G-quadruplex Oligonucleotides Research Articles

Exploring the Relationship between G-Quadruplex Nucleic Acids and Plants: From Plant G-Quadruplex Function to Phytochemical G4 Ligands with Pharmaceutic Potential.

G-quadruplex (G4) oligonucleotides are higher-order DNA and RNA secondary structures of enormous relevance due to their implication in several biological processes and pathological states in different organisms. Strategies aiming at modulating human G4 structures and their interrelated functions are first-line approaches in modern research aiming at finding new potential anticancer treatments or G4-based aptamers for various biomedical and biotechnological applications. Plants offer a cornucopia of phytocompounds that, in many cases, are effective in binding and modulating the thermal stability of G4s and, on the other hand, contain almost unexplored G4 motifs in their genome that could inspire new biotechnological strategies. Herein, we describe some G4 structures found in plants, summarizing the existing knowledge of their functions and biological role. Moreover, we review some of the most promising G4 ligands isolated from vegetal sources and report on the known relationships between such phytochemicals and G4-mediated biological processes that make them potential leads in the pharmaceutical sector.

P04.19 A combined use of a G-quadruplex oligonucleotide (GQ) and neuro-inducing small molecules inhibit glioblastoma cell proliferation

Abstract BACKGROUND According to one of the theories, gliomas can occur as a result of dysregulation of stem cell division in the subventricular region of the brain. The CD133 membrane marker is a characteristic of both normal and tumor neural stem cells therefore it can be used to isolate a stem cell population from tumor tissue. Tumor cells actively proliferate which suggests that their possible differentiation may be achieved by inhibiting of their division as these two processes are mutually exclusive. For this purpose, G-quadruplex oligonucleotides together with neural-inducers such as a brain-derived neurotrophic factor (BDNF) may be used. MATERIAL AND METHODS Five cell cultures obtained from human glioblastoma tissues were analyzed for expression of CD133 using RT-qPCR. From cell culture with the highest level of CD133 using immunomagnetic separation CD133+ and CD133- cultures were received. CD133fr/peGFP-c1 recombinant DNA consisted of a CD133 second extracellular loop fragment and a peGFP-c1 vector was constructed to determine the localization of prominin-1, that is known as CD133 when found on cell membrane, using confocal microscopy. On chosen cell cultures an oligonucleotide bi-(AID-1-T) and its combination with BDNF were tested. The mechanism of GQ’s action is cytostatic and its non-toxicity properties were proved by flow cytometry. For evaluating the proliferative activity of cells MTT assay was performed on 10th and 20th days after exposure to the factors. RESULTS Cell culture G01 was chosen for further research as it had the highest level of the CD133. Colocalization of CD133 and GFP demonstrated a membrane localization of CD133 in cells with high expression level of this marker. MTT assay on 10th day after exposure to bi-(AID-1-T) as well as its combination with BDNF on cell culture G01 CD133- showed total inhibition of cell proliferation. The same combinations tested on G01 CD133+ cell culture demonstrated no difference in proliferative activity. After 20 days after exposure to bi-(AID-1-T) and combination of bi-(AID-1-T) with BDNF the significant decrease of G01 CD133+ cells’ proliferation was observed. When tested on whole glioblastoma cell culture G01 these combinations also showed significant inhibition of cell proliferation. CONCLUSION We showed that glioblastoma cells upon transfection with recombinant DNA, that contains a fragment of CD133, mainly have a membrane localization of this marker. It was observed that CD133+ cells are more stable to external influence that can be a proof of the fact that CD133 is charactered for glioblastoma stem cells. We tested the effect of an GQ bi-(AID-1-T) and its combination with BDNF and showed that BDNF is necessary for blocking proliferation of glioblastoma cells. Altogether, the results may be used for further research as it reveals a potential treatment for patients with glioblastoma. Grant №075-15-2020-809 (13.1902.21.0030).

