High-performance affinity chromatography of messenger RNA.

A 50-mer of thymidylic acid, (dT)50, was coupled to silica inside prepacked columns using the N-hydroxysuccinimide chemistry. The resulting (dT)50-silica columns were used to resolve oligomers of adenylic acid, (dA)19-24, and to separate poly(A) mRNA (messenger RNA) from Saccharomyces. Oligomers which differed in length by a single nucleotide base were readily resolved. Using either (dT)50- or (dT)18-silica, poly(A) mRNA could be purified in as little as 8 min. The poly(A) mRNA isolated appeared to be full length and could be used directly for T4 RNA ligase and RNAse A and T1 enzymatic reactions. The (dT)50-silica column was used to fractionate total poly(A) mRNA by tail length. While the separation was primarily due to poly(A) tail length, most fractions appeared to contain multiple tail lengths. Whether this represents an intrinsic feature of the RNA or a limitation of the method is discussed. These studies show that polynucleotides in the kilobase size range can be separated rapidly and with good resolution on DNA-silica.     

Conversion of biomass to ethanol

In theEscherichia coli cell-free system, the modification of cell extract can be achieved by preparation of the strains carrying additional property or those being induced with a certain gene expression prior to harvesting. In this study, we analyzed the cell-free system with S30 extract containing T7 RNA polymerases (S30 extract-T7pol) prepared from E.coli BL21(DE3) strain, which includes T7 RNA polymerase from extrinsic genes by IPTG induction, as a model for the improvement of the cell-free system. The fact that a significant degree of mRNA degradation was observed in the cell-free system with S30 extract-T7pol indicates the increase of ribonuclease activity was an unfavorable influence derived from the cell-extract modification process. We also showed that this influence was settled by the addition of an effective ribonuclease inhibitor, such as copper (II) ion, to the reaction mixture.     

Path of an RNA ligand around the surface of the vaccinia VP39 subunit of its cognate VP39-VP55 protein heterodimer

VP39 is a vaccinia virus-encoded RNA modifying protein with roles in the modification of both mRNA ends. At the 3' end it acts as a processivity factor for the vaccinia poly(A) polymerase (VP55), promoting poly(A) tail elongation. Despite VP39's three-dimensional structure having been elucidated along with details of its mode of mRNA 5' end binding, the VP39-VP55 heterodimer's molecular mechanism of processivity is largely unknown. Here, the area immediately above almost the entire surface of the VP39 subunit was probed using chemical reporters, and the path of a previously unidentified RNA binding site was revealed. The path was indicated to fall within a cleft formed by the intersubunit interface and was consistent with both a previously reported model of the heterodimer-nucleic acid ternary complex and the known function of the heterodimer in processive poly(A) tail elongation.     

Ferrocenylnaphthalene diimide-based electrochemical ribonuclease assay.

Messenger RNA (mRNA) poly(A)+RNA (from mouse kidney) was immobilized on a N-hydroxysuccinimide(NHS)-activated carboxylic acid modified electrode prepared by the treatment of a gold electrode with 3,3'-dithiodipropionic acid, followed by NHS and 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). An electrochemical measurement using this mRNA electrode was carried out in an electrolyte containing ferrocenylnaphthalene diimide (1), and showed an electrochemical signal based on 1 concentrated on immobilized mRNA. After treating this electrode with water containing varied amounts of ribonuclease A (RNase A), the current peak based on 1 decreased with increasing in the amount of RNase A with a linear correlation in the range of 0.2-10 pg of RNase A.     

In Vitro Evolution and Selection of Proteins: Ribosome Display for Larger Libraries

The cell-free production of large protein libraries can now be achieved with the ribosome display technique. The use of intact ribosomes (R) in the translation of a mRNA library enables the rapid selection of the generated proteins (P) according to their affinity to a given immobilized binding partner (B).     

Polyamine‐Mediated Stoichiometric Assembly of Ribonucleoproteins for Enhanced mRNA Delivery

Messenger RNA (mRNA) represents a promising class of nucleic acid drugs. Although numerous carriers have been developed for mRNA delivery, the inefficient mRNA expression inside cells remains a major challenge. Inspired by the dependence of mRNA on 3′‐terminal polyadenosine nucleotides (poly A) and poly A binding proteins (PABPs) for optimal expression, we complexed synthetic mRNA containing a poly A tail with PABPs in a stoichiometric manner and stabilized the ribonucleoproteins (RNPs) with a family of polypeptides bearing different arrangements of cationic side groups. We found that the molecular structure of these polypeptides modulates the degree of PABP‐mediated enhancement of mRNA expression. This strategy elicits an up to 20‐fold increase in mRNA expression in vitro and an approximately fourfold increase in mice. These findings suggest a set of new design principles for gene delivery by the synergistic co‐assembly of mRNA with helper proteins.     

