Preparation of DNA-carrying affinity latex and purification of transcription factors with the latex

Application of Magnetic Nanoparticles for Rapid Detection and In Situ Diagnosis in Clinical Oncology

Screening, monitoring, and diagnosis are critical in oncology treatment. However, there are limitations with the current clinical methods, notably the time, cost, and special facilities required for radioisotope-based methods. An alternative approach, which uses magnetic beads, offers faster analyses with safer materials over a wide range of oncological applications. Magnetic beads have been used to detect extracellular vesicles (EVs) in the serum of pancreatic cancer patients with statistically different EV levels in preoperative, postoperative, and negative control samples. By incorporating fluorescence, magnetic beads have been used to quantitatively measure prostate-specific antigen (PSA), a prostate cancer biomarker, which is sensitive enough even at levels found in healthy patients. Immunostaining has also been incorporated with magnetic beads and compared with conventional immunohistochemical methods to detect lesions; the results suggest that immunostained magnetic beads could be used for pathological diagnosis during surgery. Furthermore, magnetic nanoparticles, such as superparamagnetic iron oxide nanoparticles (SPIONs), can detect sentinel lymph nodes in breast cancer in a clinical setting, as well as those in gallbladder cancer in animal models, in a surgery-applicable timeframe. Ultimately, recent research into the applications of magnetic beads in oncology suggests that the screening, monitoring, and diagnosis of cancers could be improved and made more accessible through the adoption of this technology.

Application of high-performance magnetic nanobeads to biological sensing devices

Nanomaterials have extensive applications in the life sciences and in clinical diagnosis. We have developed magnetic nanoparticles with high dispersibility and extremely low nonspecific binding to biomolecules and have demonstrated their application in chemical biology (e.g., for the screening of drug receptor proteins). Recently, the excellent properties of nanobeads have made possible the development of novel rapid immunoassay systems and high-precision technologies for exosome detection. For immunoassays, we developed a technology to encapsulate a fluorescent substance in magnetic nanobeads. The fluorescent nanobeads allow the rapid detection of a specific antigen in solution or in tissue specimens. Exosomes, which are released into the blood, are expected to become markers for several diseases, including cancer, but techniques for measuring the absolute quantity of exosomes in biological fluids are lacking. By integrating magnetic nanobead technology with an optical disc system, we developed a novel method for precisely quantifying exosomes in human serum with high sensitivity and high linearity without requiring enrichment procedures. This review focuses on the properties of our magnetic nanobeads, the development of novel biosensors using these nanobeads, and their broad practical applications.

Tools and methodologies capable of isolating and identifying a target molecule for a bioactive compound

Elucidating the mechanism of action of bioactive compounds, such as commonly used pharmaceutical drugs and biologically active natural products, in the cells and the living body is important in drug discovery research. To this end, isolation and identification of target protein(s) for the bioactive compound are essential in understanding its function fully. And, development of reliable tools and methodologies capable of addressing efficiently identification and characterization of the target proteins based on the bioactive compounds accelerates drug discovery research. Affinity-based isolation and identification of target molecules for the bioactive compounds is a classic, but still powerful approach. This paper introduces recent progress on affinity chromatography system, focusing on development of practical affinity matrices and useful affinity-based methodologies on target identification. Beneficial affinity chromatography systems with using practical tools and useful methodologies facilitate chemical biology and drug discovery research.

Comprehensive study of proteins that interact with microcystin-LR

We carried out a comprehensive study of proteins that exhibit specific interactions with a naturally occurring toxin, microcystin (MC)-LR, in order to gain insight into the unknown underlying mechanism of MC virulence. This audacious study employed a simple affinity test that used MC-LR immobilized on an original ethylene oxide based monolithic solid phase (Moli-gel), and swine liver lysate. Some of the proteins that interacted with MC-LR on this original affinity resin were separated by SDS-PAGE, measured by nano-LC/MS/MS after trypsin digestion, and identified using a Mascot database search. Protein sequence analyses revealed that glutathione S-transferase (GST) was one of the candidate target proteins for MC-LR. This protein was confirmed as a target protein for MC-LR based on the results of for the inhibition of an enzymatic reaction by Dhb-MC-LR. Moreover, L-3-hydroxyacyl coenzyme A dehydrogenase (HDHA) was shown to be one of the proteins that specifically interacts with MC-LR. Our results demonstrated that our analytical systems based on an original affinity resin and nano-LC/MS/MS were effective for target protein research.

