Highly Precise and Sensitive Polymerase Chain Reaction Using Mesoporous Silica-Immobilized Enzymes.

A highly precise and sensitive technology that enables DNA amplification/detection from minimal amounts of nucleic acid is expected to find applicability in genetic testing involving small amounts of samples. The use of a free enzyme in conventional DNA amplification techniques, such as the polymerase chain reaction (PCR), frequently causes side reactions (i.e., nonspecific DNA amplification) when ≤103 substrate DNA molecules are present, thereby preventing selective amplification of the target DNA. To address this issue, we have developed a novel DNA amplification system, mesoporous silica-enhanced PCR (MSE-PCR), which involves the immobilization of a thermostable DNA polymerase from Thermococcus kodakaraensis (KOD DNA polymerase) into highly ordered nanopores of the mesoporous silica to control the reaction environment around the enzyme. In the MSE-PCR system using immobilized KOD DNA polymerase, such nonspecific DNA amplification was remarkably inhibited under the same conditions. Furthermore, the optimization of mesoporous silica pore sizes enabled selective and efficient DNA amplification from DNA substrates at the single-molecule level, i.e., one ten-thousandth of the amount of substrate DNA required for a DNA amplification reaction using a free enzyme. The results obtained in this study have shown that the nanopores of mesoporous silica can inhibit nonspecific reactions in DNA amplification, thereby considerably improving the specificity and sensitivity of the DNA polymerase reaction.

Enzyme Immobilization in Mesoporous Silica for Enhancement of Thermostability.

Direct enzyme immobilization by encapsulation in the pores of mesoporous silica particles enhances protein thermal and chemical stability. In this study, we investigated the effect of pore size on the thermostability and catalytic activity of Escherichia coli glutaminase YbaS encapsulated under high temperature conditions in two SBA-type mesoporous silicas: SBA5.4 and SBA10.6 with pore diameters of 5.4 and 10.6 nm, respectively. The changes in enzyme conformation under high temperature conditions were assessed using PSA, a benzophenoxazine-based fluorescent dye that is sensitive to denatured aggregated proteins. The results showed that YbaS adsorption to SBA10.6 was higher than that to SBA5.4 and that SBA10.6-encapsulated YbaS was more resistant to heat treatment and maintained higher conformational stability than SBA5.4-encapsulated or free enzyme. Moreover, the heat-treated YbaS-SBA10.6 composite demonstrated high catalytic activity in glutamine hydrolysis. Thus, enzyme encapsulation in suitable silica mesopores can prevent heat-induced denaturation and subsequent aggregation of the enzyme.

Electrochemical enzymatic biosensor with long-term stability using hybrid mesoporous membrane.

An acetylcholinesterase-immobilized sensor unit was successfully prepared by encapsulating the enzyme within hybrid mesoporous silica membranes (F127-MST). Through a novel combination with tetracyanoquinodimethane, both acetylcholine and organophosphorus pesticides were successfully detected with high sensitivity. Furthermore, we manufactured the working prototype of an enzyme sensor with this sensor unit for detecting dichlorvos, aldicarb and parathion. At present, the detection limit in this working prototype either equaled or surpassed that of others. Also, we have the advantage of increased stability of the enzyme against the outer environment by encapsulation of the enzymes into a silica nanospace. Consequently, acetylcholinesterase immobilized in F127-MST is a practical sensor with high sensitivity, reusability, and storage stability.

An enzyme-encapsulated microreactor for efficient theanine synthesis.

A flow-type microreactor containing glutaminase-mesoporous silica composites with 10.6 nm pore diameter (TMPS10.6) was developed for the continuous synthesis of theanine, a unique amino acid. High enzymatic activity was exhibited by the local control of the reaction temperature.

Heterogeneous nucleation of protein crystals on fluorinated layered silicate.

