Interactions between meso-tetrakis(4-(N-methylpyridiumyl))porphyrin TMPyP4 and DNA G-quadruplex of telomeric repeated sequence TTAGGG

The binding properties between meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the parallel DNA G-quadruplex (G4) of telomeric repeated sequence 5′-TTAGGG-3′ have been characterized by means of circular dichroism,steady-state absorption,steady-state fluorescence and picosecond time-resolved fluorescence spectroscopies. The binding constant and the saturated binding number were determined as 1.29×106 (mol/L)-1 and 3,respectively,according to steady-state absorption spec-troscopy. Based on the findings by the use of time-resolved fluorescence spectroscopic technique,it is deduced that TMPyP4 binds to a DNA G-quadruplex with both the thread-intercalating and end-stacking modes and at the saturated binding state,one TMPyP4 molecule intercalates into the intervals of G-tetrads while the other two stack to the ends of the DNA G-quadruplex.     

Interactions between meso-tetrakis(4-(<Emphasis Type="Italic">N</Emphasis>-methylpyridiumyl))porphyrin TMPyP4 and DNA G-quadruplex of telomeric repeated sequence TTAGGG

The binding properties between meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the parallel DNA G-quadruplex (G4) of telomeric repeated sequence 5′-TTAGGG-3′ have been characterized by means of circular dichroism, steady-state absorption, steady-state fluorescence and picosecond time-resolved fluorescence spectroscopies. The binding constant and the saturated binding number were determined as 1.29×10⁶ (mol/L)⁻¹ and 3, respectively, according to steady-state absorption spectroscopy. Based on the findings by the use of time-resolved fluorescence spectroscopic technique, it is deduced that TMPyP4 binds to a DNA G-quadruplex with both the thread-intercalating and end-stacking modes and at the saturated binding state, one TMPyP4 molecule intercalates into the intervals of G-tetrads while the other two stack to the ends of the DNA G-quadruplex. Supported by the National Natural Science Foundation of China (Grant Nos. 20442004, 10576002 and 20703067)     

“Turn-off-on” fluorescent sensor for (N-methyl-4-pyridyl) porphyrin -DNA and G-quadruplex interactions based on ZnCdSe quantum dots

As a new detection model, the reversible fluorescence “turn-off-on” sensor based on quantum dots (QDs) has already been successfully employed in the detections of many biochemical materials, especially in the researches on the interactions between anticancer drugs. The previous studies, however, mainly focused on simple-structured oligonucleotides and Calf thymus DNA. G-quadruplex, an important target for anti-cancer drug with special secondary structure, has been stimulating increasing research interests. In this paper, we report a new detection method based on the fluorescence “turn-off-on” model with water-soluble ZnCdSe QDs as the fluorescent probe, to analyze the interactions between anticancer drug (N-methyl-4-pyridyl) porphyrin (TMPyP) and nucleic acid, especially the G-quadruplex. The fluorescence of QDs can be quenched by TMPyP via photo-induced electron transfer and fluorescence resonance energy transfer, while on the other hand, the combination between TMPyP and G-quadruplex releases QDs from their quenchers and thus recovers the fluorescence. Most importantly, the fluorescence “turn-off-on” model has been employed, for the first time, to analyze the impacts of special factors on the interaction between TMPyP and G-quadruplex. The excellent selectivity of the system has been verified in the studies of the interactions between TMPyP and different DNAs (double-stranded DNA, single-stranded G-quadruplex, and different types of G-quadruplexes) in Na⁺ or K⁺-containing buffer.     

