Direct evaluation of a mechanism for activation of the RecA nucleoprotein filament

The RecA protein of Escherichia coli controls the SOS response for DNA damage tolerance and plays a crucial role in recombinational DNA repair. The formation of a RecA.ATP.ssDNA complex initiates all RecA activities, and yet this process is not understood at the molecular level. An analysis of RecA.DNA interactions was performed using both a mutant RecA protein containing a tryptophan (Trp) reporter and oligodeoxyribonucleotides (ODNs) containing a fluorescent guanine analogue, 6-methylisoxanthopterin (6MI). Experiments using fluorescent ODNs allowed structurally distinct nucleoprotein filaments, formed in the absence and presence of ATPgammaS (a slowly hydrolyzed analogue of ATP), to be differentiated directly. Stopped-flow spectrofluorometry, combined with presteady-state kinetic analyses, revealed unexpected differences in the rates of RecA.ODN and RecA.ATPgammaS.ODN complex assembly. This is the first demonstration that such intrinsically fluorescent synthetic DNAs can be used to characterize definitively the real-time assembly and activation of RecA.ssDNA complexes. Surprisingly, the ssDNA binding event is almost 50-fold slower in the presence of the activating ATPgammaS cofactor. Furthermore, a combination of time-dependent emission changes from 6MI and Trp allowed the first direct chemical test of whether an inactive filament can isomerize to the active state. The results revealed that, unlike the hexameric motor proteins, the inactive RecA filament cannot directly convert to the active state upon ATPgammaS binding. These results have implications for understanding how a coincidence of functions--an ATP-communicated signal-like activity and an ATP-driven motorlike activity--are resolved within a single protein molecule.     

Atomic force microscopic study of low temperature induced disassembly of RecA-dsDNA filaments

The assembly and disassembly of RecA-DNA nucleoprotein filaments on double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) are important steps for homologous recombination and DNA repair. The assembly and disassembly of the nucleoprotein filaments are sensitive to the reaction conditions. In this work, we investigated different morphologies of the formed nucleoprotein filaments at low temperature under different solution conditions by atomic force microscopy (AFM). We found that low temperature and long keeping time could induce the incomplete disassembly of the formed nucleoprotein filaments. In addition, when the formed filaments were kept at -20 degrees C for 20 h with 1,4-dithiothreitol (DTT), the integrated filaments disassembled. It was similar to the case under the same condition without anything added. However, when glycerol was used as a substitute for DTT, there was no obvious disassembly at the same condition. Oppositely, when the formed filaments were kept at 4 degrees C for 20 h, the disassembly with additional DTT was not as obvious as the case at -20 degrees C for 20 h, whereas the case with additional glycerol disassembled. The experiments indicated the effect of cold denaturation on the interaction of DNA and RecA. Meanwhile, the study of these phenomena can supply guidelines for the property and stability of RecA as well as the relevant roles of influencing factors to RecA and DNA in further theoretical studies.     

Synthesis of multivalent N-acetyl lactosamine modified quantum dots for the study of carbohydrate and galectin-3 interactions

Ternary core/shell CdSeS/ZnS-QDs coated with N-acetyl lactosamine was prepared as a fluorescent probe to study the interactions of N-acetyl lactosamine and galectin-3. The synthesis of N-acetyl lactosamine was achieved through the ‘azidoiodoglycosylation’ method. The amount of ligand coated on QDs was determined by ¹H NMR and ICP-OES. The interactions between carbohydrates and galectin-3 were measured using SPR. The results revealed that the affinity of galectin-3 with di- and multivalent N-acetyl lactosamine increased 20 and 184-fold, respectively. The prepared glyco-QDs could be used as an efficient fluorescent probe to study carbohydrates and galectin-3 interactions.     

Detection of amyloid-beta by Fmoc-KLVFF self-assembled fluorescent nanoparticles for Alzheimer's disease diagnosis

The abnormal aggregation of amyloid-beta(Aβ) has been widely believed to play an important role in the pathogenesis of Alz heimer's disease(AD),which is also recognized as one of the main biomarkers for AD diagnosis.The peptide sequence Lys-Leu-Val-Phe-Phe(KLVFF) is considered as the main driver of the fibrillation of Aβ,which also can be utilized to target Aβ and inhibit its aggregation.In this study,KLVFF and Fmoc-KLVFF fluorescent nanoparticles were self-assembled through zinc coordination and π-πstacking.The recognition of Aβ aggregates including oligomers and fibrils by fluorescent nanoparticles can be realized through aromatic,hydrophobic,and hydrogen-bond interactions.The fluorescent nanoprobes can distinguish Aβ aggregation formats and detect Aβ at the limit of 1 pg/mL(S/N=3).Hence,the detection of Aβ aggregates by fluorescent peptide nanoparticles has great potential for AD diagnosis and progression prediction.     

