Novel fluorene/fluorenone DNA and RNA binders as efficient non-toxic ds-RNA selective fluorescent probes

A series of structurally similar 1-substitued heteroaryl fluorene derivatives were prepared in a simple single step reaction, oxidized to fluorenones and then both, fluorenes and fluorenones, were methylated to enhance the solubility and increase the affinity to DNA/RNA. Interactions of both, fluorene and fluorenone analogues with various ds-DNA, ds-RNA revealed strong ds-DNA/RNA binding, and various thermal stabilization effects. Most intriguingly, some fluorene derivatives showed opposite fluorescence change (increase for ds-RNA and decrease for ds-DNA), which was not previously reported for any fluorene analogue. CD experiments along with other methods support ds-DNA minor groove binding and major groove ds-RNA binding. All compounds showed negligible interaction with G-quadruplex DNA. Very low cell cytotoxicity of studied compounds combined with very efficient cellular uptake makes these fluorescent dyes safe for laboratory applications. Moreover, especially compounds which show opposite fluorescence response to ds-DNA and ds-RNA, are promising lead compounds for further studies aimed toward ds-RNA-specific fluorescence markers.     

Polycationic Pillar[5]arene Derivatives: Interaction with DNA and Biological Applications

Dendritic pillar[5]arene derivatives have been efficiently prepared by grafting dendrons with peripheral Boc‐protected amine subunits onto a preconstructed pillar[5]arene scaffold. Upon cleavage of the Boc‐protected groups, water‐soluble pillar[5]arene derivatives with 20 ( 13 ) and 40 ( 14 ) peripheral ammonium groups have been obtained. The capability of these compounds to form stable nanoparticles with plasmid DNA has been demonstrated by gel electrophoresis, transmission electron microscopy (TEM), and dynamic light scattering (DLS) investigations. Transfection efficiencies of the self‐assembled 13 /pCMV‐Luc and 14 /pCMV‐Luc polyplexes have been evaluated in vitro with HeLa cells. The transfection efficiencies found for both compounds are good, and pillar[5]arenes 13 and 14 show very low toxicity if any.     

Study of non-covalent interactions of luotonin A derivatives and the DNA minor groove as a first step in the study of their analytical potential as DNA probes

The interaction between DNA and several newly synthesized derivatives of the natural anticancer compound luotonin A has been studied. The results from our work reveal an effective and selective alkaloid/double-stranded DNA (ds-DNA) interaction. In the presence of increasing amounts of ds-DNA, a noticeable fluorescence quenching of the luotonin A derivatives under study was observed. However, this effect did not take place when single-stranded DNA (ss-DNA) was employed. The association constant alkaloids/ds-DNA was calculated by quantitation of such a quenching effect. The influence of other quenchers, namely Co²⁺ and Br⁻ on the native fluorescence of luotonin A and derivatives was also studied, and a remarkable quenching effect was observed for both ions. We have also investigated how by binding DNA the alkaloids could get protected from the external Co²⁺ and Br⁻ quenchers. The Stern–Volmer constants (K _SV) for Co²⁺ and Br⁻ quenching effect on the studied alkaloids were considerably reduced (10–50%) after incubation of the compounds in the presence of DNA with regard to the K _SV values in absence of DNA. An increase in the fluorescence anisotropy values of luotonins was also produced only in the presence of ds-DNA but not in the case of ss-DNA. To better characterize the nature of that interaction, viscosimetry assays and ethidium bromide displacement studies were conducted. With regard to DNA reference solutions, the viscosity of solutions containing DNA and luotonin A derivatives was reduced or not significantly increased. It was also observed that the studied compounds were unable to displace the intercalating agent ethidium bromide. All of these results, together with the obtained association constants values (K _ass = 2.2 × 10² – 1.3 × 10³), support that neither covalent nor intercalating interactions luotonin A derivatives/ds-DNA are produced, leading to the conclusion that these alkaloids bind ds-DNA through the minor groove. The specific changes in the fluorescence behavior of luotonin A and derivatives distinguishing between ss-DNA and ds-DNA binding, lead us to propose these compounds as attractive turn-off probes to detect DNA hybridization.     