Development of a light-up fluorescent probe for HRAS G-quadruplex DNA

The development of small-molecule G-quadruplex DNA probes has attracted significant attention in recent years. However, G-quadruplexes can display a wide variety of topologies, which process different structures and functions. Therefore, selective discrimination one G-quadruplex structure over another is promising. Herein, we reported the design, synthesis and biological evaluation of a long-chain fatty amine functionalized triphenylamine-quinolinium conjugate 1b. Significant enhancement of the fluorescence intensity (over 180 fold) was observed when 1b bound with HRAS G-quadruplex DNA, while much weaker enhancements were presented in the presence of other G-quadruplexes (45–90-fold) and single/double-stranded DNAs (less than 20-fold), indicating 1b had an excellent selectivity to HRAS. The details of the interactions were investigated by UV–Vis, FID and CD analysis. The results show 1b could interact and stabilize HRAS structure mainly by π-π stacking binding mode. The introduced amine chain of the structure core was found to be better in the terms of inducing selectivity toward G-quadruplex structure. In addition, the application of 1b as a fluorescent agent for living cell imaging was also demonstrated.     

利用对G-四链体环部的构型调节进行传感器的设计

对鸟嘌呤碱基G重复序列之间连接环结构对G-四链体形成的影响进行了研究。发现在连接环较长,DNA链不易形成G-四链体的情况下,可以通过将环序列设计成双链结构的方式促进G-四链体的重新形成。这就为传感器的设计提供了一个新途径,即可以利用目标分子对环部双链的调节作用控制G-四链体DNA酶的活性。为证明这一点,在双链区域引入T-T碱基错配,破坏双链结构使DNA链不能形成G-四链体。Hg2+对T-T错配的稳定作用可以促进双链结构的形成,DNA链重新折叠成G-四链体,得到的G-四链体与氯化血红素(Hemin)结合后形成具有过氧化物酶活性的G-四链体DNA酶,据此构建了Hg2+传感器。利用此传感器可在10~700 nmol/L范围内实现Hg2+的定量检测,检出限为8.7 nmol/L。在此基础上,利用半胱氨酸可以将Hg2+从T-Hg2+-T碱基对上竞争下来的能力,设计了一种半胱氨酸的检测方法。此方法可以在20~600 nmol/L范围内实现半胱氨酸的定量检测,检出限为14 nmol/L。     

Determination of Lead(II) by a Nitrocellulose Membrane Fluorescent Biosensor Based on G-Quadruplex Conformational Changes

A simple, label-free fluorescence method was developed for the sensitive determination of lead(II) using a nitrocellulose membrane biosensor. The surface of the nitrocellulose membrane was modified by glutaraldehyde to conjugate streptavidin, followed by the immobilization of a DNA probe via a biotin modifier. The biotinylated DNA probe can fold into a G-quadruplex structure in the presence of potassium ion that selectively binds to N-methyl mesoporphyrin IX and yields a strong fluorescence signal. The presence of lead(II) can induce a conformational change of the G-quadruplex to a more compact structure, which results in the release of potassium ion and N-methyl mesoporphyrin IX with a concomitant reduction of the fluorescence signal. The biosensor displayed a detection limit as low as 10 nM with excellent selectivity for lead(II) over other metal ions. The developed biosensor was employed for the determination of lead(II) in spiked river water.     

Conformational change in a urea catalyst induced by sodium cation and its effect on enantioselectivity of a Friedel-Crafts reaction

While developing bis-camphorsulfonyl urea as a hydrogen-bonding catalysts, we discovered that the native conformation of the catalyst is unsuitable for inducing enantioselectivity. By complexing the catalyst with weakly Lewis acidic sodium cations, we were able to change the conformation of the catalyst and attain a significant improvement in the selectivity. We provide structural information from X-ray crystallography to show that the uncomplexed catalyst is indeed in an unfavorable conformation. Infrared and Raman spectroscopic studies show that sodium binds the catalyst through the carbonyl and sulfonyl groups. Simulated IR and Raman spectra match well with the experimentally recorded spectra, thereby corroborating the proposed conformational change. This result shows that weak Lewis acids can be used to tune the conformation of hydrogen-bonding catalysts and enhance the selectivity of reaction catalyzed by these systems.     