Synthetic polycation: polynucleotide interactions determined using liquid chromatography with short monolithic columns

LC on short monolithic columns (Convective Interaction Medium Disks) was applied to investigate several specially synthesized water soluble polycations of different charge type (primary, tertiary, quaternary amine), as well as a copolymer of neutral saccharide and cationic monomers, regarding their ability to form reversible complexes with DNA. For this purpose, two separation modes were used, namely, pseudo-affinity and cation-exchange chromatography. Synthetic polynucleotides, namely, polyriboadenylic acid (poly(rA)) and polyribocytidylic acid (poly(rC)), were used as approximate structural analogues of DNA. In first case, the hypothetical specific binding between dissolved polymers and polynucleotide (poly(rA) or poly(rC)), covalently attached to epoxy-bearing monolithic sorbent, has been studied and compared to the results obtained using cation exchange chromatography. Quantitative parameters of interactions between macromolecules were established using frontal elution method.

Thermosensitive pickering emulsion stabilized by poly(N-isopropylacrylamide)-carrying particles

Poly(N-isopropylacrylamide) (PNIPAM)-carrying particles were characterized as thermosensitive Pickering emulsifiers. Emulsions were prepared from various oils, such as heptane, hexadecane, trichloroethylene, and toluene, with PNIPAM-carrying particles. PNIPAM-carrying particles preferentially formed oil-in-water (O/W)-type emulsions with a variety of oils. All the emulsions stabilized by PNIPAM-carrying particles were stable for more than 3 months as long as they were stored at room temperature. However, when the emulsions were heated from room temperature to 40 degrees C, at which point the PNIPAM layer caused a coil-to-globule transition, phase separation occurred. Thus, by using thermosensitive PNIPAM-carrying particles as emulsifiers, the stability of the Pickering emulsions could be controlled by a slight change in temperature.

Adeno-associated virus site-specific integration is regulated by TRP-185

Adeno-associated virus (AAV) integrates site specifically into the AAVS1 locus on human chromosome 19. Although recruitment of the AAV nonstructural protein Rep78/68 to the Rep binding site (RBS) on AAVS1 is thought to be an essential step, the mechanism of the site-specific integration, particularly, how the site of integration is determined, remains largely unknown. Here we describe the identification and characterization of a new cellular regulator of AAV site-specific integration. TAR RNA loop binding protein 185 (TRP-185), previously reported to associate with human immunodeficiency virus type 1 TAR RNA, binds to AAVS1 DNA. Our data suggest that TRP-185 suppresses AAV integration at the AAVS1 RBS and enhances AAV integration into a region downstream of the RBS. TRP-185 bound to Rep68 directly, changing the Rep68 DNA binding property and stimulating Rep68 helicase activity. We present a model in which TRP-185 changes the specificity of the AAV integration site from the RBS to a downstream region by acting as a molecular chaperone that promotes Rep68 complex formation competent for 3'-->5' DNA helicase activity.

Monodisperse hollow titania nanospheres prepared using a cationic colloidal template

Titania-coated polymeric nanoparticles were synthesized based on the cationic colloidal particles which were prepared by surfactant-free emulsion copolymerization of styrene and butylacrylate in the presence of a cationic monomer, methacryloxyethyltrimethyl ammonium chloride (MOTAC) using azobis(isobutylamidine)hydrochloride (AIBA) as an initiator. These cationic particles were stabilized by poly(vinylpyrrolidone) (PVP). Then, these particles were dispersed in ethanol and mixed with titanium(IV) butoxide. Negatively charged titania precursors were rapidly hydrolyzed onto the cationic surfaces of colloidal particles. Subsequently, the samples were heated to 450 degrees C to form anatase TiO2 and to remove the colloidal template, which resulted in hollow nanospheres. The hollow titania particles were characterized with zeta analyzer, transmission electron microscopy, scanning electron microscopy, light scattering, X-ray diffraction, thermogravimetric analysis and FT-IR.

