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1.
The interactions of three cationic distyryl dyes, namely 2,4‐bis(4‐dimethylaminostyryl)‐1‐methylpyridinium ( 1 a ), its derivative with a quaternary aminoalkyl chain ( 1 b ), and the symmetric 2,6‐bis(4‐dimethylaminostyryl)‐1‐methylpyridinium ( 2 a ), with several quadruplex and duplex nucleic acids were studied with the aim to establish the influence of the geometry of the dyes on their DNA‐binding and DNA‐probing properties. The results from spectrofluorimetric titrations and thermal denaturation experiments provide evidence that asymmetric (2,4‐disubstituted) dyes 1 a and 1 b bind to quadruplex DNA structures with a near‐micromolar affinity and a fair selectivity with respect to double‐stranded (ds) DNA [Ka(G4)/Ka(ds)=2.5–8.4]. At the same time, the fluorescence of both dyes is selectively increased in the presence of quadruplex DNAs (more than 80–100‐fold in the case of human telomeric quadruplex), even in the presence of an excess of competing double‐stranded DNA. This optical selectivity allows these dyes to be used as quadruplex‐DNA‐selective probes in solution and stains in polyacrylamide gels. In contrast, the symmetric analogue 2 a displays a strong binding preference for double‐stranded DNA [Ka(ds)/Ka(G4)=40–100), presumably due to binding in the minor groove. In addition, 2 a is not able to discriminate between quadruplex and duplex DNA, as its fluorescence is increased equally well (20–50‐fold) in the presence of both structures. This study emphasizes and rationalizes the strong impact of subtle structural variations on both DNA‐recognition properties and fluorimetric response of organic dyes.  相似文献   

2.
Small molecules are used in the G‐quadruplex (G4) research field in vivo and in vitro, and there are increasing demands for ligands that selectively stabilize different G4 structures. Thioflavin T (ThT) emits an enhanced fluorescence signal when binding to G4 structures. Herein, we show that ThT can be competitively displaced by the binding of small molecules to G4 structures and develop a ThT‐displacement high‐throughput screening assay to find novel and selective G4‐binding compounds. We screened approximately 28 000 compounds by using three different G4 structures and identified eight novel G4 binders. Analysis of the structural conformation and stability of the G4 structures in presence of these compounds demonstrated that the four compounds enhance the thermal stabilization of the structures without affecting their structural conformation. In addition, all four compounds also increased the G4‐structure block of DNA synthesis by Taq DNA polymerase. Also, two of these compounds showed selectivity between certain Schizosaccharomyces pombe G4 structures, thus suggesting that these compounds or their analogues can be used as selective tools for G4 DNA studies.  相似文献   

3.
The binuclear ruthenium complex [μ‐bidppz(phen)4Ru2]4+ has been extensively studied since the discovery of its unusual threading intercalation interaction with DNA, a binding mode with extremely slow binding and dissociation kinetics. The complex has been shown to be selective towards long stretches of alternating AT base pairs, which makes it interesting, for example, as a model compound for anti‐malaria drugs due to the high AT content of the genome of the malaria parasite P. falciparum. We have investigated the effect of bridging ligand structure on threading intercalation ability and found that length and rigidity as well as the size of the intercalated ring system are all factors that affect the rate and selectivity of the threading intercalation. In particular, we discovered a new DNA‐threading compound, [μ‐dppzip(phen)4Ru2]4+, which appears to be just at the border of being capable of threading intercalation and displays even greater selectivity for AT‐DNA than the parent compound, [μ‐bidppz(phen)4Ru2]4+.  相似文献   