Interaction of E6 Gene from Human Papilloma Virus 16 (HPV-16) with CdS Quantum Dots

The aim of this study was to analyze the interactions of blue and yellow fluorescent CdS quantum dots (CdS-QDs) with human papillomavirus 16 (HPV-16) oncogene E6. The interactions were investigated using chip capillary electrophoresis, spectrophotometry and square wave voltammetry (SWV). Using chip capillary electrophoresis we proved that blue fluorescent CdS-QDs (0.5 mM) caused an increase of the migration time of the E6 HPV-16 DNA–CdS-QDs complex by 42 s compared to control DNA (E6 HPV-16). The same concentration of yellow fluorescent CdS-QDs caused an increase in the migration time of the DNA–CdS-QDs complex by 108 s compared to the control DNA (E6 HPV-16). The difference in the migration times between both complexes was 66 s. Using square wave voltammetry (SWV), the reduction signal of cytosine and adenine (peak CA) was observed, after the complex with 2.5 µg mL^?1 DNA was formed. A decrease of the peak CA reduction signal of the complex DNA–CdS-QDs by 90 % was caused when yellow fluorescent CdS-QDs (0.03 mM) were used. The same concentration of blue fluorescent CdS-QDs caused only a 50 % decrease of the C and A reduction signal of the DNA–CdS-QDs complex. The difference between both CdS-QDs was 40 %. Electrochemical measurements and chip electrophoresis analyses confirmed that the yellow fluorescent CdS-QDs show higher affinity to the DNA (E6 HPV-16) compared to blue ones.     

Interaction of E6 Gene from Human Papilloma Virus 16 (HPV-16) with CdS Quantum Dots

The aim of this study was to analyze the interactions of blue and yellow fluorescent CdS quantum dots (CdS-QDs) with human papillomavirus 16 (HPV-16) oncogene E6. The interactions were investigated using chip capillary electrophoresis, spectrophotometry and square wave voltammetry (SWV). Using chip capillary electrophoresis we proved that blue fluorescent CdS-QDs (0.5 mM) caused an increase of the migration time of the E6 HPV-16 DNA–CdS-QDs complex by 42 s compared to control DNA (E6 HPV-16). The same concentration of yellow fluorescent CdS-QDs caused an increase in the migration time of the DNA–CdS-QDs complex by 108 s compared to the control DNA (E6 HPV-16). The difference in the migration times between both complexes was 66 s. Using square wave voltammetry (SWV), the reduction signal of cytosine and adenine (peak CA) was observed, after the complex with 2.5 µg mL⁻¹ DNA was formed. A decrease of the peak CA reduction signal of the complex DNA–CdS-QDs by 90 % was caused when yellow fluorescent CdS-QDs (0.03 mM) were used. The same concentration of blue fluorescent CdS-QDs caused only a 50 % decrease of the C and A reduction signal of the DNA–CdS-QDs complex. The difference between both CdS-QDs was 40 %. Electrochemical measurements and chip electrophoresis analyses confirmed that the yellow fluorescent CdS-QDs show higher affinity to the DNA (E6 HPV-16) compared to blue ones.

     

Interactions between local anesthetics and lipid dispersions studied with liposome electrokinetic capillary chromatography

In the case of local anesthetic intoxication, intravenous administration of lipid-based Intralipid dispersion (Fresenius Kabi) can be used for the entrapment of hydrophobic drugs. Our long-term aim is to develop a sensitive, efficient, and non-harmful lipid-based formulation to specifically trap harmful substances. In this study liposome electrokinetic capillary chromatography (LEKC) was used to study the interactions between local anesthetics and Intralipid or liposome dispersions. Intralipid dispersion and extruded liposomes with different concentrations of 1-palmitoyl-2-oleyl-sn-glycerophosphatidylcholine (POPC), phosphatidylglycerol, cardiolipin, cholesterol, oleic acid, and linoleic acid were used as a pseudostationary phase in LEKC and their interactions with lidocaine, prilocaine, and bupivacaine were studied. POPC liposomes containing 1 mol% of palmitoyl-2-[12-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]dodecanoyl]-sn-glycero-3-phosphocholine as a fluorescent marker were used for the first time in LEKC connected with laser-induced fluorescent detection in order to calculate the retention factor for anesthetics.     