Porphyrin accumulation in mitochondria is mediated by 2-oxoglutarate carrier

Heme (Fe-protoporphyrin IX), an endogenous porphyrin derivative, is an essential molecule in living aerobic organisms and plays a role in a variety of physiological processes such as oxygen transport, respiration, and signal transduction. For the biosynthesis of heme or the mitochondrial heme proteins, heme or its biosynthetic precursor porphyrin must be transported into mitochondria from cytosol. The mechanism of porphyrin accumulation in the mitochondrial inner membrane is unclear. In the present study, we analyzed the mechanism of mitochondrial translocation of porphyrin derivatives. We showed that palladium meso-tetra(4-carboxyphenyl)porphyrin (PdTCPP), a phosphorescent porphyrin derivative, accumulated in the mitochondria of several cell lines. Using affinity latex beads, we showed that 2-oxoglutarate carrier (OGC), the mitochondrial transporter of 2-oxoglutarate, bound to PdTCPP, and in vitro PdTCPP inhibited 2-oxoglutarate uptake into mitochondria in a competitive manner (Ki = 15 microM). Interestingly, all types of porphyrin derivatives examined in this study competitively inhibited 2-oxoglutarate uptake into mitochondria, including protoporphyrin IX, coproporphyrin III, and hemin. Furthermore, mitochondrial accumulation of porphyrins was inhibited by 2-oxoglutarate or OGC inhibitor. These results suggested that porphyrin accumulation in mitochondria is mediated by OGC and that porphyrins are able to competitively inhibit 2-oxoglutarate uptake into mitochondria. This is the first report of a putative mechanism for accumulation of porphyrins in the mitochondrial inner membrane.

Polyelectrolyte functionalized magnetic emulsion for specific isolation of nucleic acids

A magnetic oil in water (o/w) emulsion was cationized by adsorption of poly(ethyleneimine) (PEI). In a subsequent step, the cationic particles were derivatized with partially hydrolyzed poly(maleic anhydride-alt-methyl vinyl ether) copolymer (PMAMVE) to lead negatively charged colloids. The experimental conditions for the covalent grafting of the PMAMVE were selected on the basis of colloidal stability, charge inversion and absence of inhibition of the enzymatic DNA/RNA amplification reactions. Once the experimental conditions were selected, oligonucleotides (ODN) bearing particles were obtained according to the sequential process: (i) grafting of single stranded ODNs onto PMAMVE; (ii) grafting of the PMAMVE-ODN conjugates onto the cationic particles according to the conditions defined above. In this strategy, both steps could be independently controlled. The ODN-PMAMVE-particles conjugates were very stable with time, did not inhibit RT-PCR and were capable of hybridizing specifically with the complementary target.

High-performance fluorescent particles prepared via miniemulsion polymerization

Highly fluorescent polymer particles were prepared with Eu beta-diketonates complex as a fluorophore by miniemulsion polymerization technique. Eu beta-diketonates complex has a long decay time, a large Stokes shift, and very narrow emission bands in comparison with other organic fluorescent compounds. Aqueous miniemulsion was prepared by mixing monomer, crosslinker, hydrophobe, and Eu beta-diketonates complex and then putting the mixture into an aqueous solution of surfactant, followed by ultrasonication. An aqueous solution of initiator was added to the miniemulsion to obtain fluorescent polymer particles, which were monodispersed without aggregation. Particle size was decreased to deca-nano scale by increasing the amount of surfactant. Fluorescent intensity was increased by using Eu beta-complex coordinated with additional ligand. Further fluorescence quantum yields and fluorescent properties in the presence of DNA were investigated to the confirm superiority of Eu beta-diketonates complexes in polymer particles.