4.
A dimeric calixarene, with an aliphatic C6‐bridge and six anilinium head groups at its upper rim, preferably complexes diphosphates and oligonucleotides with more than 10 bonds between both anionic moieties. Free binding energies correlate with the length of the aliphatic bridge in a roughly linear fashion. The binding event, which is monitored by fluorescence titrations and competition experiments, relies on Coulomb interactions, as opposed to a nonpolar variant with tert‐butyl instead of ammonium groups; here, hydrophobic forces prevail, rendering the calixarene dimer selective for less polar cofactors such as FAD. The best guest for the hexaanilinium dimer is found in ssDNA, which carries multiple copies of the optimal trinucleotide for maximum attraction towards the extended cationic host. The recognition event is also observed in the environment of a lipid monolayer, and provides a means to quantify dimer diphosphate interactions by measuring p/A shifts.  相似文献   

5.
G‐quadruplex DNA show structural polymorphism, leading to challenges in the use of selective recognition probes for the accurate detection of G‐quadruplexes in vivo. Herein, we present a tripodal cationic fluorescent probe, NBTE , which showed distinguishable fluorescence lifetime responses between G‐quadruplexes and other DNA topologies, and fluorescence quantum yield (Φf) enhancement upon G‐quadruplex binding. We determined two NBTE ‐G‐quadruplex complex structures with high Φf values by NMR spectroscopy. The structures indicated NBTE interacted with G‐quadruplexes using three arms through π–π stacking, differing from that with duplex DNA using two arms, which rationalized the higher Φf values and lifetime response of NBTE upon G‐quadruplex binding. Based on photon counts of FLIM, we detected the percentage of G‐quadruplex DNA in live cells with NBTE and found G‐quadruplex DNA content in cancer cells is 4‐fold that in normal cells, suggesting the potential applications of this probe in cancer cell detection.  相似文献   

6.
A desirable goal is to synthesize easily accessible and highly K+/Na+‐selective fluoroionophores to monitor physiological K+ levels in vitro and in vivo. Therefore, highly K+/Na+‐selective ionophores have to be developed. Herein, we obtained in a sequence of only four synthetic steps a set of K+‐responsive fluorescent probes 4 , 5 and 6 . In a systematic study, we investigated the influence of the alkoxy substitution in ortho position of the aniline moiety in π‐conjugated aniline‐1,2,3‐triazole‐coumarin‐fluoroionophores 4 , 5 and 6 [R=MeO ( 4 ), EtO ( 5 ) and iPrO ( 6 )] towards the K+‐complex stability and K+/Na+ selectivity. The highest K+‐complex stability showed fluoroionophore 4 with a dissociation constant Kd of 19 mm , but the Kd value increases to 31 mm in combined K+/Na+ solutions, indicating a poor K+/Na+ selectivity. By contrast, 6 showed even in the presence of competitive Na+ ions equal Kd values (KdK+=45 mm and KdK+/Na+=45 mm ) and equal K+‐induced fluorescence enhancement factors (FEFs=2.3). Thus, the fluorescent probe 6 showed an outstanding K+/Na+ selectivity and is a suitable fluorescent tool to measure physiological K+ levels in the range of 10–80 mm in vitro. Further, the isopropoxy‐substituted N‐phenylaza[18]crown‐6 ionophore in 6 is a highly K+‐selective building block with a feasible synthetic route.  相似文献   

7.
G‐quadruplexes (G4s) are peculiar DNA or RNA tertiary structures that are involved in the regulation of many biological events within mammalian cells, bacteria, and viruses. Although their role as versatile therapeutic targets has been emphasized for 35 years, G4 selectivity over ubiquitous double‐stranded DNA/RNA, as well as G4 differentiation by small molecules, still remains challenging. Here, a new amphiphilic dicyanovinyl‐substituted squaraine, SQgl , is reported to act as an NIR fluorescent light‐up probe discriminating an extensive panel of parallel G4s while it is non‐fluorescent in the aggregated state. The squaraine can form an unconventional sandwich π‐complex binding two quadruplexes, which leads to a strongly fluorescent (Φ F=0.61) supramolecular architecture. SQgl is highly selective against non‐quadruplex and non‐parallel G4 sequences without altering their topology, as desired for applications in selective in vivo high‐resolution imaging and theranostics.  相似文献   