Pyrrolo-dC and pyrrolo-C: fluorescent analogs of cytidine and 2-deoxycytidine for the study of oligonucleotides

Pyrrolo-dC (1a, 6-methyl-3-(2-deoxy-β-d-ribofuranosyl)-3H-pyrrolo[2,3-d]pyrimidin-2-one) and its cyanoethyl phosphoramidite 2a were synthesized. The latter was incorporated into oligodeoxyribonucleotides by standard automated synthesis techniques, where pyrrolo-dC was found to serve as a fluorescent analog of deoxycytidine. The cyanoethylphosphoramidite (2b) of pyrrolo-C (2a, 6-methyl-3-(β-d-ribofuranosyl)-3H-pyrrolo[2,3-d]pyrimidin-2-one) was also synthesized and may find use for the site-specific incorporation of a fluorescent cytidine analog into oligoribonucleotides.     

Applicability of quinolizino-coumarins for monitoring free radical photopolymerization by fluorescence spectroscopy

Applicability of commercially available 2,3,5,6-1H,4H-tetrahydro-quinolizino[9,9a,1-gh]coumarin (Coumarin 6H) and its 9-methyl (Coumarin 102), 9-trifluoromethyl (Coumarin 153) and 10-carboxy (Coumarin 343) derivatives as fluorescent molecular probes for monitoring progress of free radical photopolymerization of several acrylic and methacrylic monomers by Fluorescence Probe Technique (FPT) has been tested. The progress of the photopolymerization was monitored using a specially designed cure monitoring system. It was found that all the quinolizino-coumarins shifted their fluorescence spectra towards shorter wavelengths with progress of polymerization, which enabled monitoring the progress in terms of fluorescence intensity ratios as the progress indicator. Coumarin 6H turned out to be the most sensitive to changes occurring during polymerization. Coumarin 102 and Coumarin 153 exhibit only about 20% lower sensitivity than that of Coumarin 6H, so those are also good enough for the cure monitoring of acrylic monomers, except for tetraethylene glycol diacrylate, where the quinolizino-coumarins response was disturbed by some fluorescent side product. Moreover, it has been found that the FPT technique has some limitations in the case of monofunctional monomers.     

Photochemical behaviour upon the inclusion for some volatile organic compounds in new fluorescent indolizine β-cyclodextrin sensors

The potentialities of three new fluorescent indolizine modified β-cyclodextrin have been investigated as molecular chemosensors. The pyridin-4-ylindolizine β-cyclodextrin derivatives were synthesised by an amidation between the fluorescent indolizine derivatives and 6-deoxy-6-amino-β-cyclodextrin. The multiconformational search by MM3 and AM1 method in gaseous state and in water respectively suggest the “open cavity” structure as the most probable. These compounds have been characterised spectroscopically by their emission spectra and their sensing ability towards 1-adamantanol, phenol and p-cresol. The fluorescent properties and sensitivity factor of the sensor containing an indolizine product with a perfluored aromatic fragment recommended it fairly as sensor for the detection of volatile organic compounds (VOCs), while the other two sensors, with an aliphatic fragment, can be utilised as biological markers. Finally, a significant bathochromic shift is observed for the sensor containing a t-butyl fragment, in such a way that this sensor may also lead to the detection of VOCs.     

Total synthesis of dansyl and biotin functionalized ganglioside GM3 by chemoenzymatic method

Ganglioside GM3, as well as other gangliosides, offers a variety of modifications in its sialic acid and ceramide moieties GM3 exhibits various types of important biological activities, due to the inability to effectively observe the trafficking of ganglioside GM3, developing sensitive research tools for specific monitoring of GM3 expression and activity is thus desirable. The total synthesis of a dansyl and biotin bifunctionalized fluorescent ganglioside GM3 were reported in this article. From lactose after 13 reaction steps, the compound of 2′ -biotinoylaminoethyl-6-N-dansylamido-6-deoxy-β-D-galatopyranosyl-(1→4)-β-D-glucopy-ranoside was obtained in total yield of 16.2%. Sialylation of dansyl and biotin functionalized lactose by enzymatic method gave dansyl and biotin labeled ganglioside GM3. The fluorescent property of this compound was also investigated.     