Covalent attachment of microbial lipase onto microporous styrene-divinylbenzene copolymer by means of polyglutaraldehyde

A novel method for immobilization of Thermomyces lanuginosus lipase onto polyglutaraldehyde-activated poly(styrene-divinylbenzene) (STY-DVB), which is a hydrophobic microporous support has been successfully developed. The copolymer was prepared by the polymerization of the continuous phase of a high internal phase emulsion (polyHIPE). The concentrated emulsion consists of a mixture of styrene and divinylbenzene containing a suitable surfactant and an initiator as the continuous phase and water as the dispersed phase. Lipase from T. lanuginosus was immobilized covalently with 85% yield on the internal surface of the hydrophobic microporous poly(styrene-divinylbenzene) copolymer and used as a biocatalyst for the transesterification reaction. The immobilized enzyme has been fully active 30 days in storage and retained the activity during the 15 repeated batch reactions. The properties of free and immobilized lipase were studied. The effects of protein concentration, pH, temperature, and time on the immobilization, activity, and stability of the immobilized lipase were also studied. The newly synthesized microporous poly(styrene-divinylbenzene) copolymer constitutes excellent support for lipase. It given rise to high immobilization yield, retains enzymatic activity for 30 days, stable in structure and allows for the immobilization of large amount of protein (11.4mg/g support). Since immobilization is simple yet effective, the newly immobilized lipase could be used in several application including oil hydrolysis, production of modified oils, biodiesel synthesis, and removal of fatty acids from oils.     

Fabrication of poly(ethylene glycol) hydrogel microstructures using photolithography

The fabrication of hydrogel microstructures based upon poly(ethylene glycol) diacrylates, dimethacrylates, and tetraacrylates patterned photolithographically on silicon or glass substrates is described. A silicon/silicon dioxide surface was treated with 3-(trichlorosilyl)propyl methacrylate to form a self-assembled monolayer (SAM) with pendant acrylate groups. The SAM presence on the surface was verified using ellipsometry and time-of-flight secondary ion mass spectrometry. A solution containing an acrylated or methacrylated poly(ethylene glycol) derivative and a photoinitiator (2,2-dimethoxy-2-phenylacetophenone) was spin-coated onto the treated substrate, exposed to 365 nm ultraviolet light through a photomask, and developed with either toluene, water, or supercritical CO2. As a result of this process, three-dimensional, cross-linked PEG hydrogel microstructures were immobilized on the surface. Diameters of cylindrical array members were varied from 600 to 7 micrometers by the use of different photomasks, while height varied from 3 to 12 micrometers, depending on the molecular weight of the PEG macromer. In the case of 7 micrometers diameter elements, as many as 400 elements were reproducibly generated in a 1 mm2 square pattern. The resultant hydrogel patterns were hydrated for as long as 3 weeks without delamination from the substrate. In addition, micropatterning of different molecular weights of PEG was demonstrated. Arrays of hydrogel disks containing an immobilized protein conjugated to a pH sensitive fluorophore were also prepared. The pH sensitivity of the gel-immobilized dye was similar to that in an aqueous buffer, and no leaching of the dye-labeled protein from the hydrogel microstructure was observed over a 1 week period. Changes in fluorescence were also observed for immobilized fluorophore labeled acetylcholine esterase upon the addition of acetyl acholine.     

Synthesis of Long Chain Fatty Acids Acylated Coumarin Glycoside Esters with Lipase as Catalyst

A series of novel coumarin glycoside esters(1―9) was synthesized through the acylation reaction of 4-methylcoumarin-7-O-β-D-glucoside(11) with different long chain fatty acids catalyzed by lipase in organic medium. The acylation occurred regioselectively at the 6'-OH of glycosyl moiety. The enzymatic synthesis was optimized to achieve 54%―70% yield using immobilized lipase(Novozym 435, 10 mg/mL) as catalyst and acetone and pyridine(9:1, volume ratio, water content<1%) as solvent with an acyl donor/coumarin glycoside molar ratio of 10:1 at a temperature of 40―50 ℃ for 96 h. All the synthesized compounds were confirmed.     

Novel biosensor for the rapid measurement of estrogen based on a ligand-receptor interaction.