Magnetic colloids for the generic capture of viruses

In molecular biology or in the diagnostic field, a strong interest has been devoted to the use of magnetic nanoparticles as an efficient tool for a fast and easy biomolecule extraction. Various methods allow the synthesis of numerous types of magnetic particles, but very few of them can be adapted to biological protocols. For biological tests based on the final detection of nucleic acids, the major difficulties in the choice of these magnetic beads are their fast magnetic separation, requiring a high magnetic oxide content and overall a good compatibility with enzymes used for nucleic acid amplification. In this study, magnetic colloids were obtained from oil in water (o/w) magnetic emulsion by a two-step polymer immobilization procedure. First, a polycation, poly(ethyleneimine), was adsorbed to ensure charge inversion of the emulsion droplets. Then poly(maleic anhydride-co-methyl vinyl ether) was either chemically grafted or adsorbed if under its hydrolyzed form. The obtained colloids were characterized in terms of colloidal stability, surface charge density, and morphology and were evaluated in a reverse transcription-PCR (RT-PCR) inhibition test. Selected colloids were used for the nonspecific capture of viruses, with RT-PCR being used as a means of detection. Particle size and charge studies allowed us to follow each step of their synthesis, showing the relevance of these methods. The prepared magnetic particles exhibit a good RT-PCR compatibility when used in the range of 5-40 microg in the 50 microl amplification mix. Finally, virus capture tests revealed a capture efficiency of 90% with an average detection sensitivity of 10(3)pfu/ml.

Chromatographic investigation of macromolecular affinity interactions

High-performance monolithic disk affinity chromatography was applied to the investigation of formation of complexes between (1) complementary polyriboadenylic and polyribouridylic acids, e.g. poly(A) and poly(U), respectively, (2) poly(A) and synthetic polycation poly(allylamine), pAA. Polyriboadenylic acid and poly(allylamine) were immobilized on macroporous disks (CIM disks). Quantitative parameters of affinity interactions between macromolecules were established using frontal analysis at different flow rates.

Development of Polymer Latex Particles for Selective Cleavage of Mismatched DNA and Their Application for DNA Diagnosis

We developed functional polymer latex particles that can catch and cleave mismatched DNA selectively and propose a new mismatch detection system using the functional particles. The aimed particles possess two functional units composed of mismatch binding protein (MutS) and an anthraquinone derivative (AQ), a light-activated agent that photocleaves dsDNA. Use of the functional particles made it possible to discriminate complementary and mismatched DNAs and photocleave mismatched DNA selectively. The efficiency of photocleavage of mismatched DNA by the functional particles increased with UV irradiation time. It was also found that the functional particles were reusable and had dissociation constants (K(d)) of 1000 and 68.5 nM for G/C homoduplex and G/T heteroduplex, respectively. Using the functional particles and a dsDNA-binding fluorescent dye, SYBR-Gold, we could construct the system for detection of mismatched DNA that was 40 base pairs. The functional particles prepared in this study will be an absolutely new tool for mismatch detection in DNA diagnosis.

Flow-stress-induced discrimination of a K-ras point mutation by sandwiched polymer microsphere-enhanced surface plasmon resonance

The highly sensitive detection of a K-ras point mutation with the aid of DNA-carrying microspheres as a flow-stress receptor is proposed at the surface of a surface plasmon resonance (SPR) biosensor. Single-stranded DNAs were immobilized onto epoxy-group-derivatized gold surfaces and the hybridization of DNA targets was monitored. The subsequent interaction with DNA-carrying micospheres enhanced the SPR response. The increase of flow rate during the event of dissociation changed the amount of detachment of the DNA-carrying microspheres for the mismatched pair. In addition, the viscosity was changed by addition of glycerol to the buffer. The increase of shear stress from the flow resulted in detachment of DNA-carrying microspheres hybridized with the mismatched sequence and increased the ability to discriminate a point mutation. This is a new method which not only increases the lower detection limit of evanescent wave-based biosensors, but also the ability to discriminate a point mutation which is a critical factor for ultrasensitive DNA detection in flow devices.