Covalent Bi-Modular Parallel and Antiparallel G-Quadruplex DNA Nanocostructs Reduce Viability of Patient Glioma Primary Cell Cultures.

G-quadruplex oligonucleotides (GQs) exhibit specific anti-proliferative activity in human cancer cell lines, and they can selectively inhibit the viability/proliferation of cancer cell lines vs. non-cancer ones. This ability could be translated into a cancer treatment, in particular for glioblastoma multiform (GBM), which currently has a poor prognosis and low-efficiency therapeutic treatments. A novel bi-modular GQ, bi-(AID-1-T), a twin of the previously described three-quartet AID-1-T, was designed and studied in terms of both its structure and function. A covalent conjugation of two AID-1-Ts via three thymidine link, TTT, did not interfere with its initial GQ structure. A comparison of bi-(AID-1-T) with its mono-modular AID-1-T, mono-modular two-quartet HD1, and bi-modular bi-HD1, as well as conventional two-quartet AS1411, was made. Among the five GQs studied, bi-(AID-1-T) had the highest anti-proliferative activity for the neural cancer cell line U87, while not affecting the control cell line, human embryonic fibroblasts. GQs, for the first time, were tested on several primary glioma cultures from patient surgical samples. It turned out that the sensitivity of the patient primary glioma cultures toward GQs varied, with an apparent IC50 of less than 1 μM for bi-(AID-1-T) toward the most sensitive G11 cell culture (glioma, Grade III).

Fluorescent Visualization of Nucleolar G-Quadruplex RNA and Dynamics of Cytoplasm and Intranuclear Viscosity

The nucleolus, the locus of ribosome biogenesis, was found to be the predominant intracellular target of a new fluorescent probe, V-P1. In solution, the probe demonstrated both a selectivity to RNA...

Development of an Aptamer-Conjugated Polyrotaxane-Based Biodegradable Magnetic Resonance Contrast Agent for Tumor-Targeted Imaging.

Gadolinium-based magnetic resonance imaging (MRI) contrast agents with biodegradability, biosafety, and high efficiency are highly desirable for tumor diagnosis. Herein, a biodegradable, AS1411-conjugated, α-cyclodextrin polyrotaxane-based MRI contrast agent (AS1411-G2(DTPA-Gd)-SS-PR) was developed for targeted imaging of cancer. The polyrotaxane-based contrast agent was achieved by the complexation of α-cyclodextrin (α-CD) and a linear poly(ethylene glycol) (PEG) chain containing disulfide linkages at two terminals. The disulfides enable the dethreading of the polyrotaxane into excretable small units due to cleavage of the disulfide linkages by reducing agents such as intracellular glutathione (GSH). Furthermore, the second-generation lysine dendron conjugated with gadolinium chelates and AS1411, a G-quadruplex oligonucleotide that has high binding affinity to nucleolin generally presenting a high level on the surface of tumor cells, coupled to the α-CD via click chemistry. The longitudinal relaxivity of AS1411-G2(DTPA-Gd)-SS-PR (11.7 mM-1 s-1) was two times higher than the clinically used Gd-DTPA (4.16 mM-1 s-1) at 0.5 T. The in vitro degradability was confirmed by incubating with 10 mM 1,4-dithiothreitol (DTT). Additionally, the cytotoxicity, histological assessment, and gadolinium retention studies showed that the prepared polyrotaxane-based contrast agent had a superior biocompatibility and was predominantly cleared renally without long-term accumulation toxicity. Importantly, AS1411-G2(DTPA-Gd)-SS-PR displayed the enhanced performance in MRI of breast cancer cells in vitro as well as a subcutaneous breast tumor in vivo due to the targeting ability of the AS1411 aptamer. The enhanced performance was due to efficient multivalent interactions with tumor cells, producing faster accumulation and longer contrast imaging time at the tumor site. This work clearly confirms that the specially designed and fabricated α-CD-based polyrotaxane is a promising contrast agent with an excellent contrast imaging performance and biosafety for tumor MR imaging.