Direct screening of G-quadruplex ligands from Kalopanax septemlobus (Thunb.) Koidz extract by high performance liquid chromatography

G-quadruplex DNA structure is considered to be a very attractive target for antitumor drug design due to its unique role in maintaining telomerase activities. Therefore, discovering ligands with high stability of G-quadruplex structure is of great interest. In this paper, high-performance liquid chromatography (HPLC) was used for fast screening of G-quadruplex ligands from the crude extract of Kalopanax septemlobus (Thunb.) Koidz, a traditional Chinese medicine. Four potent G-quadruplex ligands were firstly selected through HPLC by comparing the peak profiles and absorption intensity of the crude sample before and after interaction with G-quadruplex DNA. Then the target compounds were isolated and purified by high-speed countercurrent chromatography (HSCCC) for further confirmation of their stabilities of G-quadruplex by temperature-dependent circular dichroism (CD). Four compounds were isolated and identified as 2,4-dihydroxybenzoic acid (I), chlorogenic acid (II), caffeic acid (III) and 5-feruloylquinic acid (IV) each by MS and NMR. Finally, compound I, II, III were each proved to be potent G-quadruplex ligands by decreasing the peak intensity in HPLC chromatogram after complexation with G-quadruplex, which stabilize G-quadruplex by 7±2 °C, 10±2 °C, and 3±2 °C respectively, based on CD analyses. However, compound IV showed no G-quadruplex stability. The decrease of peak absorption intensity in HPLC chromatogram is the most important signal to find G-quadruplex ligands. This provides a very promising strategy for fast screening G-quadruplex ligands from natural plant extracts.     

Study on inclusion complexes of meso-tetrakis(2-thienyl)porphyrin and Cu-meso-tetrakis(2-thienyl)porphyrin with cyclodextrins by spectroscopy method

In phosphate buffer solution of pH5.4, the interaction of meso-tetrakis(2-thienyl)porphyrin(H₂TTP) and Cu-meso-tetrakis(2-thienyl)porphyrin(Cu-TTP) with α-cyclodextrin(α-CD), β-CD, γ-CD, heptakis(2,3,6-tri-O-methyl)-β-CD(TM-β-CD) has been studied by means of UV-vis, fluorescence and ¹HNMR spectroscopy, respectively. The H₂TTP and Cu-TTP can form 1:2 inclusion complexes with TM-β-CD and 1:1 inclusion complexes with the other three cyclodextrins. In this paper, the inclusion constants (K) of H₂TTP and Cu-TTP for the formation of the inclusion complexes have been estimated from the changes of absorbance and fluorescence intensity in phosphate buffer solution. The inclusive capabilities of different kinds of cyclodextrins are compared. The result shows that the inclusion ability of α-CD with H₂TTP and Cu-TTP is the strongest among the three native CDs. The inclusion ability of modified β-CD with H₂TTP and Cu-TTP is stronger, compared to the native β-CD, which indicates that the capacity matching plays a crucial role in the inclusion procedure except for the hydrophobic effect. In addition ¹HNMR spectra supports the inclusion conformation of the TM-β-CD-Cu-TTP inclusion complex, indicating the interaction mechanism of inclusion processes.     

Synthesis of a ruthenium(II) polypyridine complex with 1,10-phenanthrolineselenazole as ligand and investigation of its G-quadruplex DNA-binding properties

A new Ru(II) complex, [Ru(bpy)₂L](ClO₄)₂ (bpy?=?2,2′-bipyridine, L?=?1,10-phenanthrolineselenazole), has been synthesized and structurally characterized by elemental analysis, ESI-MS, and ¹H NMR. The interaction of human telomeric oligomer 5′-AG₃(T₂AG₃)₃-3′ with the Ru(II) complex was explored by competition FRET experiment, ?uorescence titration, circular dichroism spectroscopy, thermal denaturation, polymerase chain reaction stop assay, and TRAP assay. The Ru(II) complex can selectively bind to G-quadruplex DNA. The results indicated that the complex not only induces a remarkable conformational change of human telomeric DNA, but also has the ability to stabilize the G-quadruplex.     