Here, we describe an improved system for protein crystallization based on heterogeneous nucleation using fluorinated layered silicate. In addition, we also investigated the mechanism of nucleation on the silicate surface. Crystallization of lysozyme using silicates with different chemical compositions indicated that fluorosilicates promoted nucleation whereas the silicates without fluorine did not. The use of synthesized saponites for lysozyme crystallization confirmed that the substitution of hydroxyl groups contained in the lamellae structure for fluorine atoms is responsible for the nucleation-inducing property of the nucleant. Crystallization of twelve proteins with a wide range of pI values revealed that the nucleation promoting effect of the saponites tended to increase with increased substitution rate. Furthermore, the saponite with the highest fluorine content promoted nucleation in all the test proteins regardless of their overall net charge. Adsorption experiments of proteins on the saponites confirmed that the density of adsorbed molecules increased according to the substitution rate, thereby explaining the heterogeneous nucleation on the silicate surface.

Detection of hetero-proteins-mesoporous silica assembly by BRET.

The assembly of a hetero-protein (Renilla reniformis luciferase (Rluc) and a green fluorescence protein (sGFP)) encapsulated in folded-sheet mesoporous material with 7.1 nm pore diameter (FSM7.1), which was used for studying protein-protein interactions in pores of mesoporous silica, has been confirmed by the detection of bioluminescence resonance energy transfers (BRET).

Enhancement in thermal stability and resistance to denaturants of lipase encapsulated in mesoporous silica with alkyltrimethylammonium (CTAB).

We assembled a highly durable conjugate with both a high-density accumulation and a regular array of lipase, by encapsulating it in mesoporous silica (FSM) with alkyltrimethylammonium (CTAB) chains on the surface. The activity for hydrolyzing esters of the lipase immobilized in mesoporous silica was linearly related to the concentration of lipase, whereas that of non-immobilized lipase showed saturation due to self-aggregation at a high concentration. The lipase conjugate also had increased resistance to heating when stayed in the silica coupling with CTAB. In addition, encapsulating the enzyme with FSM coupled CTAB caused the lipase to remain stable even in the presence of urea and trypsin, suggesting that the encapsulation prevented dissociation and denaturing. This conjugate had much higher activity and much higher stability for hydrolyzing esters when compared to the native lipase. These results show that FSM provides suitable support for the immobilization and dispersion of proteins in mesopores with disintegration of the aggregates.

High-throughput protein refolding screening method using zeolite.

We established a 96-well-plate-based refolding screening system using zeolite. In this system, protein denatured and solubilized with 6 M guanidine hydrochloride is adsorbed onto zeolite placed in a 96-well plate. The refolding conditions can be tested by incubating the samples with refolding buffers under various conditions of pH, salts, and additives. In this study, we chose green fluorescent protein as the model protein. Green fluorescent protein was expressed as inclusion bodies, and we tested the effects of four pH conditions and six additives on its refolding. The results demonstrate that green fluorescent protein was more efficiently refolded with zeolite than with the conventional dilution method.

Refolding of lactate dehydrogenase by zeolite beta.

We used zeolite beta as an adsorbing matrix to refold recombinant lactate dehydrogenase (LDH) protein collected as an insoluble aggregate from a bacterial expression system. The adsorption isotherm revealed that 1 g of zeolite adsorbed 200 mg of denatured LDH solubilized with a buffer containing 6 M of guanidine hydrochloride. The pH of the buffer had little effect on the adsorption, but this property was abolished by preincubation of the zeolite with polyethylene glycol (PEG) in a weight ratio of 1:10. These data suggest that the adsorption of LDH depends on the hydrophobicity of the zeolite surface, and that the adsorption of PEG to zeolite is sufficient to release LDH from its surface. LDH was thus released by refolding buffer containing PEG and arginine, and soluble LDH was obtained in its active enzymatic form. The addition of arginine dramatically increased the yield of LDH in a dose-dependent manner. The overall refolding efficiency was optimized to 35%.

Use of zeolite to refold a disulfide-bonded protein.

Zeolites are microporous crystalline aluminosilicates with a highly ordered structure. Using zeolite beta as an adsorbent, denatured/reduced hen egg lysozyme was refolded to the active form at high concentrations. The denatured/reduced lysozyme was adsorbed onto the zeolite and the protein was refolded by desorbing it into refolding buffer, consisting of redox reagents, guanidine hydrochloride, polyethylene glycol, and L-arginine. This zeolite refolding method could be highly effective for various kinds of proteins, refolding them with high efficiency even when they contain disulfide bonds.

