplex-based adenosine detection assay in aqueous solution. Two different detection strategies were investigated for adenosine detection, and the results showed that initial addition of adenosine to the adenosine aptamer gave superior results. The assay exhibited a linear response for adenosine in the concentration range of 5 to 120 μM (R(2) = 0.992), and the limit of detection for adenosine was 5 μM. Moreover, this assay was highly selective for adenosine over other nucleosides, and exhibited potential use for biological sample analysis.

Iridium(iii) complexes with 1,10-phenanthroline-based N^N ligands as highly selective luminescent G-quadruplex probes and application for switch-on ribonuclease H detection

A study was performed to investigate the relationship between molecular structure and G4 sensing ability for a series of iridium(iii) complexes. The complex7was used to construct a G4-based assay for RNase H.

Determination of cell metabolite VEGF₁₆₅ and dynamic analysis of protein-DNA interactions by combination of microfluidic technique and luminescent switch-on probe

In this paper, we rationally design a novel G-quadruplex-selective luminescent iridium (III) complex for rapid detection of oligonucleotide and VEGF165 in microfluidics. This new probe is applied as a convenient biosensor for label-free quantitative analysis of VEGF165 protein from cell metabolism, as well as for studying the kinetics of the aptamer-protein interaction combination with a microfluidic platform. As a result, we have successfully established a quantitative analysis of VEGF165 from cell metabolism. Furthermore, based on the principles of hydrodynamic focusing and diffusive mixing, different transient states during kinetics process were monitored and recorded. Thus, the combination of microfluidic technique and G-quadruplex luminescent probe will be potentially applied in the studies of intramolecular interactions and molecule recognition in the future.

Computational Prediction of RNA-Binding Proteins and Binding Sites

Proteins and RNA interaction have vital roles in many cellular processes such as protein synthesis, sequence encoding, RNA transfer, and gene regulation at the transcriptional and post-transcriptional levels. Approximately 6%–8% of all proteins are RNA-binding proteins (RBPs). Distinguishing these RBPs or their binding residues is a major aim of structural biology. Previously, a number of experimental methods were developed for the determination of protein–RNA interactions. However, these experimental methods are expensive, time-consuming, and labor-intensive. Alternatively, researchers have developed many computational approaches to predict RBPs and protein–RNA binding sites, by combining various machine learning methods and abundant sequence and/or structural features. There are three kinds of computational approaches, which are prediction from protein sequence, prediction from protein structure, and protein-RNA docking. In this paper, we review all existing studies of predictions of RNA-binding sites and RBPs and complexes, including data sets used in different approaches, sequence and structural features used in several predictors, prediction method classifications, performance comparisons, evaluation methods, and future directions.

G-quadruplex induced chirality of methylazacalix[6]pyridine via unprecedented binding stoichiometry: en route to multiplex controlled molecular switch

Nucleic acid based molecular device is a developing research field which attracts great interests in material for building machinelike nanodevices. G-quadruplex, as a new type of DNA secondary structures, can be harnessed to construct molecular device owing to its rich structural polymorphism. Herein, we developed a switching system based on G-quadruplexes and methylazacalix[6]pyridine (MACP6). The induced circular dichroism (CD) signal of MACP6 was used to monitor the switch controlled by temperature or pH value. Furthermore, the CD titration, Job-plot, variable temperature CD and ¹H-NMR experiments not only confirmed the binding mode between MACP6 and G-quadruplex, but also explained the difference switching effect of MACP6 and various G-quadruplexes. The established strategy has the potential to be used as the chiral probe for specific G-quadruplex recognition.

Using a sequence of estrogen response elements as a DNA aptamer for estrogen receptors in vitro

Estrogen receptors (ERs) are overexpressed in approximately 70% of breast cancer cases, and they play an important role in tumorigenesis. ERs are strong predictive factors for measuring responses to hormonal therapies. Aptamers are short and single stranded oligonucleotides that are able to recognize target molecules with high affinity. In the present study, we selected and synthesized an oligonucleotide, which has a similar sequence to estrogen response element in the Xenopus Vitellogenin A2 gene. The synthesized oligonucleotide was evaluated by using immunostaining of paraffin-embedded breast cancer tissues and treating MCF-7 human mammary carcinoma cell line in vitro. We found that the synthesized oligonucleotide had a high binding affinity to ER similar to estradiol. Using a specific anti-ER antibody as a standard control, we showed that the synthesized oligonucleotide specifically recognized and immunostained tumor cells of breast cancer without cross-reaction with normal tissues. The overall agreement of ER detection between the anti-ER antibody and the ER aptamer was 97.1% (kappa value=0.943; 95% CI=0.879-1.006; p<0.002). Similar to tamoxifen or fulvestrant, the oligonucleotide also had an inhibitory effect on cell proliferation of MCF-7 cell line in a dose- and time-dependent fashion but had no cytotoxic effect on human normal mammary epithelial cells. Therefore, the synthesized oligonucleotide may be used as an aptamer for immunostaining of paraffin-embedded tissue sections for breast cancer diagnosis, as well as a potential ER antagonist in the treatment of breast cancer.

A multiple amplification strategy for nucleic acid detection based on host-guest interaction between the β-cyclodextrin polymer and pyrene

A multiple amplification strategy has been developed for nucleic acid detection based on host-guest interaction between the β-cyclodextrin polymer (β-CDP) and pyrene. Briefly, the detection system consists of three parts: the polymerase and nicking enzyme-assisted isothermal strand displacement amplification (SDA) activated by a target DNA or microRNA; the exonuclease III-aided cyclic enzymatic amplification (CEA); and the fluorescence enhancement effect based on host-guest interaction between β-CDP and pyrene. This strategy showed a good positive linear correlation with target DNA concentrations in the range from 75 fM to 1 pM with a detection limit of 41 fM. Significantly, our amplification platform was further validated and evaluated successfully by assaying miRNA-21 in human serum. The proposed assay has great potential as a nucleic acid quantification method for use in biomedical research, clinical analysis and disease diagnostics.

Colorimetric and fluorescence detection of G-quadruplex nucleic acids with a coumarin–benzothiazole probe

A colorimetric and red-emitting fluorescent dual probe for G-quadruplexes was devised with a conjugated coumarin–benzothiazole scaffold.

A G-triplex luminescent switch-on probe for the detection of mung bean nuclease activity

A G-triplex luminescent switch-on probe for the detection of nuclease activity.

G-quadruplex-based logic gates for HgII and AgI ions employing a luminescent iridium(iii) complex and extension of metal-mediated base pairs by polymerase

We report herein the synthesis of a series of cyclometallated iridium(iii) complexes as luminescent G-quadruplex-selective probes to construct AND, OR and INHIBIT logic gates for the detection of Hg^II and Ag^I ions.

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.

A colorimetric and luminescent dual-modal assay for Cu(II) ion detection using an iridium(III) complex

A novel iridium(III) complex-based chemosensor bearing the 5,6-bis(salicylideneimino)-1,10-phenanthroline ligand receptor was developed, which exhibited a highly sensitive and selective color change from colorless to yellow and a visible turn-off luminescence response upon the addition of Cu(II) ions. The interactions of this iridium(III) complex with Cu2+ ions and thirteen other cations have been investigated by UV-Vis absorption titration, emission titration, and 1H NMR titration.