Synthesis and characterization of a sensitive and selective Fe3+ fluorescent sensor based on novel sulfonated calix[4]arene‐based host‐guest complex

A novel fluorescent sensor was prepared from sulfonated calix[4]arene (SC4A) by the host-guest complexation method using the fluorescent dye rhodamine B (RB) as a structure-directing agent. The crystal structure of the host-guest complex (RB@(SC4A)₃) was confirmed by X-ray diffraction studies while its performance and sensing mechanism for metal ion pollutants were characterized using fluorescence and nuclear magnetic resonance spectroscopies. The results showed that RB@(SC4A)₃ had a triangular branch structure resulting from host-guest mediation of the interactions between the three SC4A host molecules and the three terminal groups of the guest molecule RB. The host-guest complex exhibited sensitive and selective sensing towards Fe³⁺ ions via a fluorescence quenching mechanism. The results indicated that RB@(SC4A)₃ could be a promising sensitive and selective fluorescent sensor for metal ion pollutants monitoring. It also provided new insights into the synthesis of calixarene-based host-guest complex.     

Facile synthesis and optical resolution of inherently chiral fluorescent calix[4]crowns: enantioselective recognition towards chiral leucinol

A series of tri-O-alkylated inherently chiral fluorescent calix[4]crowns in the cone conformations and a series of tetra-O-alkylated inherently chiral fluorescent calix[4]crowns in the partial cone conformations have been synthesized. By condensing with chiral auxiliary (S)-BINOL, the resulting diastereomers could be separated via preparative TLC. We found that the size of the crown moiety effected the separation of the diastereomers. Further, removal of the BINOL unit by hydrolysis furnished pairs of enantiomers with optical purity. Moreover, we found that a tetra-O-alkylated inherently chiral fluorescent calix[4]crown-6 in the partial cone conformation 6c showed considerable enantioselective recognition capability towards chiral leucinol.     

Colorimetric and electrochemical detection of ligase through ligation reaction-induced streptavidin assembly

We propose a concept for ligase detection by conversion of aggregation-based homogeneous analysis into surface-tethered electrochemical assay through streptavidin（SA）-biotin interaction. Sortase A（Srt A）served as the model analyte and two biotinylated peptides（bio-LPETGG and GGGK-bio） were used as the substrates. Srt A-catalyzed ligation of the peptide substrates led to the generation of bio-LPETGGGKbio. The ligation product（bio-LPETGGGK-bio） induced the aggregation and color change of SA-modifi...     

Novel water-soluble fluorescent polymer containing recognition units: Synthesis and interactions with PC12 cell

New water-soluble fluorescent poly(N-vinylpyrrolidone) (PVP) containing carbonylhydrazide recognition units was synthesized by free radical polymerization of N-vinylpyrrolidone in the presence of mercaptoacetic acid as chain transfer agent and then being modified by 1-pyrenebutyric acid hydrazide. FT-IR, ¹H NMR, gel permeation chromatography-multi-angle laser light scattering and fluorescence spectroscopy were used to characterize these polymers. Results of fluorescence measurements show that these polymers have a good affinity for deoxyribonucleic acid (DNA). The interactions with PC12 cell results indicated that the polymer with suitable molecular weight could penetrate into PC12 cell and emit fluorescence. This water-soluble polymer with recognition units and high luminescence can be used as a promising fluorescent probe for measurements of biomacromolecules and cells.     

Aggregation behavior of naphthalimide fluorescent surfactants in aqueous solution

A group of novel fluorescent surfactants, N-n-alkyl-4-(1-methylpiperazine)-1,8-naphthalimide iodine [C_nndi]I (n?=?8, 10, and 12), have been synthesized and their aggregation behavior in aqueous solution have been explored by surface tension, electric conductivity, hydrogen-1 NMR spectra, absorption, and fluorescence spectra. Compared with traditional cationic surfactants, the [C_nndi]I have a rather lower critical micelle concentration and higher surface activity. Absorption and fluorescence spectra were proved to be facile method to monitor directly the aggregation states of fluorescent surfactant molecules in solution and revealed clearly the formation of face-to-face stacked structure of the [C_nndi]I molecules driven by the π–π interactions. The micelle formation process for [C_nndi]I was demonstrated to be enthalpy-driven in the temperature range investigated. Possible aggregation process was given based on the experimental results. The combination of dye and surfactant provides a way for monitoring the formation process of micelle directly by fluorescence spectra.     