Sensitive pseudobienzyme electrocatalytic DNA biosensor for mercury(II) ion by using the autonomously assembled hemin/G-quadruplex DNAzyme nanowires for signal amplification

Herein, a novel sensitive pseudobienzyme electrocatalytic DNA biosensor was proposed for mercury ion (Hg²⁺) detection by using autonomously assembled hemin/G-quadruplex DNAzyme nanowires for signal amplification. Thiol functionalized capture DNA was firstly immobilized on a nano-Au modified glass carbon electrode (GCE). In presence of Hg²⁺, the specific coordination between Hg²⁺ and T could result in the assembly of primer DNA on the electrode, which successfully triggered the HCR to form the hemin/G-quadruplex DNAzyme nanowires with substantial redox probe thionine (Thi). In the electrolyte of PBS containing NADH, the hemin/G-quadruplex nanowires firstly acted as an NADH oxidase to assist the concomitant formation of H₂O₂ in the presence of dissolved O₂. Then, with the redox probe Thi as electron mediator, the hemin/G-quadruplex nanowires acted as an HRP-mimicking DNAzyme that quickly bioelectrocatalyzed the reduction of produced H₂O₂, which finally led to a dramatically amplified electrochemical signal. This method has demonstrated a high sensitivity of Hg²⁺ detection with the dynamic concentration range spanning from 1.0 ng L⁻¹ to 10 mg L⁻¹ Hg²⁺ and a detection limit of 0.5 ng L⁻¹ (2.5 pM) at the 3S_blank level, and it also demonstrated excellent selectivity against other interferential metal ions.     

Multiplex binding modes of toluidine blue with calf thymus DNA and conformational transition of DNA revealed by spectroscopic studies

It is noteworthy to understand the details of interactions between antitumor drugs and DNA because the binding modes and affinities affect their antitumor activities. Here, The interaction of toluidine blue (TB), a potential antitumor drug for photodynamic therapy of tumor, with calf thymus DNA (ctDNA) was explored by UV–vis, fluorescence, circular dichroism (CD) spectroscopy, UV-melting method and surface-enhance Raman spectroscopy (SERS). The experimental results suggest that TB could bind to ctDNA via both electrostatic interaction and partial intercalation. The fluorescence quenching of TB by ctDNA was static and due to electron transfer from bases to the excited singlet state of TB. At low [TB]/[DNA] ratio, TB mainly partially intercalated into ctDNA resulting in the slight increase of base stacking degree; at high [TB]/[DNA] ratio, excessive TB externally stacked along the helix surface via coupling with partially intercalated ones, thereby inducing B-A transition of ctDNA. The conformational transition of DNA was confirmed by the obvious improvement of the thermal stability of ctDNA. The SERS spectra suggest that TB could partially intercalate into DNA basepairs with its ring C₁NC_1′ side buried.     

Label-free fluorescent probing of G-quadruplex formation and real-time monitoring of DNA folding by a quaternized tetraphenylethene salt with aggregation-induced emission characteristics

Biosensing processes such as molecular beacons require non-trivial effort to covalently label or mark biomolecules. We report here a label-free DNA assay system with a simple dye with aggregation-induced emission (AIE) characteristics as the fluorescent bioprobe. 1,1,2,2-Tetrakis[4-(2-bromoethoxy)phenyl]ethene is nonemissive in solution but becomes highly emissive when aggregated. This AIE effect is caused by restriction of intramolecular rotation, as verified by a large increase in the emission intensity by increasing viscosity and decreasing temperature of the aqueous buffer solution of 1,1,2,2-tetrakis[4-(2-triethylammonioethoxy)phenyl]ethene tetrabromide (TTAPE). When TTAPE is bound to a guanine-rich DNA strand (G1) via electrostatic attraction, its intramolecular rotation is restricted and its emission is turned on. When a competitive cation is added to the G1 solution, TTAPE is detached and its emission is turned off. TTAPE works as a sensitive poststaining agent for poly(acrylamide) gel electrophoresis (PAGE) visualization of G1. The dye is highly affinitive to a secondary structure of G1 called the G-quadruplex. The bathochromic shift involved in the G1 folding process allows spectral discrimination of the G-quadruplex from other DNA structures. The strong affinity of TTAPE dye to the G-quadruplex structure is associated with a geometric fit aided by the electrostatic attraction. The distinct AIE feature of TTAPE enables real-time monitoring of folding process of G1 in the absence of any pre-attached fluorogenic labels on the DNA strand. TTAPE can be used as a K+ ion biosensor because of its specificity to K+-induced and -stabilized quadruplex structure.     