8.
Pure and palladium‐loaded Co3O4 hollow hierarchical nanostructures consisting of nanosheets have been prepared by solvothermal self‐assembly. The nanostructures exhibited an ultrahigh response and selectivity towards p‐xylene and toluene. The responses (resistance ratio) of the palladium‐loaded Co3O4 hollow hierarchical nanostructures to 5 ppm of p‐xylene and toluene were as high as 361 and 305, respectively, whereas the selectivity values (response ratios) towards p‐xylene and toluene over interference from ethanol were 18.1 and 16.1, respectively. We attributed the giant response and unprecedented high selectivity towards methylbenzenes to the abundant adsorption of oxygen by Co3O4, the high chemiresistive variation in the Co3O4 nanosheets (thickness≈11 nm), and the catalytic promotion of the specific gas‐sensing reaction. The morphological design of the p‐type Co3O4 nanostructures and loading of the palladium catalyst have paved a new way to monitoring the most representative indoor air pollutants in a highly selective, sensitive, and reliable manner.  相似文献   

9.
The electronic excited states populated upon absorption of UV photons by DNA are extensively studied in relation to the UV‐induced damage to the genetic code. Here, we report a new unexpected relaxation pathway in adenine–thymine double‐stranded structures (AT)n. Fluorescence measurements on (AT)n hairpins (six and ten base pairs) and duplexes (20 and 2000 base pairs) reveal the existence of an emission band peaking at approximately 320 nm and decaying on the nanosecond time scale. Time‐dependent (TD)‐DFT calculations, performed for two base pairs and exploring various relaxation pathways, allow the assignment of this emission band to excited states resulting from mixing between Frenkel excitons and adenine‐to‐thymine charge‐transfer states. Emission from such high‐energy long‐lived mixed (HELM) states is in agreement with their fluorescence anisotropy (0.03), which is lower than that expected for π–π* states (≥0.1). An increase in the size of the system quenches π–π* fluorescence while enhancing HELM fluorescence. The latter process varies linearly with the hypochromism of the absorption spectra, both depending on the coupling between π–π* and charge‐transfer states. Subsequently, we identify the common features between the HELM states of (AT)n structures with those reported previously for alternating (GC)n: high emission energy, low fluorescence anisotropy, nanosecond lifetimes, and sensitivity to conformational disorder. These features are also detected for calf thymus DNA in which HELM states could evolve toward reactive π–π* states, giving rise to delayed fluorescence.  相似文献   

10.
Reported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH3)2}2(μ‐trans‐Pt(NH3)2{NH2(CH2)6NH2}2)]4+ (BBR3464, 1 ), [{trans‐PtCl(NH3)2}2(μ‐NH2(CH2)6NH2)]2+ (BBR3005, 2 ), [{trans‐PtCl(NH3)2}2(μ‐H2N(CH2)3NH2(CH2)4)]3+ (BBR3571, 3 ) and [{trans‐PtCl(NH3)2}2{μ‐H2N(CH2)3‐N(COCF3)(CH2)4}]2+ (BBR3571‐COCF3, 4 ) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [1H, 15N] HSQC NMR spectroscopy studies of the reaction of [15N]‐ 1 with the sequence 5′‐d{TATACATGTATA}2 allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)2. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [15N]‐ 2 . Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.  相似文献   

11.
We have developed a straightforward synthetic pathway to a set of six photoactivatable G‐quadruplex ligands with a validated G4‐binding motif (the bisquinolinium pyridodicarboxamide PDC‐360A) tethered through various spacers to two different photo‐cross‐linking groups: benzophenone and an aryl azide. The high quadruplex‐versus‐duplex selectivity of the PDC core was retained in the new derivatives and resulted in selective alkylation of two well‐known G‐quadruplexes (human telomeric G4 and oncogene promoter c‐myc G4) under conditions of harsh competition. The presence of two structurally different photoactivatable functions allowed the selective alkylation of G‐quadruplex structures at specific nucleobases and irreversible G4 binding. The topology and sequence of the quadruplex matrix appear to influence strongly the alkylation profile, which differs for the telomeric and c‐myc quadruplexes. The new compounds are photoactive in cells and thus provide new tools for studying G4 biology.  相似文献   