Redox Potentials and Electronic States of Iron Porphyrin IX Adsorbed on Single Crystal Gold Electrode Surfaces.

Metalloporphyrins are active sites in metalloproteins and synthetic catalysts. They have also been studied extensively by electrochemistry as well as being prominent targets in electrochemical scanning tunneling microscopy (STM). Previous studies of FePPIX adsorbed on graphite and alkylthiol modified Au electrodes showed a pair of reversible Fe(III/II)PPIX peaks at about -0.41 V (vs NHE) at high solution pH. We recently used iron protoporphyrin IX (FePPIX) as an intercalating probe for long-range electrochemical electron transfer through a G-quadruplex oligonucleotide (DNAzyme); this study disclosed two, rather than a single pair of voltammetric peaks with a new and dominating peak, shifted 200 mV positive relative to the ≈-0.4 V peak. Prompted by this unexpected observation, we report here a study of the voltammetry of FePPIX itself on single-crystal Au(111), (100), and (110) and polycrystalline Au electrode surfaces. In all cases the dominating pair of new Fe(III/II)PPIX redox peaks, shifted positively by more than 200 mV compared to those of previous studies appeared. This observation is supported by density functional theory (DFT) which shows that strong dispersion forces in the FePPIX/Au electronic interaction drive the midpoint potential toward positive values. The FePPIX spin states depend on interaction with the Au(111) interface, converting all the Fe(II)/(III)PPIX species into low-spin states. These results support electrochemical evidence for the nature of the electronic coupling between FePPIX and Au-surfaces, and the electronic states of adsorbate molecules, with a bearing also on recent reports of magnetic FePPIX/Au(111) interactions in ultrahigh vacuum (UHV).

Spectroscopic study of fluorescent probes based on G-quadruplex oligonucleotides labeled with ethynylpyrenyldeoxyuridine

The design, synthesis, and spectral properties of four pyrene labeled oligonucleotide probes with G-quadruplex structure (Tel22–Tpy, Tel22–Upy, Tel22–6Upy, Tel22–18Upy) based on the 22-mer human telomeric sequence (Tel22) have been reported. Pyrene labels in the form of ethynylpyrenyldeoxyuridine have been inserted efficiently into oligodeoxynucleotides probes using phosphoramidite chemistry. The probes exhibited abilities to fold into G-quadruplex structures and to bind metal cations (Na+ and K+). Folding properties of probes and their spectral behavior were examined by recording the UV–vis, fluorescence, and CD spectra as well as by analyzing melting profiles. Fluorescence characteristics and G-quadruplex folding of probes were also studied at the interface of cationic dioctadecyldimethylammonium bromide (DODAB) monolayer. Investigations included film balance measurements (π–A isotherms) and fluorescence spectra recording using a fiber optic accessory interfaced with a spectrofluorimeter.

Abstract 1521: hTERT G-quadruplex-targeted oligonucleotides inhibit glioblastoma cell growth