Rhodamine B aggregation in self-assembled multilayers induced by polyelectrolyte and interfacial fluorescence recognition for DNA

Photophysical properties of Rhodamine B bound to water-soluble polyanion sodium poly(4-styrenesulfonate) (PSS) in solution and Quartz/APES/PSS/RB SAMs were investigated. Experiments showed that Rhodamine B aggregated in Quartz/APES/PSS/RB SAMs and its fluorescence behavior was different from that in Quartz/APES/RB SAMs without PSS. The constructed Quartz/APES/PSS/RB SAMs were applied for label-free interfacial fluorescence sensing of DNA with extremely high sensitivity.     

Use of a porphyrin platform and 3,4-HPO chelating units to synthesize ligands with N4 and O4 coordination sites

Piperazine and 1,2-diaminobenzene have been previously used as anchoring molecules to synthesize 3-hydroxy-4-pyridinone (3,4-HPO) tetradentate ligands affording ligands with different flexibility and coordination properties. In order to have a relatively rigid and hindered structure, a porphyrin platform was selected to anchor one or two 3,4-HPO chelating units. This platform provides an additional N₄ coordination sphere and also very interesting optical properties to the synthesized conjugates. Depending on the metal ion present in the porphyrin core, conjugates with different spectroscopic properties are obtained. EPR spectroscopy has been used to characterize the copper(II) metalloporphyrins and to monitor and identify the species formed upon addition of copper(II) to solutions of two porphyrin conjugates with one and two 3,4-HPO arms. The porphyrin conjugates having two 3,4-HPO units are ligands that provide two separate binding sites with N₄ and O₄ coordination spheres, which allow accommodation of two metal ion centers that may be distinguished by spectroscopic methods.     

Coil-globule transition of DNA molecules induced by cationic surfactants: a dynamic light scattering study

The compaction and aggregation of DNA induced by cationic surfactants was studied by dynamic light scattering (DLS). Furthermore, the effect on surfactant-compacted DNA of the addition of nonionic amphiphiles and salt was studied. When using sufficiently low amounts of DNA and cetyltrimethylammonium bromide (CTAB), compacted DNA molecules could be monitored by the appearance of a band characterized by lower hydrodynamic radius and by the decrease in the intensity of the peak corresponding to extended DNA molecules. Notably, we observed a region where compacted molecules coexist with extended ones; these two populations were found to be stable with time. For higher concentrations of CTAB, only compacted molecules were observed and the size of the particles increased with time indicating aggregation. The number of globules present in the coexistence region increased linearly with the surfactant concentrations, as given by the area of the band corresponding to this population, which indicates a double-cooperativity of the binding. The DLS experiments were in good agreement with previous fluorescence microscopy studies, with certain advantages over this technique since there is no need to add fluorescence dyes and antioxidants. Furthermore, it allows the study of molecules which are too small to be visualized by fluorescence microscopy.     

A kinetic study of methane conversion by a dinitrogen microwave plasma

Conversion of CH₄ with a N₂ microwave plasma (2.45 GHz) is studied. The experiments cover the absorbed microwave power range 300–700 W with 17–62% of methane in the gas mixture, with pressures of 10–40 mbar and flow rates of 140–650 ml· min^–1. The yields of C₂ hydrocarbons and dihydrogen are analyzed by gas chromatography. The distance of methane addition downstream of the plasma plays an important role on the composition and the concentration of the products obtained. This distance mainly determines the energy concentrated in the active species of the plasma when they react with methane. Different behaviors for acetylene formation, on the one hand, and for ethane and ethene formation, on the other hand, have been observed, and this finding allows us to propose a kinetic mechanism for the decay of methane and for the formation of C₂ hydrocarbons.     

