Digital logic circuit based on a single molecular system of salicylidene Schiff base

The salicylidene Schiff base N-3,5-dichloro-salicylidene-(S)-alpha-phenylethylamine (SPEA) has been synthesized and characterized. Stimulated by one optical input (UV light) and two chemical inputs (OH(-) and Zn(2+)), SPEA undergoes reactions of photochemistry, deprotonation, and complexation. Tailing these reactions by means of the UV-vis absorption spectra and fluorescence spectra, two obvious optical outputs, an absorption band at 323 nm and a fluorescent emission peak at 460 nm, have been obtained. On the basis of encoding binary digits in these inputs and outputs applying positive logic conventions, one monomolecular circuit, which integrates one OR, two NOT, and four AND gates, has been achieved.     

Alcohol-FET sensor based on a complex cell membrane enzyme system

An alcohol -FET sensor was developed by use of a complex enzyme system in a cell membrane and an ion-sensitive field effect transistor (ISFET). The cell membrane of Gluconobacter suboxydans IFO 12528, which converts ethanol to acetic acid, was immobilized on the gate of an ISFET with calcium alginate gel coated with nitrocellulose. This ISFET (1), a reference ISFET without the cell membrane (ISFET 2) and an Ag/AgCl reference electrode were placed in 5 mM Trismalate buffer (pH 5.5, 25°C), and the differential output between ISFETS 1 and 2 was measured. The output of the sensor was stabilized by adding pyrroloquinoline quinone. The response time was ca. 10 min., and there was a linear relationship between the differential output voltage and the ethanol concentration up to 20 mg l^?1. The output of the sensor was stable for 40 h below 30°C. The sensor responded to ethanol, propan- 1-ol and butan- 1-ol, but not to methanol, propan-2-ol and butan-2-ol. The sensor was used to determine blood ethanol.     

Single-molecule DNA logic nanomachines based on origami

<正>Nowadays, it is a truism that chemists, bioengineers and others must be schooled in cell and molecular biology, including knowledge of the cellular, elemental and molecular building blocks of living systems. Inspired by exquisite and efficient biomolecular machines in living cells, such as ATPases that catalyze the decomposition of ATP into ADP and free phosphate ion, researchers representing multiple dis-     

Colorimetric logic gates based on aptamer-crosslinked hydrogels

We have developed a novel molecular logic gate system based on the incorporation of aptamer-crosslinked hydrogels. Modified gold nanoparticles are used as the output signal, which is visible to the naked eye. This system is designed for AND and OR operations using two chemicals as stimulus inputs.     

Molecular logic: a half-subtractor based on tetraphenylporphyrin

Spectroscopic changes from a solution of the amphophile 5,10,15,20-tetraphenylporphyrin in N,N-dimethylformamide using inputs of acid (HClaq) and base (KOBut) are interpreted as XOR and INHIBIT logic operations. The combination of these two operations gives rise to a device that acts as a molecular half-subtractor.     

Photonic Boolean logic gates based on DNA aptamers

We designed a pair of DNA-based logic gates that sense single-stranded DNAs and aptamer ligands to produce fluorescence outputs according to Boolean logic functions AND and OR.     

Molecular logic gates based on 2-tyrylquinoline derivatives

Various logical operations can be performed by molecular logic gates (MLG) based on 2-styrylquinoline derivatives using irradiation with light and protonation as input signals and absorbance (optical density) as output signal. The MLG operation type (“INH”, “OR”, “AND”) depends on the observation wavelength.     

