Kinetic studies of DNA cleavage reactions catalyzed by an ATP-dependent deoxyribonuclease on a 27-MHz quartz-crystal microbalance

Catalytic DNA cleavage reactions by an ATP-dependent deoxyribonuclease (DNase) from Micrococcus luteus were monitored directly with a DNA-immobilized 27-MHz quartz-crystal microbalance (QCM). The 27-MHz QCM is a very sensitive mass-measuring device in aqueous solution, as the frequency decreases linearly with increasing mass on the electrode at a nanogram level. Three steps in ATP-dependent DNA hydrolysis reactions, including (1) binding of DNase to the end of double-stranded DNA (dsDNA) on the QCM electrode (mass increase), (2) degradation of one strand of dsDNA in the 3' --> 5' direction depending on ATP (mass decrease), and (3) release of the enzyme from the nonhydrolyzed 5'-free-ssDNA (mass decrease), could be monitored stepwise from the time dependencies of QCM frequency changes. Kinetic parameters for each step were obtained as follows. The binding constant (K(a)) of DNase to the dsDNA was determined as (28 +/- 2) x 10(6) M(-)(1) (k(on) = (8.0 +/- 0.3) x 10(3) M (-)(1) s(-)(1) and k(off) = (0.29 +/-0.01) x 10(-)(3) s(-)(1)), and it decreased to (0.79 +/- 0.16) x 10(6) M(-)(1) (k'(on) = (2.3 +/- 0.2) x 10(3) M (-)(1) s(-)(1) and k'(off) = (2.9 +/- 0.1) x 10(-)(3) s(-)(1)) for the completely nonhydrolyzed 5'-free ssDNA. This is the reason the DNase bound to the dsDNA substrate can easily release from the nonhydrolyzed 5'-free-ssDNA after the complete hydrolysis of the 3' --> 5' direction of the complementary ssDNA. K(a) values depended on the DNA structures on the QCM, and the order of these values was as follows: the dsDNA having a 4-base-mismatched base-pair end (3) > the dsDNA having a 5' 15-base overhanging end (2) > the dsDNA having a blunt end (1) > the ssDNA having a 3'-free end (4) > the ssDNA having a 5'-free end (5). Thus, DNase hardly recognized the free 5' end of ssDNA. Michaelis-Menten parameters (K(m) for ATP and k(cat)) of the hydrolysis process also could be obtained, and the order of k(cat)/K(m) was as follows: the dsDNA having a blunt end (1) approximately the dsDNA having a 4-base-mismatched base-pair end (3) > the ssDNA having a free 3' end (4) > the ssDNA having a free 5' end (5). Thus, DNase could not recognize and not hydrolyze the free 5' end of ssDNA. The DNA hydrolysis reaction could be driven by dATP and GTP (purine base) as well as ATP, whereas the cleavage efficiency was very low driven with UTP, CTP (pyrimidine base), ADP, and AMP.     

Wireless electrodeless piezomagnetic biosensor with an isolated nickel oscillator

This study presents a fundamental concept of piezomagnetic biochemical sensor driven in a wireless-electrodeless manner. A stepped cylindrical rod of nickel is used as the oscillator, which traps the vibrational energy of axially-polarized surface-shear waves in the central part, where the diameter is slightly larger. A meander-line coil surrounding the oscillator with an air gap can cause and detect the resonant vibrations of the surface-shear waves via the piezomagnetic effect. The resonant frequency of the trapped-mode resonance is continuously measured to detect human immunoglobulin G (IgG). It decreased by 0.08% when a solution containing IgG was injected into the glass cell where the oscillator was placed alone. This oscillator is useful for fundamental studies of various biochemical reactions in a closed system in different environmental gases and different pressures.     

Interaction of tea catechins with lipid bilayers investigated by a quartz-crystal microbalance analysis

The quartz-crystal microbalance (QCM) technique was applied to investigate the interaction of tea catechins with lipid bilayers. The association constants obtained from the frequency changes of QCM revealed that (-)epicatechin gallate and (-)epigallocatechin gallate interacted with 1,2-dimyristoyl-sn-glycero-3-phosphocholine ca. 1000 times more strongly than (-)epicatechin and (-)epigallocatechin. The results exhibited good correlation with the strength of biological activity.     