Studies on interaction of porphyrin and its complexes with DNA at interface on gold electrode modified by thiol-porphyrin self-assembled monolayer

The interaction of 5-[p-(mercaptopropyloxy)-phenyl]-10, 15, 20-triphenylporphyrin (H₂MPTPP) and its metalloporphyrin (Co, Ni-MPTPP) with calf thymus deoxyribonucleic acid (DNA) has been studied on gold electrode modified by thiol-porphyrin self-assembled monolayer (SAM). The mode and characteristics of their interaction with DNA have been studied by cyclic voltammetry, scanning electrochemical microscope (SECM), and alternating current (AC) impedance. Some electrochemical parameters have been determined, i.e., apparent heterogeneous reaction rate constant (k _eff from SECM and k _f from AC impedance) and the hindrance (B) of electrode. K₃[Fe(CN)₆] was used as probe to obtain some electrochemical information of electrode interface. SECM images obtained from interface on SAM interacted with DNA showed very good resolution with different topography. Based on a comparison with the results from experiments, a reasonable agreement between SECM and AC impedance can be obtained, which means a conjunction of them. It is proposed to be electrostatic interaction of H₂MPTPP, Co-MPTPP and Ni-MPTPP with DNA, and the attractive force between porphyrins and DNA follows the order Ni-MPTPP > Co-MPTPP > H₂MPTPP.     

Oxidations of alkenes catalyzed by a Mn(III) porphyrin and cationic polymer latexes

Three types of cationic polymer latexes were prepared by emulsion copolymerization of vinylbenzyl chloride, divinylbenzene and a third monomer, vinyl octadecyl ether, styrene, or n-decyl methacrylate, followed by quaternization with trimethylamine. The latexes had 44–71 nm diam and polydispersity indices of 1.06–1.10. Vinyl octadecyl ether did not copolymerize but hydrolyzed under the polymerization conditions to produce 1-octadecanol, which as a coemulsifier gave highly viscous latexes. The tetraanion 5,10,15,20-tetrakis-(2,6-dichloro-3-sulfonatophenyl) porphinatomanganese (III) chloride bound irreversibly to the cationic latexes and was an active catalyst for oxidations of alkenes by sodium hypochlorite and potassium peroxymonosulfate in the absence of added organic solvent. The porphyrin catalyst in the latexes was more active than in solution. Porphyrin catalysis gave epoxides concurrently with competing uncatalyzed hypochlorous acid oxidations to complex mixtures of allylic chlorides, allylic alcohols, α,β-unsaturated ketones, and chlorohydrins.     

Electrochemical studies of the interaction of Basic Brown G with DNA and determination of DNA

A new method of electrochemical probe has been proposed for the determination of Herring Sperm DNA (DNA) based on its interaction with Basic Brown G (BBG). The electrochemical behavior of interaction of BBG with DNA was investigated on Hg electrode. In 0.1 mol L⁻¹ NH₃-NH₄Cl buffer solution (pH 8.0), BBG can be reduced on Hg electrode with a well-defined voltammetric peak at −0.67 V (versus SCE). In the presence of DNA, the reduction peak current of BBG decreases and the peak potential shifts to a more positive potential without the appearance of new peak. The study shows that a new BBG-DNA complex is formed by linear sweep voltammetry (LSV) and spectrophotometry. The decrease of the second order derivative of reductive peak current (Δi^″p) of BBG is proportional to the concentration of DNA in the range of 0.10-36 μg mL⁻¹. Limit of detection of DNA is 0.04 μg mL⁻¹. DNA of Hepatitis B Virus in serum samples was determined satisfactorily. Additionally, the binding mechanism was preliminarily discussed. The mode of interaction between BBG and DNA was found to be intercalation binding.