Molecular logic gates based on pentacyanoferrate complexes: from simple gates to three-dimensional logic systems

The article presents new aspects of reactivity of two pentacyanoferrates: [Fe(CN)5NO]2- and [Fe(CN)5N(O)SR]3-. The dependence of thermodynamic functions on cations was found for the reaction between nitroprusside and thiolate. The thermodynamic data are interpreted in terms of ion pairing and changes in the solvation shell of the cations. It was found that the reaction enthalpies and entropies depend strongly on the cation radius. The reaction volume in turn is strongly affected by the structure and properties of the hydration shell. Careful data analysis allowed the contribution of partial cation dehydration to the total reaction volume to be determined. The experimental results were also interpreted in terms of chemical logic gates. Complex logic systems were built from a number of cells containing a switching compound arranged in different geometric patterns. Increasing the dimensionality of these arrangements leads to really complex logic systems containing up to 20 AND and OR logic gates. The system is capable of processing up to 16 bits of input data.     

Multiple logic gates based on electrically wired surface-reconstituted enzymes

The electrode functionalized with glucose oxidase (GOx) and microperoxidase-11 (MP-11) performs various Boolean logic operations (OR, XOR, AND-OR) upon addition of glucose and/or H2O2 and application of different potentials. The output signal coming from the electrically wired enzymes is electrochemically readable, allowing interfacing of biochemical computing systems with ordinary electronics.     

A glucose-responsive controlled release of insulin system based on enzyme multilayers-coated mesoporous silica particles

A novel glucose-responsive controlled release of insulin system is constructed through coating enzyme multilayers on mesoporous silica particles (MSPs). The MSPs serve as the drug reservoir, and the enzyme multilayers cross-linked with glutaraldehyde act as a valve to control the release of insulin in response to the external glucose level.     

Versatile logic devices based on programmable DNA-regulated silver-nanocluster signal transducers

A DNA-encoding strategy is reported for the programmable regulation of the fluorescence properties of silver nanoclusters (AgNCs). By taking advantage of the DNA-encoding strategy, aqueous AgNCs were used as signal transducers to convert DNA inputs into fluorescence outputs for the construction of various DNA-based logic gates (AND, OR, INHIBIT, XOR, NOR, XNOR, NAND, and a sequential logic gate). Moreover, a biomolecular keypad that was capable of constructing crossword puzzles was also fabricated. These AgNC-based logic systems showed several advantages, including a simple transducer-introduction strategy, universal design, and biocompatible operation. In addition, this proof of concept opens the door to a new generation of signal transducer materials and provides a general route to versatile biomolecular logic devices for practical applications.     

Multiquantum processes in the enzyme molecules immobilized on biological membranes

A physical model of an oxidation–reduction reaction for immobilized enzyme is considered. The influence of the electric-field intensity of a biological membrane on the enzyme reaction rate is analyzed. It is shown that the low-frequency dipole-active vibration of the oppostite charge groups of the substrate and enzyme relative to each other leads to multiquantum excitation of the system over the conformational degree of freedom. This excitation provides an abrupt increasing of the tunnel decay rate of the substrate–enzyme complex on a free product and a free enzyme. This way of the reaction is more probable in comparison with the usual overbarrier process. Some consequences for the immobilized cytochrome P-450 are discussed. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 66 : 255–260, 1998     

Optoelectronic reader for CET dosimeter, a radiation accident chemical dosimetry system

The use of chlorobenzene–ethanol–trimethylpentane solution (CET) in radiation dosimetry is based on radiolytic formation of hydrochloric acid which protonates a pH indicator, thymolsulphonphthalein. The high molar absorptivity of its red form at 552 nm is responsible for a high sensitivity of the system: doses in the range 0.2–15 Gy can be measured. Together with a visual colour comparator it has formed a personnel dosimetry system suitable for accident and civil defense use.

A newly constructed optoelectronic reader with two two-colour light emitting diodes (550 and 690 nm) as light sources and a silicone photocell as a detector uses the differential absorbance at these two wavelengths as the response. The response is a direct function of dose and can be recorded and processed electronically.     