Abstract Glioblastoma is one of the most common and deadly forms of brain cancer, representing roughly 75% of all brain malignancies. These tumors generally have poor prognoses and are resistant to conventional therapy. It has recently been shown that as many as 80% of all glioblastomas contain mutations in a G-rich 68 base pair region of the hTERT promoter. hTERT is the catalytic subunit of telomerase, a holoenzyme responsible for lengthening the ends of chromosomes, thereby conferring immortality to cells. Normally, hTERT is not expressed in somatic cells and its expression is tightly controlled in stem cells. However, hTERT is upregulated in up-to 95% of human tumors and is considered a key activator of cancer progression and a sign of poor clinical outcome. Therefore, hTERT has been under investigation for the past decade as a potential therapeutic target. We have shown that the mutations in hTERT promoter occur in a G-rich region that is part of a silencer element which forms a secondary G-quadruplex structure required for function, and that these mutations destabilize the G-quadruplex structure, allowing hTERT expression. We have also demonstrated that oligonucleotides encoding the G-quadruplex forming sequence in the c-MYC promoter can stabilize the G-quadruplex structure and downregulate c-MYC expression. Therefore, we hypothesized that oligonucleotides targeted to the G-quadruplex of the hTERT promoter could downregulate this gene expression and inhibit glioblastoma cell proliferation in a similar manner. We designed several G-quadruplex-forming oligonucleotides covering the mutated sites in the hTERT promoter either in totality (68 nucleotides) or separately (25 nucleotides) to stabilize the G-quadruplex region. Two glioblastoma cell lines (A172 and U87) and one neuroblastoma cell line (CHP134) were exposed to these oligonucleotides and evaluated for growth inhibition using the MTT assay and for gene expression by QRT-PCR. All oligonucleotides tested were found to induce between 40 to 90% growth inhibition in the 3 cell lines. The cell growth inhibition was both time and dose dependent and showed effectiveness as early as 3 days suggesting that this effect is not solely due to telomere shortening. Four oligonucleotides with the most consistent efficacy in growth inhibition were evaluated for their effect on hTERT gene expression in the 3 cell lines at 4 day exposure and revealed that two of the G-quadruplex forming oligonucleotides significantly decreased hTERT expression compared to untreated cells. In conclusion, we have defined G-quadruplex oligonucleotides targeted to the hTERT promoter that downregulate hTERT gene expression and are effective growth inhibitors in glioblastoma cells. Our findings indicate that downregulation of hTERT with targeted oligonucleotides affects non-canonical functions of hTERT conferring an advantage to this therapeutic approach. Note: This abstract was not presented at the meeting. Citation Format: Alex West, Francine Rezzoug, Shelia D. Thomas, Donald M. Miller. hTERT G-quadruplex-targeted oligonucleotides inhibit glioblastoma cell growth [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1521. doi:10.1158/1538-7445.AM2017-1521

Conjugation of hemin to G-quadruplex forming oligonucleotide using click chemistry

Peroxidase-mimicking DNAzyme is one of the systems that recently gained a great interest. It has been successfully applied for designing numerous bioassays. The success of this system is connected to its advantages over a protein enzyme, horseradish peroxidase. Promising strategy for further improvement of performance of DNAzyme with peroxidase-like activity was proposed recently. It was based on the covalent attachment of hemin moiety to the G-quadruplex scaffold. We report here the first attempt of conjugating hemin to the G-quadruplex DNA using click chemistry approach. We modified hemin molecule through attachment of an azide-terminated linker to the porphyrin carboxylic group. Two click chemistry approaches were examined to conjugate the azide-modified hemin to a G-quadruplex oligonucleotide: copper-catalyzed and Cu-free cycloaddition reactions. Using Cu-free click reaction, we successfully synthesized G-quadruplex-hemin conjugate that exhibited promising peroxidase activity.

G-quadruplex oligonucleotide AS1411 as a cancer-targeting agent: Uses and mechanisms.

AS1411 is a 26-mer G-rich DNA oligonucleotide that forms a variety of G-quadruplex structures. It was identified based on its cancer-selective antiproliferative activity and subsequently determined to be an aptamer to nucleolin, a multifunctional protein that preferentially binds quadruplex nucleic acids and which is present at high levels on the surface of cancer cells. AS1411 has exceptionally efficient cellular internalization compared to non-quadruplex DNA sequences. Recent developments related to AS1411 will be examined, with a focus on its use for targeted delivery of therapeutic and imaging agents. Numerous research groups have used AS1411 as a targeting agent to deliver nanoparticles, oligonucleotides, and small molecules into cancer cells. Studies in animal models have demonstrated that AS1411-linked materials can accumulate selectively in tumors following systemic administration. The mechanism underlying the cancer-targeting ability of AS1411 is not completely understood, but recent studies suggest a model that involves: (1) initial uptake by macropinocytosis, a form of endocytosis prevalent in cancer cells; (2) stimulation of macropinocytosis by a nucleolin-dependent mechanism resulting in further uptake; and (3) disruption of nucleolin-mediated trafficking and efflux leading to cargoes becoming trapped inside cancer cells. Human trials have indicated that AS1411 is safe and can induce durable remissions in a few patients, but new strategies are needed to maximize its clinical impact. A better understanding of the mechanisms by which AS1411 targets and kills cancer cells may hasten the development of promising technologies using AS1411-linked nanoparticles or conjugates for cancer-targeted therapy and imaging. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.