Quantitative detection of a DNA ligase reaction on a quartz-crystal microbalance.

We report here kinetic analyses of DNA ligation by using a DNA-immobilized quartz-crystal microbalance (QCM), which enables in situ real-time monitoring of both the binding of ligase and ligation reaction on DNA strands, as mass changes.     

Kinetic studies of site-directed mutational isomalto-dextranase-catalyzed hydrolytic reactions on a 27 MHz quartz-crystal microbalance

A quartz-crystal microbalance (QCM) technique was applied to analyze effects of site-directed mutagenesis of a glycosidase (isomalto-dextranase) on the hydrolysis mechanism of the substrate binding (k(on), k(off), and K(d)) and the catalytic process (k(cat)), separately, by using a dextran-immobilized QCM in buffer solution. D266N, D198N, and D313N mutants, which are predicted as critical residues of the isomalto-dextranase hydrolytic activity, dramatically decreased the apparent enzyme activity. The D266N mutant, however, did not change the substrate binding ability (K(d)), and the D198N and D313N mutants largely increased K(d) values due to the increase of k(off) and/or the decrease of k(on) values, as well as the negatively small k(cat) values. From these results, we estimate the reaction mechanism, in which Asp266 acts as only a general acid in the catalytic process, Asp198 acts as both nucleophile in the catalytic process and binding the substrate, and Asp313 acts as only the substrate binding.     

In situ monitoring of peptide-bound dsDNA selection on a GCN4-bZIP-immobilized quartz-crystal microbalance.

A highly sensitive 27 MHz quartz-crystal microbalance (QCM) was applied as a device of dsDNA in vitro selection. When GCN4-bZIP peptides were immobilized on the small Au electrode of the QCM, dsDNAs having TGACTCA sequences could be mainly selected from DNA library having a 15-bp random region, which was consistent with the sequence observed by X-ray crystallography.     

Resonance acoustic microbalance with naked-embedded quartz (RAMNE-Q) biosensor fabricated by microelectromechanical-system process

A resonance acoustic microbalance with a naked-embedded quartz (RAMNE-Q) is realized by a microfabrication method, aiming at broader applications of quartz-crystal microbalance (QCM) biosensors. The RAMNE-Q biosensor consists of three layers; a silicon layer with an engraved microchannel and sandwiching glass layers. The naked AT-cut quartz resonator of 9.3 or 28.5 μm thick is located in the microchannel and supported by the silicon micropillars and semicircular walls without fixing, and it is encapsulated by the rigid body. Cupper antennas are used for generating and receiving electromagnetic fields to excite and detect the shear vibration of the quartz oscillator during the solution flow, thereby achieving the noncontact measurement of the resonance frequency. Because of the isolated resonator, the Q factor is high enough (about 1500 at 170-180 MHz) even in the flowing solution. We succeeded in detecting 1 ng/ml human immunoglobulin G in phosphate-buffered-saline solution via Staphylococcus aureus protein A immobilized nonspecifically on the quartz surfaces, demonstrating the high sensitivity and high signal-to-noise ratio of the RAMNE-Q biosensor. It does not require electrodes and is a replacement-free biosensor, and its reusability is confirmed.     

Quantitative detection of binding of PCNA protein to DNA strands on a 27 MHz quartz-crystal microbalance.

We report here binding kinetics of proliferating cell nuclear antigen (PCNA) to the dsDNA immobilized on a 27 MHz quartz-crystal microbalance. PCNA is a toroidal-shaped protein and encircles dsDNA sliding along the strand. The binding behavior of this sliding clamp protein was compared with those of other side binding proteins such as GCN4-bZIP and Zn-finger peptides.     