Separation of thiopurine derivatives by thin-layer electrophoresis using low-temperature fluorescence detection

A method using thin-layer electrophoresis to separate thiopurine derivatives is described. Of the thin-layer media studied only Ecteola-cellulose and silica gel have been found to give satisfactory separations. Picomole quantities of the separated compounds have been made detectable by low-temperature fluorescence using liquid nitrogen. The sensitivity limit of this low-temperature technique for various purine derivatives is reported.     

Responsive polymer gels: double-stranded versus single-stranded DNA

Cross-linking of polyelectrolytes such as DNA gives gels that are osmotically highly swollen but contract upon addition of electrolytes and, in particular, upon association of oppositely charged cosolutes with the polyelectrolyte chain. The deswelling behavior of cross-linked DNA gels thus reflects the DNA-cosolute interactions and provides a basis for the development of responsive DNA formulations. Gels of both single- and double-stranded DNA have interesting applications, and a comparison between them provides the basis for understanding mechanisms. Denaturation of cross-linked ds-DNA gels was induced by heating them above the melting temperature and then cooling. This process, studied by fluorescence using ethidium bromide, appeared to be reversible when a heating/cooling cycle was performed. The swelling behavior upon addition of different cosolutes, such as metal ions, polyamines, charged proteins, and surfactants, was investigated for different DNA gel samples, including long and short ds-DNA and long and short ss-DNA. The DNA molecular weight was found to have only a slight effect on the deswelling curves, whereas conformation exhibited a pronounced effect. In general, single-stranded DNA gels exhibited a larger collapse in the presence of cations than did double-stranded DNA. This difference was more pronounced with surfactants than with the other cosolutes investigated. The difference between double- and single-stranded DNA was attributed to differences in linear charge density, chain flexibility, and hydrophobicity. For surfactants with different chain lengths, the swelling behavior displayed by ss-DNA can be interpreted in terms of an interplay between hydrophobic and electrostatic interactions, the latter being influenced by polymer flexibility. Increasing hydrophobicity of the network leads to a decreased critical aggregation concentration (cac) for the surfactant/gel complex, as a result of the strengthened hydrophobic attractive force between the surfactant and the gel chain. The swelling of DNA gels appears to be reversible and to be independent of DNA conformation. Surfactant-induced deswelling of DNA gels under some conditions appears to be quite homogeneous, whereas under other conditions, there is a separation into a collapsed region in the outer parts of the gel sample and an inside swollen part. Such "skin" formation is quite different for ss- and ds-DNA, with ss-DNA giving more pronounced skin formation over a wider range of binding ratio, beta. For example, no macroscopic separation into collapsed and swollen regions was observed at intermediate degrees of binding for ds-DNA gels, whereas a dense surfactant-rich surface phase (skin) was found to coexist with a swollen core network for ss-DNA gels with beta>0.5. One explanation for this difference is the large deformation energy required for the compression of the very stiff ds-DNA chains.     

Urea derivatives as low-molecular-weight gelators

This paper reports an overview of low-molecular-weight gelators (LMWGs) that have a ureide moiety as a hydrogen-bonding site. Various mono-, bis-, tris-, and tetrakis-urea compounds can form supramolecular gels with organic solvents. The author developed a C ₃-symmetrical tris-urea molecule that can form a ubiquitous framework of LMWGs. The supramolecular organogel of the tris-urea molecule exhibited a chemical-stimuli-responsive reversible gel–sol phase transition. Supramolecular hydrogels are constructed from self-assemblies of amphiphilic urea derivatives. Sugar-connected amphiphilic tris-urea was found to form a gel with water, and the hydrogels showed chemical-stimuli-responsive gel–sol phase transitions. The potential of supramolecular hydrogels as matrices of electrophoresis has been demonstrated through the supramolecular gel electrophoresis (SUGE) of protein samples using our developed amphiphilic tris-urea LMWG.     

The experimental and theoretical QM/MM study of interaction of chloridazon herbicide with ds-DNA