Stable and Reusable Electrochemical Biosensor for Poly(ADP-ribose) Polymerase and Its Inhibitor Based on Enzyme-Initiated Auto-PARylation.

A stable and reusable electrochemical biosensor for the label-free detection of poly(ADP-ribose) polymerase (PARP) is designed in this work. C-kit-1, a thiol-modified G-quadruplex oligonucleotide, is first self-assembled on a gold electrode surface. The G-quadruplex structure of c-kit-1 can specifically tether and activate PARP, resulting in the generation of negatively charged poly(ADP-ribose) polymer (PAR). On the basis of electrostatic attraction, PAR facilitates the surface accumulation of positively charged electrochemical signal molecules. Through the characterization of electrochemical signal molecules, the label-free quantification of PARP is simply implemented. On the basis of the proposed method, selective quantification of PARP can be achieved over the linear range from 0.01 to 1 U with a calculated detection limit of 0.003U. Further studies also demonstrate the applicability of the proposed method to biosamples revealing the broad potential in practical applications. Furthermore, inhibitor of PARP has also been detected with this biosensor. Meanwhile, benefited from self-assembly on solid surface, this biosensor possesses two important features, i.e., reusability and stability, which are desirable in related biosensors.

Using gold aggregation to probe the inhibition and destruction of the G-quadruplex structure by TT-dimerization.

Thrombin binding G-quadruplex oligonucleotide containing two TT-dimer fragments and a gold attachment (ODN G1-G) was designed and synthesized with the aim of understanding the TT-dimer effect in G-quadruplex formation. Our results showed that TT-dimer mutation induced by UV light inhibits the formation of and even destroys the G-quadruplex structure, as confirmed by UV, CD and melting temperature measurements. The structural change resulting from TT-dimer formation with DNA was additionally probed and was found to be accompanied by significant gold aggregation that was observed in the form of a signal change from red to blue.

Inhibition of mdr1 by G-quadruplex oligonucleotides and reversal of paclitaxel resistance in human ovarian cancer cells.

The expression of ATP-dependent efflux pump P-glycoprotein (P-gp) in cancer cells generally results in multidrug resistance (MDR) to chemotherapeutic drugs, which is the main cause of chemotherapy failure in cancer treatment. The intracellular drug levels could be increased by some MDR reversal agents that inhibited the drug efflux activity of P-gp. The synthesized DNA nucleic acids of G-quadruplex represent a novel and unique class of anti-cancer agents. While there was no report on the roles of DNA G-quadruplex oligonucleotides (GQ-ODNs) in the MDR reversal, the present study was performed to investigate the ability of synthesized GQ-ODNs to reverse P-gp-mediated MDR and its mechanism in paclitaxel (PTX)-resistant SKOV3 (SKOV3/PTX) cells and their sensitive cell lines SKOV3. The ability of GQ-ODNs to reverse drug resistance was evaluated by MTS assay. The results showed that GQ-ODNs can reverse PTX resistance effectively. The potential of GQ-ODNs as reversal agents was evaluated with the nude mice tumor xenograft model and showed that the co-administration of the GQ-ODNs and PTX had better effects and was also more evident than treatment with only PTX. The P-gp expression was assessed by the Western blot; it showed that SKOV3/PTX cells showed highly expressed P-gp protein, while their sensitive cells scarcely showed P-gp. The presence of GQ-ODNs efficiently decreased the P-gp expression, showing that GQ-ODNs could reverse P-gp-mediated MDR by decreasing the expression of P-gp. This study indicated that GQ-ODNs could effectively reverse P-gp-mediated PTX resistance by inhibiting the expression of P-gp and by the co-administration of GQ-ODNs and PTX that could increase the apoptosis of SKOV3/PTX cells. Thus, the synthesized GQ-ODNs may be a potential inhibitor to overcome drug resistance.