A bioaffinity sensor was developed aiming at the detection of estrogen. This biosensor system is based on the specific binding of estrogen to its receptor immobilized on a gold disk electrode. The recombinant DNA encoding human estrogen receptor ligand-binding domain was expressed in bacteria using the histidine-tag fusion system. The expression of the fusion protein was under control of a bacteriophage T7 promoter, and the protein was purified under native conditions by affinity chromatography, which is based on a specific interaction between a histidine-tag, located in the N-terminus of the protein, and the Ni(II) chelate adsorbent. The protein was immobilized on an Au-electrode with Ni(II)-mediated chemisorption using a histidine tag and thiol-modified iminodiacetic acid. Cyclic voltammetric measurements showed that the reversible electrochemical reaction of a ferrocyanide/ferricyanide redox couple was suppressed by the presence of estrogen in a concentration-dependent manner. It seems reasonable to suppose that the electrostatic property of the protein layer on the electrode surface was altered by complexation with estrogen. These data suggest that this biosensor is applicable to the evaluation binding activities of the chemicals toward the human estrogen receptor.     

Internal degrees of freedom,structural motifs,and conformational energetics of the 5'-deoxyadenosyl radical: implications for function in adenosylcobalamin-dependent enzymes. A computational study

The potential energy surface of the free 5'-deoxyadenosyl radical in the gas phase is explored using density functional and second-order M?ller-Plesset perturbation theories with 6-31G(d) and 6-31++G(d,p) basis sets and interpreted in terms of attractive and repulsive interactions. The 5',8-cyclization is found to be exothermic by approximately 20 kcal/mol but kinetically unfavorable; the lowest cyclization transition state (TS) lies about 7 kcal/mol higher than the highest TS for conversion between most of the open isomers. In open isomers, the two energetically most important attractive interactions are the hydrogen bonds (a) between the 2'-OH group and the N3 adenine center and (b) between the 2'-OH and 3'-OH groups. The relative ribose-adenine rotation about the C1'-N9 glycosyl bond in a certain range changes the energy by as much as 10-15 kcal/mol, the origin being (i) the repulsive 2'-H.H-C8 and O1'.N3 and (ii) the attractive 2'-OH.N3 ribose-adenine interactions. The hypothetical synergy between the glycosyl rotation and the Co-C bond scission may contribute to the experimentally established labilization of the Co-C bond in enzyme-bound adenosylcobalamin. The computational results are not inconsistent with the rotation about the C1'-N9 glycosyl bond being the principal coordinate for long-range radical migration in coenzyme B(12)-dependent enzymes. The effect of the protein environment on the model system results reported here remains an open question.     

Surface-anchored poly(2-vinyl-4,4-dimethyl azlactone) brushes as templates for enzyme immobilization

We explored surface-anchored poly(2-vinyl-4,4-dimethyl azlactone) (PVDMA) brushes as potential templates for protein immobilization. The brushes were grown using atom transfer radical polymerization from surface-anchored initiators and characterized by a combination of ellipsometry, atomic force microscopy, and X-ray photoelectron spectroscopy. RNase A was immobilized as a model enzyme through the nucleophilic attack of azlactone by the amine groups in the lysines located in the protein. The surface density of RNase A increased linearly from 5 to 50 nm. For 50 nm thick poly(2-vinyl-4,4-dimethyl azlactone) brushes, 7.5 microg/cm2 of RNase A was bound. The kinetics and thermodynamics of RNase A immobilization, the activity relative to surface density, and the pH and temperature dependence were examined. A Langmuir-like model for binding kinetics indicates that the kinetics are controlled by the rate of adsorption of RNase A and has an adsorption rate constant, k(ads), of 2.8 x 10(-8) microg(-1) s(-1) cm3. A maximum relative activity of approximately 0.95, which is near the activity of free RNase A, was reached at 1.2 microg/cm2 (approximately 3.0 monolayers) of immobilized RNase A. The immobilized RNase A had a similar temperature and pH dependence as free RNase A, indicating no significant change in conformation. The PVDMA template was extended to other biotechnologically relevant enzymes, such as deoxyribonuclease I, glucose oxidase, glucoamylase, and trypsin, with relative activities higher than or comparable to those of enzymes immobilized by other means. PVDMA brushes offer an efficient route to immobilize proteins via the ring opening of azlactone without the need for activation or pretreatment while retaining high relative activities of the bound enzymes.     