We report a multispectroscopic, voltammetric and theoretical hybrid of QM/MM study of the interaction between double-stranded DNA containing both adenine-thymine and guanine-cytosine alternating sequences and chloridazon (CHL) herbicide. The electrochemical behavior of CHL was studied by cyclic voltammetry on HMDE, and the interaction of ds-DNA with CHL was investigated by both cathodic differential pulse voltammetry (CDPV) at a hanging mercury drop electrode (HMDE) and anodic differential pulse voltammetry (ADPV) at a glassy carbon electrode (GCE). The constant bonding of CHL-DNA complex that was obtained by UV/vis, CDPV and ADPV was 2.1×10(4), 5.1×10(4) and 2.6×10(4), respectively. The competition fluorescence studies revealed that the CHL quenches the fluorescence of DNA-ethidium bromide complex significantly and the apparent Stern-Volmer quenching constant has been estimated to be 1.71×10(4). Thermal denaturation study of DNA with CHL revealed the ΔTm of 8.0±0.2°C. Thermodynamic parameters, i.e., enthalpy (ΔH), entropy (ΔS°), and Gibbs free energy (ΔG) were 98.45 kJ mol(-1), 406.3 J mol(-1) and -22.627 kJ mol(-1), respectively. The ONIOM, based on the hybridization of QM/MM (DFT, 6.31++G(d,p)/UFF) methodology, was also performed using Gaussian 2003 package. The results revealed that the interaction is base sequence dependent, and the CHL has more interaction with ds-DNA via the GC base sequence. The results revealed that CHL may have an interaction with ds-DNA via the intercalation mode.     

Tandem mass spectrometry methods for definitive protein identification in proteomics research

Optimized procedures have been developed for the addition of sulfonic acid groups to the N-termini of low-level peptides. These procedures have been applied to peptides produced by tryptic digestion of proteins that have been separated by two-dimensional (2-D) gel electrophoresis. The derivatized peptides were sequenced using matrix-assisted laser desorption/ionization (MALDI) post-source decay (PSD) and electrospray ionization-tandem mass spectrometry methods. Reliable PSD sequencing results have been obtained starting with sub-picomole quantities of protein. We estimate that the current PSD sequencing limit is about 300 fmol of protein in the gel. The PSD mass spectra of the derivatized peptides usually allow much more specific protein sequence database searches than those obtained without derivatization. We also report initial automated electrospray ionization-tandem mass spectrometry sequencing of these novel peptide derivatives. Both types of tandem mass spectra provide predictable fragmentation patterns for arginine-terminated peptides. The spectra are easily interpreted de novo, and they facilitate error-tolerant identification of proteins whose sequences have been entered into databases.     

Hexagonal → cholesteric phase transition of DNA molecules in liquid-crystalline dispersion particles

To assess the character of packing of double-stranded (ds) DNA molecules in liquid-crystalline dispersion particles formed by phase exclusion of DNA molecules from aqueous salt solutions of poly(ethylene glycol), the circular dichroism spectra of these dispersions at different temperatures have been compared. It has been shown for the first time that heating dispersion particles with the hexagonal packing of ds-DNA molecules is accompanied by the hexagonal → cholesteric phase transition. This result can be described using the notion of quasi-nematic layers composed of orientationally ordered adjacent ds-DNA molecules in the structure of dispersion particles; these layers can be packed in two ways dictating their hexagonal or cholesteric spatial structure.     

Computer simulation of DNA gel electrophoresis: influence of solid friction on linear and circular chains

The effect of solid friction between DNA molecules and gel fibres during gel electrophoresis has been studied using Brownian dynamics simulations. To investigate the effect of the topology of the polyelectrolyte chains, we have studied both linear and circular molecules. The results show that the migration properties of linear molecules seem to be almost uneffected by solid friction. There is, however, a significant effect on the mobility of circular molecules of the same size. Increasing the electric field strength increases the mobility of the linear molecules while for the circular chains, the mobility goes through a maximum when friction is included.     

3D打印便携式凝胶电泳装置用于蛋白质的快速检测

随着现场分析对于快速、便携和经济型检测的需求,分析仪器的便携化和微型化备受关注。3D打印技术的不断发展,将会极大推动小型化、便携式实验设备的开发和研制。分析仪器的微型化有助于促进资源不足地区在医疗现场、食品安全和环境污染等方面的现场监测。目前,用于蛋白质分离的凝胶电泳装置多为实验室用小型化分析仪器,可用于现场快速分离蛋白质的小型化仪器尚未见报道。该研究设计加工了一款便携式凝胶电泳装置,用于蛋白质的快速分离检测。首先,通过3D打印加工的凝胶电泳装置可在实验室内方便、快捷、低成本的复制。其次,通过对预染蛋白质相对分子质量标准的分离测试,对该系统结构进行优化。优化后该凝胶电泳装置电泳槽的尺寸仅为15 mm×20 mm×17 mm,采用3D打印技术可在5 h内加工完成,耗费打印材料10 mL。正负极所用电泳缓冲液共需4 mL,所使用的25 V锂电池可实现100 h左右的工作时间。装置优化后可实现蛋白质的快速高效分离。随后,在5种常用蛋白质相对分子质量标准的分离中,该装置与商业化平板凝胶电泳分离效果相当,同时具备更快的分离速度。该研究在便携式凝胶电泳装置的开发及其在蛋白质快速分离方面取得了初步成果,但在分离完成后立即对蛋白质进行定量分析以及更多实际样品的应用方面还需要进一步研究。     