Selective adsorption of bacterial cells onto zeolites.

Zeolites adsorb microbial cells on their surfaces and selective adsorption for specific microorganisms was seen with certain zeolites. Tests for the adsorption ability of zeolites were conducted using various established microbial cell lines. Specific cell lines were shown to selectively absorb to certain zeolites, species to species. In order to understand the selectivity of adsorption, we tested adsorption under various pH conditions and determined the zeta-potentials of zeolites and cells. The adsorption of some cell lines depended on the pH, and some microorganisms were preferentially adsorbed at acidic pH. The values of zeta-potentials were used for calculating the electric double layer interaction energy between zeolites and microbial cells. There was a correlation between the experimental adsorption results and the interaction energy. Moreover, we evaluated the surface hydrophobicity of bacterial cells by using the microbial adherence to hydrocarbon (MATH) assay. In addition, we also applied this method for zeolites to quantify relative surface hydrophobicity. As a result, we found a correlation between the adsorption results and the hydrophobicity of bacterial cells and zeolites. These results suggested that adsorption could be explained mainly by electric double layer interactions and hydrophobic interactions. Finally, by using the zeolites Na-BEA and H-Y, we succeeded in clearly separating three representative microbes from a mixture of Escherichia coli, Bacillus subtilis and Staphylococcus aureus. Zeolites could adsorb each of the bacterial cell species with high selectivity even from a mixed suspension. Zeolites can therefore be used as effective carrier materials to provide an easy, rapid and accurate method for cell separation.

The ensemble of hetero-proteins in inorganic nanochannels.

The assembly and proper alignment of two heterofluorescent proteins (sGFP and DsRed) in the mesoporous channels of ethanol-treated FSM6.2 (a folded-sheet mesoporous material with a pore diameter of 6.2 nm) was confirmed using a fluorescence resonance energy transfer (FRET) technique. The sGFP-DsRed-FSM6.2 conjugate showed a large decrease in the emission of donor (sGFP) fluorescence, indicating that the conjugate functions as an energy transfer system through the combination of the two heteroproteins, due to the successful encapsulation of the sGFP-DsRed pairs in the mesopores. Fluorescence spectral analysis demonstrated that the proteins were highly dispersed and homogeneously encapsulated in the mesopores of FSM6.2, even at high concentration, although they spontaneously aggregated and showed a red shift in solution at the concentration corresponding to that in the conjugate. Furthermore, an increase in the amount of sGFP and DsRed adsorbed to the pores of FSM6.2 led to a decrease in the distance between these proteins, resulting in enhancement of FRET efficiency.

Formation of cage-like hollow spherical silica via a mesoporous structure by calcination of lysozyme-silica hybrid particles.

Calcination of lysozyme-silica hybrid hollow particles gives novel cage-like hollow spherical silicas with differently patterned through-holes on their shell structure.

Encapsulation of hemoglobin in mesoporous silica (FSM)-enhanced thermal stability and resistance to denaturants.

Hemoblogin (Hb), which is a typical oligomeric protein, was introduced into the pores of mesoporous silica (FSM: folded-sheet mesoporous material) that had a diameter of 7.5 nm. Soret CD spectra of Hb-FSM-7.5 conjugates showed a peak that was identical to that of free Hb. This suggests that Hb retained its highly ordered structure in the mesoporous silica. In addition, the UV-visible absorption spectrum showed that Hb had an increased resistance to heat denaturation in the silica. Even after heat treatment at 85 degrees C, Hb-FSM-7.5 retained its ligand-binding activity. The stability of Hb-FSM-7.5 was examined further by measuring its peroxidase-like activity. Encapsulation of Hb resulted in the retention of activity in the presence of high NaCl or Gdn-HCl levels. This suggests that encapsulation prevented dissociation and denaturing. Thus, it seems that the mesopores created a favorable environment for the oligomeric protein to perform its function, even under harsh conditions.

Synthesis of protein-silica hybrid hollow particles through the combination of protein catalysts and sonochemical treatment.

Hollow spherical particles with protein-silica hybrid shell structures have been synthesized through a combination of the catalytic activity of the protein and sonochemical treatment; the morphologies of the particles were controlled by varying the protein concentration.