Covalent grafting of polythymidylic acid onto amine-containing polystyrene latex particles

The covalent grafting of a 35-base poly(thymidylic) acid (dT35) onto aminated polystyrene latex has been studied. The oligonucleotide was activated by 1,4-phenylene diisothiocyanate (PDC) prior to grafting reaction. The influence of various experimental conditions related either to the medium (pH, ionic strength) or to the latex (nature and surface charge density, presence of adsorbed nonionic surfactant) was studied. Discrimination between covalent grafting and adsorption was achieved by desorbing the non-covalently grafted dT35 induced by consecutive washings with a suitable buffer solution. The amount of covalently grafted oligonucleotide directly correlated to the concentration and accessible functional groups at the particle surface.

High-performance affinity beads for identifying drug receptors

We have developed a method using novel latex beads for rapid identification of drug receptors using affinity purification. Composed of a glycidylmethacrylate (GMA) and styrene copolymer core with a GMA polymer surface, the beads minimize nonspecific protein binding and maximize purification efficiency. We demonstrated their performance by efficiently purifying FK506-binding protein using FK506-conjugated beads, and found that the amount of material needed was significantly reduced compared with previous methods. Using the latex beads, we identified a redox-related factor, Ref-1, as a target protein of an anti-NF-kappaB drug, E3330, demonstrating the existence of a new class of receptors of anti-NF-kappaB drugs. Our results suggest that the latex beads could provide a tool for the identification and analysis of drug receptors and should therefore be useful in drug development.

Hydrophilic and cationic latex particles for the specific extraction of nucleic acids

The adsorption of BSA and RNA onto hydrophilic and thermosensitive poly(N-isopropyl-acrylamide) (NIPAM) latex particles was described as a function of pH, ionic strength and temperature. The hydrogel poly(NIPAM) latex was synthesized by precipitation polymerization in the presence of a cationic amino-containing monomer. The latex obtained was characterized in terms of particle size, and electrophoretic mobility as a function of pertinent variables: pH, temperature and ionic strength. The adsorption of BSA onto the latex was investigated to identify the conditions at which the adsorbed amount of BSA was negligible. The adsorption of RNA was studied to establish the conditions which give rise to maximal adsorption of RNA. In order to favor the desorption of RNA, desorption was investigated by changing the pH, ionic strength, and temperature. The adsorption of BSA was found to be lower at 20 than at 40 degrees C. However, the adsorption of RNA is drastically affected by the pH and the ionic strength of the medium. Maximal adsorbed amounts were obtained at acidic pH, 20 degrees C, and low ionic strength. The adsorption is shown to decrease when the pH, temperature and ionic strength increase, implying that the adsorption was mainly governed by electrostatic interactions. Maximal release of RNA molecules was obtained at high ionic strength and basic pH.

Functional interactions of transcription factor human GA-binding protein subunits

The transcription factor human GA-binding protein (hGABP) is composed of two subunits, the Ets-related hGABPalpha, which binds to a specific DNA sequence, and either one of two hGABPalpha-associated subunits, hGABPbeta or hGABPgamma. The DNA-binding protein hGABPalpha cannot affect transcription by itself, but can modify hGABP-dependent transcription in vitro and in vivo in the presence of its associated subunits. In this study, co-transfection assays showed that the ratio of hGABPbeta to hGABPgamma affected transcription from a promoter containing hGABP binding sites. Biochemical analysis showed that they bind to hGABPalpha competitively, indicating that the ratio of hGABPbeta to hGABPgamma is important for hGABP complex formation. Kinetic analysis of the protein-protein interaction using the surface plasmon resonance system showed that hGABPalpha binds to hGABPbeta or hGABPgamma with similar equilibrium constants. Kinetic analysis of the DNA-hGABP interaction showed that the binding of hGABPgamma to hGABPalpha stabilized the interaction of hGABPalpha with its DNA binding site. In addition, the kinetic analysis revealed that this was due to a slower dissociation of the protein complex from the DNA. These results suggest that hGABPalpha-associated subunits influence the DNA binding stability of hGABPalpha and regulate hGABP-mediated transcription by competing with each other.