12.
A new biomolecular device for investigating the interactions of ligands with constrained DNA quadruplex topologies, using surface plasmon resonance (SPR), is reported. Biomolecular systems containing an intermolecular‐like G‐quadruplex motif 1 (parallel G‐quadruplex conformation), an intramolecular G‐quadruplex 2 , and a duplex DNA 3 have been designed and developed. The method is based on the concept of template‐assembled synthetic G‐quadruplex (TASQ), whereby quadruplex DNA structures are assembled on a template that allows precise control of the parallel G‐quadruplex conformation. Various known G‐quadruplex ligands have been used to investigate the affinities of ligands for intermolecular 1 and intramolecular 2 DNA quadruplexes. As anticipated, ligands displaying a π‐stacking binding mode showed a higher binding affinity for intermolecular‐like G‐quadruplexes 1 , whereas ligands with other binding modes (groove and/or loop binding) showed no significant difference in their binding affinities for the two quadruplexes 1 or 2 . In addition, the present method has also provided information about the selectivity of ligands for G‐quadruplex DNA over the duplex DNA. A numerical parameter, termed the G‐quadruplex binding mode index (G4‐BMI), has been introduced to express the difference in the affinities of ligands for intermolecular G‐quadruplex 1 against intramolecular G‐quadruplex 2 . The G‐quadruplex binding mode index (G4‐BMI) of a ligand is defined as follows: G4‐BMI=KDintra/KDinter, where KDintra is the dissociation constant for intramolecular G‐quadruplex 2 and KDinter is the dissociation constant for intermolecular G‐quadruplex 1 . In summary, the present work has demonstrated that the use of parallel‐constrained quadruplex topology provides more precise information about the binding modes of ligands.  相似文献   

13.
The use of stimuli to induce reversible structural transformations in metallosupramolecular systems is of keen interest to chemists seeking to mimic the way that Nature effects conformational changes in biological machinery. While a wide array of stimuli have been deployed towards this end, stoichiometric changes have only been explored in a handful of examples. Furthermore, switching has generally been between only two distinct states. Here we use a simple 2‐(1‐(pyridine‐4‐methyl)‐1H‐1,2,3‐triazol‐4‐yl)pyridine “click” ligand in combination with PdII in various stoichiometries and concentrations to quantitatively access and cycle between three distinct species: a [PdL2]2+ monomer, a [Pd2L2]4+ dimer, and a [Pd9L12]18+ cage.  相似文献   

14.
Telomerase inhibition is an attractive strategy for cancer chemotherapy. In the current study, we have synthesized and characterized two chiral ruthenium(II) complexes, namely, Λ‐[Ru(phen)2(p‐MOPIP)]2+ and Δ‐[Ru(phen)2(p‐MOPIP)]2+, where phen is 1,10‐phenanthroline and p‐MOPIP is 2‐(4‐methoxyphenyl)‐imidazo[4,5f][1,10]phenanthroline. The chiral selectivity of the compounds and their ability to discriminate quadruplex DNA were investigated by using UV/Vis, fluorescence spectroscopy, circular dichroism spectroscopy, fluorescence resonance energy transfer melting assay, polymerase chain reaction stop assay and telomerase repeat amplification protocol. The results indicate that the two chiral compounds could induce and stabilize the formation of antiparallel G‐quadruplexes of telomeric DNA in the presence or absence of metal cations. We report the remarkable ability of the two complexes Λ‐[Ru(phen)2(p‐MOPIP)]2+ and Δ‐[Ru(phen)2(p‐MOPIP)]2+ to stabilize selectively G‐quadruplex DNA; the former is a better G‐quadruplex binder than the latter. The anticancer activities of these complexes were evaluated by using the MTT assay. Interestingly, the antiproliferative activity of Λ‐[Ru(phen)2(p‐MOPIP)]2+ was higher than that of Δ‐[Ru(phen)2(p‐MOPIP)]2+, and Λ‐[Ru(phen)2(p‐MOPIP)]2+ showed a significant antitumor activity in HepG2 cells. The status of the nuclei in Λ/Δ‐[Ru(phen)2(p‐MOPIP)]2+‐treated HepG2 cells was investigated by using real‐time living cell microscopy to determine the effects of Λ/Δ‐[Ru(phen)2(p‐MOPIP)]2+ on intracellular accumulation. The results show that Λ/Δ‐[Ru(phen)2(p‐MOPIP)]2+ can be taken up by HepG2 cells and can enter into the cytoplasm as well as accumulate in the nuclei; this suggests that the nuclei were the cellular targets of Λ/Δ‐[Ru(phen)2(p‐MOPIP)]2+.  相似文献   