Electrophoresis of cereal storage proteins

Cereal proteins have been studied by a number of analytical techniques over the years. One of the major methodologies utilized by cereal chemists has been electrophoresis. Starting with moving boundary electrophoresis and progressing to slab gels and high-performance capillary electrophoresis, innovative methods have been developed to provide high resolution separations of difficult to separate proteins. Sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (PAGE), acid-PAGE, isoelectric focusing, free zone CE, and even high-resolution two-dimensional HPLC-HPCE methods have been developed to separate cereal proteins. This review focuses on electrophoretic methods for separating and characterizing cereal storage proteins.     

Comprehensive characterization of surface-functionalized poly(amidoamine) dendrimers with acetamide,hydroxyl, and carboxyl groups

Terminal amine groups of poly(amidoamine) (PAMAM) dendrimers can be substituted with different functional groups for various applications. In this study, PAMAM derivatives with acetamide, hydroxyl, and carboxyl termini were synthesized from ethylenediamine (EDA) core generation 4 and 5 primary amine-terminated PAMAM dendrimers. The reaction products were purified with dialysis and subsequently characterized by polyacrylamide gel electrophoresis (PAGE), capillary electrophoresis (CE), size exclusion chromatography (SEC), matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry, potentiometric titration, ¹H NMR, and ¹³C NMR. PAGE and CE electropherograms provide data regarding the purity, charge distribution, and electrophoretic mobility of the dendrimers and their derivatives. SEC and MALDI-TOF mass spectrometry detect the average absolute molar mass and the individual mass fractions, respectively. The combination of SEC with potentiometric titration provides quantitative evidence of the degree of the functional group substitution, while NMR techniques (both ¹H NMR and ¹³C NMR) confirmed the changes in dendrimer surface functionalization. This study provides a general example for the comprehensive characterization of surface-functionalized PAMAM dendrimer nanoparticles. The synthesized dendrimer derivatives hold promise for environmental and medical applications.     

Topoisomerase Inhibition,Nucleolytic and Electrolytic Contribution on DNA Binding Activity Exerted by Biological Active Analogue of Coordination Compounds

The neutral mononuclear copper complexes with the quinolone antibacterial drug ciprofloxacin and bipyridine derivatives have been synthesized and characterized. Complexes were screened for their antibacterial activity against three Gram⁽⁻⁾ and two Gram⁽⁺⁾ bacteria, and study suggests inhibition of gyrase activity by metal complexes as the possible mechanism. The nucleolytic activity of adducts was carried out on double stranded pUC19 DNA using gel electrophoresis in the presence of radical scavenging agents that suggest hydrolytic cleavage mechanism for plasmid DNA.     

Fluorescence quenching studies of potential-dependent DNA reorientation dynamics at glassy carbon electrode surfaces

The potential-dependent reorientation dynamics of double-stranded DNA (ds-DNA) attached to planar glassy carbon electrode (GCE) surfaces were investigated. The orientation state of surface-bound ds-DNA was followed by monitoring the fluorescence from a 6-carboxyfluorescein (FAM6) fluorophore covalently linked to the distal end of the DNA. Positive potentials (i.e., +0.2 V vs open circuit potential, OCP) caused the ds-DNA to align parallel to the electrode surface, resulting in strong dipole-electrode quenching of FAM6 fluorescence. Switching of the GCE potential to negative values (i.e., -0.2 V vs OCP) caused the ds-DNA to reorient perpendicular to the electrode surface, with a concomitant increase in FAM6 fluorescence. In addition to the very fast (submilliseconds) dynamics of the initial reorientation process, slow (0.1-0.9 s) relaxation of FAM6 fluorescence to intermediate levels was also observed after potential switching. These dynamics have not been previously described in the literature. They are too slow to be explained by double layer charging, and chronoamperometry data showed no evidence of such effects. Both the amplitude and rate of the dynamics were found to depend upon buffer concentration, and ds-DNA length, demonstrating a dependence on the double layer field. The dynamics are concluded to arise from previously undetected complexities in the mechanism of potential-dependent ds-DNA reorientation. The possible origins of these dynamics are discussed. A better understanding of these dynamics will lead to improved models for potential-dependent ds-DNA reorientation at electrode surfaces and will facilitate the development of advanced electrochemical devices for detection of target DNAs.     