Effect of ultrasound on DNA polymerase reactions: monitoring on a 27-MHz quartz crystal microbalance

Effects of ultrasound irradiation on DNA polymerase (Klenow fragment, KF) reactions were studied on the template/primer DNA-immobilized quartz crystal microbalance (QCM). Under ultrasound irradiation, binding of KF to the DNA was suppressed due to the decrease of the binding rate constant (k(1)) and the increase of the dissociation rate constant (k(-)(1)). The catalytic elongation rate (k(cat)) was increased, but the stability of the KF/DNA/monomer ternary complex (K(m)) was decreased by the ultrasound irradiation. Ultrasound effects are discussed in correlation with the conformation changes of domain structures in KF.     

LSPR biomolecular assay with high sensitivity induced by aptamer-antigen-antibody sandwich complex

Herein we demonstrate a sensitive approach for protein detection based on peak shifts of localized surface plasmon resonance (LSPR) induced by aptamer-antigen-antibody sandwich structures. The applicability of the proposed method is demonstrated using human α-thrombin as a model analyte. While the binding of thrombin to its specific receptor, thrombin binding aptamer (TBA) modified on Au nanorods (AuNRs), causes a measurable LSPR shift, a subsequent binding of an anti-thrombin antibody to the captured thrombin can exhibit a nearly 150% amplification in the LSPR response. This enhanced signal essentially leads to an improvement of limit of detection (LOD) by more than one order of magnitude. In addition, the use of TBA as thrombin recognition units makes the biosensor reusable. The feasibility of the proposed method was further exploited by the detection of thrombin in human serum, opening the possibility of a real application for diagnostics and medical investigations.     

Development and validation of sandwich ELISA microarrays with minimal assay interference

Sandwich enzyme-linked immunosorbent assay (ELISA) microarrays are emerging as a strong candidate platform for multiplex biomarker analysis because of the ELISA's ability to quantitatively measure rare proteins in complex biological fluids. Advantages of this platform are high-throughput potential, assay sensitivity and stringency, and the similarity to the standard ELISA test, which facilitates assay transfer from a research setting to a clinical laboratory. However, a major concern with the multiplexing of ELISAs is maintaining high assay specificity. In this study, we systematically determine the amount of assay interference and noise contributed by individual components of a multiplexed 24-assay system. We find that nonspecific reagent cross-reactivity problems are relatively rare. We did identify the presence of contaminant antigens in a "purified antigen". We tested the validated ELISA microarray chip using paired serum samples that had been collected from four women at a 6-month interval. This analysis demonstrated that protein levels typically vary much more between individuals than within an individual over time, a result which suggests that longitudinal studies may be useful in controlling for biomarker variability across a population. Overall, this research demonstrates the importance of a stringent screening protocol and the value of optimizing the antibody and antigen concentrations when designing chips for ELISA microarrays.     

A biotin-hydrogel-coated quartz crystal microbalance biosensor and applications in immunoassay and peptide-displaying cell detection

A biotin-coated quartz crystal microbalance (QCM) chip was prepared by dip-coating a long-chain alkanethiol-modified crystal with precoupled dextran-biotin hydrogels. The resulting biotin chip was used to affinity-immobilize streptavidin (SAv) and was then further employed for various biosensor assays. First, the SAv chip allowed efficient on-line binding of biotinylated bovine serum albumin (bBSA), followed by a sensitive and specific response toward anti-bovine serum albumin (BSA) antibodies. Three consecutive immunoassays were reproducibly demonstrated with a single chip. The apparent binding kinetics with k_on = 5.9 μM⁻¹ h⁻¹, k_off = 10.1 h⁻¹, and K_D = 1.71 μM was readily resolved by fitting the real-time sensorgrams. Second, the capability of the SAv chip to selectively recognize recombinant Escherichia coli with flagella displaying an artificial SAv binding peptide, Strep-tag II, was demonstrated by QCM analysis and verified by scanning transmission electron microscope (STEM) image analysis with biotin-coated gold nanoparticles as the label. Finally, the affinity of the cell-displayed Strep-tag II peptide to surface-coated SAv, K_D = 6.8 × 10⁸ CFU/ml, was resolved on-line using equilibrium binding kinetics by QCM. This study presents an easy, economical, and reliable method of preparing high-performance SAv-coated biotin chips with potential for application in real-time repetitive immunoassays, on-line binding kinetics studies, and high-affinity peptide screening.     