15.
A 13mer DNA duplex containing the artificial 4‐aminophthalimide:2,4‐diaminopyrimidine (4AP:DAP) base pair in the central position was characterized by optical and NMR spectroscopy. The fluorescence of 4AP in the duplex has a large Stokes shift of Δλ =124 nm and a quantum yield of Φ F=24 %. The NMR structure shows that two interstrand hydrogen bonds are formed and confirms the artificial base pairing. In contrast, the 4‐N ,N ‐dimethylaminophthalimide moiety prefers the syn conformation in DNA. The fluorescence intensity of this chromophore in DNA is very low and the NMR structure shows no significant interaction with DAP. Primer‐extension experiments with DNA polymerases showed that not only is the 4AP C nucleotide incorporated at the desired position opposite DAP in the template, but also that the polymerase is able to progress past this position to give the full‐length product. The observed selectivity supports the NMR results.  相似文献   

16.
A series of small diamidines with thiophene and modified N-alkylbenzimidazole σ-hole module represent specific binding to single G⋅C base pair (bp) DNA sequence. The variation of N-alkyl or aromatic rings were sensitive to microstructures of the DNA minor groove. Thirteen new compounds were synthesized to test their binding affinity and selectivity. The dicyanobenzimidazoles needed to synthesize the target diamidines were made via condensation/cyclization reactions of different aldehydes with different 3-amino-4-(alkyl- or phenyl-amino) benzonitriles. The final diamidines were synthesized using lithium bis-trimethylsilylamide (LiN[Si(CH3)3]2) or Pinner methods. The newly synthesized compounds showed strong binding and selectivity to AAAGTTT compared to similar sequences AAATTT and AAAGCTTT investigated by several biophysical methods including biosensor-SPR, fluorescence spectroscopy, DNA thermal melting, ESI-MS spectrometry, circular dichroism, and molecular dynamics. The binding affinity results determined by fluorescence spectroscopy are in accordance with those obtained by biosensor-SPR. These small size single G⋅C bp highly specific binders extend the compound database for future biological applications.  相似文献   

17.
The trinuclear platinum compound [{trans‐PtCl(NH3)2}2(μ‐trans‐Pt(NH3)2{NH2(CH2)6NH2}2)]4+ (BBR3464) belongs to the polynuclear class of platinum‐based anticancer agents. These agents form in DNA long‐range (Pt,Pt) interstrand cross‐links, whose role in the antitumor effects of BBR3464 predominates. Our results show for the first time that the interstrand cross‐links formed by BBR3464 between two guanine bases in opposite strands separated by two base pairs (1,4‐interstrand cross‐links) exist as two distinct conformers, which are not interconvertible, not only if these cross‐links are formed in the 5′‐5′, but also in the less‐usual 3′‐3’ direction. Analysis of the conformers by differential scanning calorimetry, chemical probes of DNA conformation, and minor groove binder Hoechst 33258 demonstrate that each of the four conformers affects DNA in a distinctly different way and adopts a different conformation. The results also support the thesis that the molecule of antitumor BBR3464 when forming DNA interstrand cross‐links may adopt different global structures, including different configurations of the linker chain of BBR3464 in the minor groove of DNA. Our findings suggest that the multiple DNA interstrand cross‐links available to BBR3464 may all contribute substantially to its cytotoxicity.  相似文献   