PHOTOCHEMICAL BINDING OF PHENOTHIAZINES ON BIOLOGICAL MEMBRANE PROTEINS

Abstract— The photobinding of phenothiazine derivatives (chlorpromazine, fluphenazine, promazine and promethazine) was studied on four different types of biological membranes (microsomes, myelin and synaptosomes from rat brain as well as human erythrocytes). The photoreaction was performed by ultraviolet irradiation of the tritiated compounds in their long wavelength absorption band (313 nm) and bound photoproducts were analysed by autoradiography of the proteins separated by polyacrylamide gel electrophoresis. The specificity of binding is low, however, a 34000 dalton band is intensely labeled on synaptic membranes with chlorpromazine and fluphenazine. All the phenothiazines bind on erythrocyte membrane proteins and specially on band 4.2 and on a peptide located before actin on the electrophoresis gel. These results show the generality of the phenothiazine photobinding on membrane proteins. These photobinding properties can be used for the identification and localization of some of these proteins.     

The role of separation science in proteomics research.

In the last few years there has been an increased effort into the separation, quantification and identification of all proteins in a cell or tissue. This is a review of the role gel electrophoresis, high performance liquid chromatography (HPLC), and capillary electrophoresis (CE) play in proteomics research. The capabilities and limitations of each separation technique have been pointed out. Instrumental strategies for the resolution of cell proteins which are based on efficient separation employing either a single high-resolution procedure or a multidimensional approach on-line or off-line, and a mass spectrometer for protein identification have been reviewed. A comparison of the advantages of multi-dimensional separations such as two-dimensional polyacrylamide gel electrophoresis, HPLC-HPLC, and HPLC-CE to the separation of cell and tissue proteins are discussed. Also, a discussion of novel approaches to protein concentration, separation, detection, and quantification is given.     

Identification of proteins from Escherichia coli using two-dimensional semi-preparative electrophoresis and mass spectrometry

Escherichia coli is a gram-negative bacterium that causes sepsis and infections of the nervous system, and the digestive and urinary tracts. The availability of the complete nucleotide sequence encoding the E. coli K-12 genome has made this organism an excellent model for proteomic studies. Semi-preparative two-dimensional electrophoresis, including liquid phase isoelectric focusing (IEF), one-dimensional sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis (PAGE) and gel elution, have for the first time been used in combination with matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOFMS), electrospray tandem mass spectrometry and database searching for rapid separation of proteins from a uropathogenic strain of E. coli. The identity of 30 proteins, including the membrane protein nmpC, was obtained using this approach.     

Self-assembling and photophysical properties of the organogelators based on cyanostyryl-substituted carbazoles

Four cyanostyryl-substituted carbazole derivatives (CN-ODEC1, CN-ODEC2, CN-DDEC1, and CN-DDEC) were synthesized and their self-assembly properties have been studied. It was found that they could form organogels especially in aromatic solvents. Scanning electron microscopy and light microscopy images show that the xerogels formed from monosubstituted derivatives (CN-O/DDEC1) gave well-organized tapes, and those from disubstituted derivatives (CN-O/DDEC2) exhibited heavy entangled three-dimensional structures. The UV–vis absorption and fluorescence emission spectra, as well as X-ray diffraction patterns, suggest that carbazole derivatives underwent J-type π-stacking. Meanwhile, we suggested that strong H-bonding and moderate π–π interactions were the key driving force for the gelation of the monosubstituted derivatives, and head-to-tail “ladder-type” J-aggregates were formed in the gel state. On the other hand, strong π–π interaction might be considered as the main driving force for the gelation of disubstituted derivatives, and J-aggregates with no well-organized packing mode of molecules were obtained in the gel phase. It should be noticed that aggregation-induced emission was observed during the gelation processes.