A biosensor based on urate oxidase-peroxidase coupled enzyme system for uric acid determination in urine

A new amperometric biosensor based on urate oxidase-peroxidase coupled enzyme system for the specific and selective determination of uric acid in urine was developed. Commercially available urate oxidase and peroxidase were immobilized with gelatin by using glutaraldehyde and fixed on a pretreated teflon membrane. The method is based on generation of H₂O₂ from urine uric acid by urate oxidase and its consuming by peroxidase and then measurement of the decreasing of dissolved oxygen concentration by the biosensor. The biosensor response depends linearly on uric acid concentration between 0.1 and 0.5 μM. In the optimization studies of the biosensor, phosphate buffer (pH 7.5; 50 mM) and 35 °C were obtained as the optimum working conditions. In addition, the most suitable enzyme activities were found as 64.9×10⁻³ U cm⁻² for urate oxidase and 512.7 U cm⁻² for peroxidase. And also some characteristic studies of the biosensor such as reproducibility, substrate specificity and storage stability were carried out.     

Labile zinc-assisted biological phosphate chemosensing and related molecular logic gating interpretations

Herein, molecular fluorescence 'OFF-ON' behavior with aqueous addition of biological phosphate and Zn(2+) is studied with Zn(2)(slys)(2)Cl(2) [H(2)slys = 6-amino-2-{(2-hydroxybenzylidene)amino}hexanoic acid], a fluorescent water-soluble complex, using various spectroscopic tools (e.g., (31)P NMR, UV-vis, emission, and CD spectroscopy) at the micromolar level. Adduct-dependent fluorescence intensity changes can be interpreted as a two-input (cation/anion) implication molecular logic gating system. A displacement study of PPi from the dizinc complex is also reported. Diphosphate and triphosphate addition/displacements were also studied. (31)P NMR spectroscopy shows gradual NMR peak shifts from bound ADP/GDP to free ADP/GDP with increasing [PPi]. In the emission spectrum, fluorescence quenching is shown: CD signal maxima decrease with addition of PPi. These displacement events are also tested with triphosphates (ATP, GTP), and their binding strength/displacement ability over ADP/GDP is quantified: PPi > ATP ≈ GTP (3.35 ± 0.77 × 10(4) M(-1) for PPi, 7.73 ± 1.79 × 10(3) M(-1) for ATP, 9.21 ± 2.88 × 10(3) M(-1) for GTP over 1·ADP). Many anions and cations were also screened for selectivity. Tubulin polymerization was assayed in the presence of 1 and its copper analogue which reflected a slight inhibition in polymerization.     

A natural-product-inspired photonic logic gate based on photoinduced electron-transfer-generated dual-channel fluorescence

[structure: see text] Modified 1-benzylisoquinoline N-oxides can operate as molecular logic gates. The combination of dual-channel fluorescence emissions and the preferred interaction for selected chemical inputs allows one to design multifunction and self-reprogrammable molecular logic gates.     

Building a biological space based on protein sequence similarities and biological ontologies

Assignment of function to protein sequence is a task of growing importance in the life sciences, as new high-throughput sequencing DNA technologies generate ever increasing quantities of genomic and meta-genomic data. Patterns within the sequence space, caused by the evolutionary conservation and assembly of protein domains, make possible the inference of function from sequence similarity. Clustering similar sequences is a useful technique for finding conserved sequences; the CluSTr database is a publicly-available database arranging proteins in a hierarchy structured by similarity. The protein classification tool InterProScan builds on this approach by applying a range of methods to detect proteins that contain signatures indicative of the presence of particular conserved domains. The use of ontologies to describe protein function provides a flexible and abstract language to classify proteins. Together, these techniques can provide an understanding of the shape of the protein space, and can be used to explore the unchartered waters of the emerging metagenomic world.     