Phase Transitions and Structural Changes in DPPC Liposomes Induced by a 1-Carba-Alpha-Tocopherol Analogue

Steady-state emission spectroscopy of 1-anilino-8- naphthalene sulfonate (ANS) and 1,6-diphenyl-1,3,5-hexatriene (DPH), fluorescence anisotropy, and DSC methods were used to characterize the interactions of the newly synthesized 1-carba-alpha-tocopherol (CT) with a 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) membrane. The DSC results showed significant perturbations in the DPPC structure for CT concentrations as low as 2 mol%. The main phase transition peak was broadened and shifted to lower temperatures in a concentration-dependent manner, and pretransition was abolished. Increasing CT concentrations induced the formation of new phases in the DPPC structure, leading to melting at lower temperatures and, finally, disruption of the ordered DPPC structure. Hydration and structural changes of the DPPC liposomes using ANS and DPH fluorescent probes, which are selectively located at different places in the bilayer, were studied. With the increased concentration of CT molecules in the DPPC liposomes, structural changes with the simultaneous formation of different phases of such mixture were observed. Temperature studies of such mixtures revealed a decrease in the temperature of the main phase transition and fluidization at decreasing temperatures related to increasing hydration in the bilayer. Contour plots obtained from concentration–temperature data with fluorescent probes allowed for identification of different phases, such as gel, ordered liquid, disordered liquid, and liquid crystalline phases. The CT molecule with a modified chromanol ring embedded in the bilayer led to H-bonding interactions, expelling water molecules from the interphase, thus introducing disorder and structural changes to the highly ordered gel phase.     

Application of a green fluorescent fusion protein to study protein-protein interactions by electrophoretic methods

A screening procedure for protein-protein interactions in cellular extracts using a green fluorescent protein (GFP) and affinity capillary electrophoresis (ACE) was established. GFP was fused as a fluorescent indicator to the C-terminus of a cyclophilin (rDmCyp20) from Drosophila melanogaster. Cyclophilins (Cyps) belong to the ubiquitously distributed enzyme family of peptidyl-prolyl cis/trans isomerases (PPlases) and are well known as cellular targets of the immunosuppressive drug cyclosporin A (CsA). The PPlase activity of the GFP fused rDmCyp20 as well as the high affinity to CsA remain intact. Using native gel electrophoresis and ACE mobility-shift assays, it was demonstrated that the known moderate affinity of Cyp20 to the capsid protein p24 of HIV-1 was detectable in the case of rDmCyp20 fused to the fluorescent tag. For the p24 / rDmCyp20-GFP binding an ACE method was established which allowed to determine a dissociation constant of Kd = 20+/-1.5 x 10(-6) M. This result was verified by size-exclusion chromatography and is in good agreement with published data for the nonfused protein. Moreover the fusion protein was utilized to screen rDmCyp20-protein interactions by capillary electrophoresis in biological matrices. A putative ligand of rDmCyp20 in crude extracts of embryonic D. melanogaster was discovered by mobility-shift assays using native gel electrophoresis with fluorescence imaging and ACE with laser-induced fluorescence detection. The approach seems applicable to a wide range of proteins and offers new opportunities to screen for moderate protein-protein interactions in biological samples.     

Fluorescent Orthopalladated Complexes of 4-Aryliden-5(4H)-oxazolones from the Kaede Protein: Synthesis and Characterization

The goal of the work reported here was to amplify the fluorescent properties of 4-aryliden-5(4H)-oxazolones by suppression of the hula-twist non-radiative deactivation pathway. This aim was achieved by simultaneous bonding of a Pd center to the N atom of the heterocycle and the ortho carbon of the arylidene ring. Two different 4-((Z)-arylidene)-2-((E)-styryl)-5(4H)-oxazolones, the structures of which are closely related to the chromophore of the Kaede protein and substituted at the 2- and 4-positions of the arylidene ring (1a OMe; 1b F), were used as starting materials. Oxazolones 1a and 1b were reacted with Pd(OAc)₂ to give the corresponding dinuclear orthometalated palladium derivates 2a and 2b by regioselective C–H activation of the ortho-position of the arylidene ring. Reaction of 2a (2b) with LiCl promoted the metathesis of the bridging carboxylate by chloride ligands to afford dinuclear 3a (3b). Mononuclear complexes containing the orthopalladated oxazolone and a variety of ancillary ligands (acetylacetonate (4a, 4b), hydroxyquinolinate (5a), aminoquinoline (6a), bipyridine (7a), phenanthroline (8a)) were prepared from 3a or 3b through metathesis of anionic ligands or substitution of neutral weakly bonded ligands. All species were fully characterized and the X-ray determination of the molecular structure of 7a was carried out. This structure has strongly distorted ligands due to intramolecular interactions. Fluorescence measurements showed an increase in the quantum yield (QY) by up to one order of magnitude on comparing the free oxazolone (QY < 1%) with the palladated oxazolone (QY = 12% for 6a). This fact shows that the coordination of the oxazolone to the palladium efficiently suppresses the hula-twist deactivation pathway.