Binding to G-quadruplex RNA activates the mitochondrial GTPase NOA1

NOA1 is an evolutionary conserved, nuclear encoded GTPase essential for mitochondrial function and cellular survival. The function of NOA1 for assembly of mitochondrial ribosomes and regulation of OXPHOS activity depends on its GTPase activity, but so far no ligands have been identified that regulate the GTPase activity of NOA1. To identify nucleic acids that bind to the RNA-binding domain of NOA1 we employed SELEX (Systemic Evolution of Ligands by EXponential Enrichment) using recombinant mouse wildtype NOA1 and the GTPase mutant NOA1-K353R. We found that NOA1 binds specifically to oligonucleotides that fold into guanine tetrads (G-quadruplexes). Binding of G-quadruplex oligonucleotides stimulated the GTPase activity of NOA1 suggesting a regulatory link between G-quadruplex containing RNAs, NOA1 function and assembly of mitochondrial ribosomes.

Transfecting RNA quadruplexes results in few transcriptome perturbations

Guanine-rich nucleic acid sequences can form four-stranded structures called G-quadruplexes. Previous studies showed that transfecting G-quadruplex DNA oligonucleotides inhibits proliferation in many cancer cell lines and can induce apoptosis. However, little is known about the effects of transfecting RNA quadruplexes. In this study, we transfected a G-quadruplex RNA oligonucleotide (GqRNA) into HEK293T cells and observed that it did not alter cell viability. Subsequent transcriptome expression profiling revealed that only two genes, EGR1 and FOS, were significantly altered in the presence of GqRNA (upregulated 2- to 4-fold). Sequence analysis showed that both genes contained putative quadruplex sequences (PQS) in their 3′-UTRs, immediately adjacent to the stop codons. Transfection of the EGR1 PQS as an RNA oligonucleotide also caused an increase in EGR1 expression. Similar motifs are found in a variety of genomes, but are relatively rare and have been missed by previous annotations. A bioinformatic analysis revealed stop codon-proximal enrichment of such motifs compared with the rest of the 3′-UTR, although these genes were not affected by RNA quadruplex transfection, and their function remains unknown. Overall, transfecting RNA quadruplexes results in relatively few alterations in gene expression.

Evidence of different G-quadruplex DNA binding with biogenic polyamines probed by electrospray ionization-quadrupole time of flight mass spectrometry, circular dichroism and atomic force microscopy

The binding properties of five G-quadruplex oligonucleotides (humtel24, k-ras32, c-myc22, c-kit1 and c-kit2) with polyamines have been investigated by electrospray ionization-quadrupole time of flight mass spectrometry, circular dichroism, melting temperature, atomic force microscopy (AFM) and molecular simulation. The MS results demonstrated that the polyamines and G-quadruplex DNA can form complexes with high affinity, and one molecule of G-quadruplex DNA can combine several molecules (1-5) of polyamines. The binding affinities of the polyamines to DNA were in the order of spermine > spermidine > putrescine. After binding with polyamines, the conformations of the G-quadruplex DNA were significantly changed, and spermine can induce the configurations of k-ras32 and c-kit1 to deviate from their G-quadruplex structures at high concentrations. In the presence of K(+), the conformations of G-quadruplex DNA were stabilized, while polyamines can also induced alterations of their configurations. Melting temperature experiments suggested that the Tm of the DNA-polyamine complexes obviously increased both in the absence and presence of K(+). The AFM results indicated that polyamines can induce aggregation of G-quadruplex DNA. Above results illustrated that the polyamines bound with the phosphate backbone and the base-pairs of G-quadruplex structures. Combining with the molecular simulation, the binding mode of the G-quadruplex DNA and polyamines were discussed. The results obtained would be beneficial for understanding the biological and physiological functions of polyamines and provide useful information for development of antitumor drugs.