18.
By intelligently utilizing the different interacting strengths between different moieties according to the displacement method, general biosensors with aggregation‐induced emission (AIE) characteristics for biomacromolecules without selectivity were converted to excellent, highly selective probes for one specific biomacromolecule with the aid of graphene oxide (GO) in an aqueous medium. Importantly, thanks to the different interactions between the AIE molecule and biomacromolecules, just by simply changing the AIE molecule the sensing system could detect different types of biomacromolecules, thereby providing a new approach to the development of AIE‐based sensors with high selectivity and sensitivity. More specifically, the complex of A2HPS?HCl—a derivative of hexaphenylsilone (HPS) functionalized by two amino (A2) groups (N(CH2CH3)3)—and GO only gives an “off–on” response to DNA, with a detection limit of 2.3 μg mL?1 toward DNA‐CT (calf thymus); interestingly, the complex of TPE‐N2C4 (1,2‐bis{4‐[4‐(N,N,N‐triethylammonium)butoxy]phenyl}‐1,2‐diphenylethene dibromide) and GO could only detect the presence of bovine serum albumin (BSA), whereas other biomacromolecules, including DNA, RNA, and even other proteins have very little influence.  相似文献   

19.
Nucleic acids can adopt non‐duplex topologies, such as G‐quadruplexes in vitro. Yet it has been challenging to establish their existence and function in vivo due to a lack of suitable tools. Recently, we identified the triangulenium compound DAOTA‐M2 as a unique fluorescence probe for such studies. This probe's emission lifetime is highly dependent on the topology of the DNA it interacts with opening up the possibility of carrying out live‐cell imaging studies. Herein, we describe the origin of its fluorescence selectivity for G‐quadruplexes. Cyclic voltammetry predicts that the appended morpholino groups can act as intra‐ molecular photo‐induced electron transfer (PET) quenchers. Photophysical studies show that a delicate balance between this effect and inter‐molecular PET with nucleobases is key to the overall fluorescence enhancement observed upon nucleic acid binding. We utilised computational modelling to demonstrate a conformational dependence of intra‐molecular PET. Finally, we performed orthogonal studies with a triangulenium compound, in which the morpholino groups were removed, and demonstrated that this change inverts triangulenium fluorescence selectivity from G‐quadruplex to duplex DNA, thus highlighting the importance of fine tuning the molecular structure not only for target affinity, but also for fluorescence response.  相似文献   

20.
Anion‐selective solvent polymeric membrane based on hydrogen bond‐forming, neutral ionophores with amide or acyl‐hydrazine groups are described. The use of the two calix[4]arenes results in anion‐selective electrodes with a selectivity for phosphate. The electrodes of the optimum characteristic have the composition of 1 wt% ionophore, 66 wt% o‐NPOE, 33 wt% poly (vinyl chloride) (PVC) and TDMACl (15 or 30 mol% relative to the ionophore 1 and 2 , respectively). The optimized membrane electrodes show Nernstian responses towards monohydrogen phosphate (?29.1 and ?29.3 mV/decade) based on ionophore 1 and 2 , respectively, in a wide concentration range (1.0×10?5 to 1.0×10?2 or 1.0×10?5 to 1.0×10?1 M). The selectivity coefficients are determined with the fixed interference method and the activity ratio method. The electrodes display an anti‐Hofmeister series selectivity pattern and highly selective for HPO42? over Cl?, Br?, CH3COO?, NO3? and SO42?. The lifetime of the electrodes is at least 1 month and their response time is found to be 25 s. The proposed sensors could be put to analytical use both by direct potentiometry as well as potentiometric titration.  相似文献   

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