TheTalaromyces emersonii enzyme system

In typical fermentations at 45‡C on cellulose/corn steep liquor/ammonium and mineral salts medium, growth of the thermophilic fungusTalaromyces emersonii increases rapidly up to about 50 h and then decreases, presumably because of cell lysis, sporulation, or both. The accumulation of cellulase activity follows closely on growth and essentially reaches a maximum at about the same time that cell protein does. By contrast, two peaks of Β-glucosidase activity are observed, one maximal at about 36 h and the second at about 75 h. Fractionation of culture filtrates showed that the cellulase system is comprised of at least four endoglucanases (EC 3.2.1.4), four or five exoglucanases (cello-biohydrolase; EC 3.2.1.91), and three types of Β-glucosidase (cellobiase; EC 3.2.1.21). All are glycoproteins. Indeed, variation in carbohydrate content may account for some of the observed multiplicity of enzyme forms. Although none of the individual components is active against cellulose, reconstitution experiments show that appropriate mixtures of each type act synergistically to effect hydrolysis of substrate. In addition to the three extracellular Β-glucosidases I (M_r, 135,000), II (M_r, 100,000), and III (M_r, 45,700), an intracellular form, IV (M_r, 57,600), has been isolated. All exist as single polypeptides. The extracellular forms I and III are most active at 70‡C, pH 5, and have half-lives under these conditions of 6 and 3 h, respectively. By contrast, the intracellular form (IV) is most active at 35‡C and is rapidly denatured at higher temperatures. Substrate specificity and other studies provide clues to their possible roles in vivo. Β-Glucosidase III acts as an exoglucohydrolase by removing glucose residues from cellooligosaccharides arising from the action of endocellulases. Β-Glucosidase I is the major enzyme involved in cleaving cellobiose and short chain cellooligosaccharides. In doing so it relieves the inhibition by cellobiose of cellulase action. The intracellular form, Β-glucosidase IV, may have a dual role. By virtue of its transferase activity it may convert incoming cellobiose to the active inducer of cellulase synthesis, whereas by cleaving cellobiose to glucose (hydrolase action) it provides energy for the cell and a repressor of cellulase formation. Four endocellulases have been purified to apparent homogeneity as judged by electrophoresis. Preliminary results show that they all have M_r values of about 70,000 and pI values less than 4. However, they differ from one another in carbohydrate content, thermal stability, and affinity for substrate. The complete cellulase system is most active at pH 4.2, 60–65‡C, and retains about 80% of its original activity after 5 d incubation at 60‡C, pH 5. Avicel and filter paper most effectively induce synthesis of the complete cellulase system, as measured by the ability of culture filtrate to digest filter paper. Cotton, Solka floc, and α-cellulose are also effective inducers, as are “wastes” such as newspaper, straw, and beet pulp. Little or no cellulase synthesis is evident when lactose, cellobiose, or glucose replaces cellulose in growth media. From a practical viewpoint we find that saccharification of beet pulp is most readily achieved by using enzyme (i.e., culture filtrate) obtained by growing the organism on medium containing beet pulp as the source of cellulose. Of the various strains ofTalaromyces emersonii investigated for cellulase production, we found CBS 814.70 to be the best, yielding approx. 0.5 IU/mL of culture filtrate. By medium optimization and genetic manipulation we have isolated a number of mutants of this strain giving 2 IU/mL or more and enzyme productivities of 20–25 IU/L/h. Xylanase, arabinogalactanase, and pectinase activities have also been detected in culture filtrates of the organism when grown on beet pulp. Various lignocellulosic materials, including cotton, Solka floc, Avicel, filter paper, newspaper, and straw, can be degraded by the enzyme system. However, much of our effort has been directed to investigation of the saccharification of beet pulp since it is available in large quantities at central locations and because its lignin content is low. About 85% of the dry weight of this material is accounted for by cellulose, hemicellulose, and pectin in roughly equal proportions. Culture filtrates effect significant saccharification of pulp as measured by the release of reducing sugars or of glucose. Ball-milling the pulp prior to incubation with enzyme effects considerable improvement in the extent of digestion. Alkali or peracetic acid pretreatment of the ball-milled substrate facilitates enzymic hydrolysis even further. Good results are also obtained when unmilled pulp is (a) pretreated with pectinase prior to incubation with normal culture filtrates or (b) incubated with more concentrated culture filtrates with good pectinase activity. Under suitable conditions, 80% hydrolysis of beet pulp polysaccharides was achieved in 5 d at 60‡C, pH 5.