Unlocking G-quadruplex: Effect of unlocked nucleic acid on G-quadruplex stability

G-quadruplexes are common structural motifs in aptamers. UNA or unlocked nucleic acid is the latest nucleic acid modification. We have attempted to evaluate the impact of UNA modification on the structure and stability of G-quadruplex oligonucleotides for application in aptamer design. We show using CD spectroscopy that UNA modifications can cause structural transitions in some cases although they retain the inherent G- quadruplex signature. From UV melting studies we showed a position dependent effect of UNA modifications such that quadruplexes with UNA modified loops are further stabilized whereas UNA modifications in stem of the G-quadruplex significantly destabilize the structure. The impact of UNA modification on different nucleobases is also investigated. From the analysis of UV melting results, thermodynamic profile was computed and it was concluded that all the sequences are stable at 37 °C. Finally, a greater serum stability of the modified oligonucleotides in comparison with unmodified ones is also demonstrated. Overall, the position dependent effect of single UNA substitutions was observed and analysed.

Naphthalene diimide scaffolds with dual reversible and covalent interaction properties towards G-quadruplex

Selective recognition and alkylation of G-quadruplex oligonucleotides has been achieved by substituted naphathalene diimides (NDIs) conjugated to engineered phenol moieties by alkyl-amido spacers with tunable length and conformational mobility. FRET-melting assays, circular dichroism titrations and gel electrophoresis analysis have been carried out to evaluate both reversible stabilization and alkylation of the G-quadruplex. The NDIs conjugated to a quinone methide precursor (NDI-QMP) and a phenol moiety by the shortest alkyl-amido spacer exhibited a planar and fairly rigid geometry (modelled by DFT computation). They were the best irreversible and reversible G-quadruplex binders, respectively. The above NDI-QMP was able to alkylate the telomeric G-quadruplex DNA in the nanomolar range and resulted 100–1000 times more selective on G-quadruplex versus single- and double-stranded oligonucleotides. This compound was also the most cytotoxic against a lung carcinoma cell line.

Emission lifetime study of fluorescence probes based on G-quadruplex oligonucleotides end-labeled with pyrene moieties

Fluorescence lifetime study of two probes abbreviated as Py-Htelom-Py and Py-TBA-Py, carrying pyrene moieties at both termini and sequences of Human telomere and Thrombin Binding Aptamer, respectively are reported. The effect of potassium ion on the photophysical processes was examined in order to elucidate factors that facilitate the production of excimer emission. Emission kinetics data indicated that the relative orientation of pyrene and neighboring nucleobase (guanine, adenine, thymine) plays a crucial role in determining both the rate of electron-transfer quenching of pyrene excited state and the efficiency of excimer emission.

Emission lifetime study of fluorescence probes based on G-quadruplex oligonucleotides end-labeled with pyrene moieties

Fluorescence lifetime study of two probes abbreviated as Py-Htelom-Py and Py-TBA-Py, carrying pyrene moieties at both termini and sequences of Human telomere and Thrombin Binding Aptamer, respectively are reported. The effect of potassium ion on the photophysical processes was examined in order to elucidate factors that facilitate the production of excimer emission. Emission kinetics data indicated that the relative orientation of pyrene and neighboring nucleobase (guanine, adenine, thymine) plays a crucial role in determining both the rate of electron-transfer quenching of pyrene excited state and the efficiency of excimer emission.