Protein immobilization on the surface of poly-L-lactic acid films for improvement of cellular interactions

To covalently immobilize gelatin or collagen type I on poly-L-lactic acid (PLLA) film surfaces poly(hydroxyethyl methacrylate) (PHEMA) or poly(methacrylic acid) (PMAA) was grafted via photooxidization and subsequent UV-induced polymerization [Makromol. Chem. 186 (1985) 1533.1]. For films grafted with PHEMA, methyl sulfonyl chloride was used to activate the hydroxyl groups and for films grafted with PMAA 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide was used to activate the carboxyl groups. Gelatin and collagen were finally reacted with the activated hydroxyl or carboxyl groups to obtain covalently immobilized protein layers. Grafting of PHEMA, PMAA and protein on the surfaces was confirmed using ATR-IR and XPS. Surface wettability of the modified films was improved. The protein immobilized PLLA may be widely used as a biocompatible material.     

Flow-injection determination of L-histidine with an immobilized histidine oxidase from Brevibacillus borstelensis KAIT-B-022 and chemiluminescence detection.

A chemiluminometric flow injection analytical system for the quantitation of L-histidine is described. Histidine oxidase (EC 1.4.3.-) from Brevibacillus borstelensis KAIT-B-022 was immobilized on tresylated poly(vinyl alcohol) beads and packed into a stainless-steel column. The hydrogen peroxide produced was detected chemiluminometrically by a flowthrough sensor containing immobilized peroxidase (EC 1.1 1.1.7). The maximum sample throughput was 10 h(-1). The calibration graph was linear from 0.05 to 5 mM; the detection limit (signal to noise ratio = 3) was 0.01 mM. The activity of immobilized histidine oxidase reduced to 65% of the initial value after 350 injections. The system was applied to the determination of L-histidine in fish meat, such as salmon, tunny, bonito, and mackerel.     

Radiation synthesis of a water-soluble temperature sensitive polymer, activated copolymer and applications in immobilization of proteins

In this work the radiation polymerization of N-isopropylacrylamide (NIPAAM) in aqueous solutions has been carried out and a water-soluble, temperature sensitive polymer and copolymer were obtained by using γ-rays from Co-60 source at room temperature. We have gained the optimum dose and dose—rate of radiation synthesis of linear polyNIPAAM through determining conversion yield and viscosity. In order to immobilize protein (BSA) and enzyme (HRP) into this water-soluble polymer, we prepared an activated copolymer, poly ( N-isopropylacrylamide-co-N-acryloxysuccinimide). The BSA and HRP has been immobilized onto the activated copolymer. The BSA (HRP) / copolymer conjugates still kept the original thermally sensitive properties of the linear polyNIPAAM. The conjugation yield of BSA to the activated copolymer decreased with increasing of dose. The thermal stability of the immobilized HRP was stable at 0 °C for a long time and has, at least, 4 days stability at room temperature. Immobilized HRP activity was lowered when the temperature was raised above its LCST. This phenomenon was reversible and the immobilized HRP regained activity below its LCST. The optimum pH of the immobilized HRP shifted from ca.5 upward to ca.7.     

Lipase-catalyzed synthesis and properties of poly[(12-hydroxydodecanoate)-co-(12-hydroxystearate)] directed towards novel green and sustainable elastomers

Novel green and sustainable elastomers having both good biodegradability and chemical recyclability properties were designed and synthesized using potentially biobased materials and lipase as an environmentally benign catalyst. High molecular weight poly[(12-hydroxydodecanoate)-co-(12-hydroxystearate)] [poly(12HD-co-12HS)] samples with varying monomer ratios were prepared by the polycondensation of 12-hydroxydodecanoic acid and methyl 12-hydroxystearate using immobilized lipase from Candida antarctica (IM-CA) in toluene in the presence of molecular sieves 4A at 90 degrees C. Although poly(12HD) is a highly crystalline polyester having a melting temperature (T(m)) of 87.6 degrees C and crystalline temperature (T(c)) of 64 degrees C, by the copolymerization of 12HD with 12HS, both the T(m) and T(c) of the copolymer decreased with increasing 12HS contents, and poly(12HD-co-12HS) containing more than 60 mol-% 12HS was a viscous liquid at room temperature. At the same time, the Young's modulus and hardness also decreased with increasing 12HS content, and poly(12HD-co-36 mol-% 12HS) exhibited an elastic behavior, having a hardness of 70 A using a durometer A. In addition, it showed an excellent biodegradability by activated sludge and chemical recyclability by lipase.