An antibody-lectin sandwich assay for quantifying protein glycoforms

We describe an antibody-lectin sandwich assay for quantitation of glycoforms of proteins. The assay uses deglycosylated IgG antibody immobilized on a microtiter plate to capture the protein of interest from the sample. The particular glycoform is then identified by reaction with biotin-labeled lectin, which is measured using streptavidin/alkaline phosphatase. The assay can be adapted to quantitate any protein’s glycoforms by simply substituting the antibody and lectin with specific alternatives,     

Estrogen receptor binding assay of chemicals with a surface plasmon resonance biosensor

We have developed a simple assay method for the evaluation of estrogen receptor (ER) binding capacity of chemicals without the use of radio- or fluorescence-labeled compounds. We used the solution competition assay by the BIACORE biosensor, a surface plasmon resonance biosensor, with estradiol as a ligand, human recombinant ER(alpha) (hrER(alpha)) as a high molecular weight (hmw) interactant and test chemicals as analytes. For the ligand, aminated estradiol with a spacer molecule (E2-17PeNH) was synthesized and immobilized on a carboxymethyl dextran-coated sensor chip by the amine coupling method. The injection of the hmw interactant hrER(alpha) to the biosensor raised the sensorgram, indicating its binding to the ligand E2-17PeNH. The binding of test chemicals to hrERalpha was determined as a reduction in the hrER(alpha) binding to E2-17PeNH. The dissociation constant for the binding to hrER(alpha) was calculated for estrone (4.29 x 10(-9)M), estradiol (4.04 x 10(-10)M), estriol (8.35 x 10(-10)M), tamoxifen (2.16 x 10(-8)M), diethylstilbestrol (1.46 x 10(-10)M), bisphenol A (1.35 x 10(-6)M) and 4-nonylphenol (7.49 x 10(-6)M), by plotting the data according to an equation based on mass action law. This method can also be used as a high throughput screening method.     

Molecularly imprinted ligand-exchange recognition assay of glucose by quartz crystal microbalance

Molecular imprinted polymers (MIP) as a recognition element for sensors are increasingly of interest and MIP-quartz crystal microbalance (QCM) have started to appear in the literature. In this study, we have combined quartz crystal microbalance with MIP to prepare a sensor using the ability of glucose to chelate of copper (II) ion of methacrylamidohistidine (MAH) monomer to create ligand exchange (LE) assembled monolayer which is suitable for glucose determination. The study includes the measurement of binding interaction of molecularly imprinted QCM sensor via ligand interaction, investigation of the pH effect on frequency shift and recognition selectivity studies of glucose-imprinted polymer with respect to methyl-alpha-d-glucopyranoside and sucrose. Bmax (number of binding sites) and K(D) (dissociation constant of the metal-chelate copolymer) were also calculated using Scathard plot and the detection limit was found as 0.07 mM. MIP showed higher glucose-binding affinity than a well-known glucose binding protein, conconavalin A.     

A novel label-free live-cell biosensor for G-protein-coupled receptor functional assay with enhanced sensitivity

This study developed a surface plasmon resonance (SPR)-based live-cell biosensor with enhanced sensitivity for label-free ligand binding assay of G-protein-coupled receptors (GPCRs). The β2-adrenoceptor was heterologously expressed in human embryonic kidney-293 cells. The specific ligand binding function of expressed β2-adrenoceptor was monitored by SPR via refractive index measurement. The results indicate the expressed β2-adrenoceptor can respond to isoprenaline with high specificity. The SPR signals can be enhanced more than three times by the use of LY294002. This biosensor can be applied in the functional assay of GPCRs by detecting the specific interactions between GPCRs and their target ligands.     

Fermentation glucose assay using the Exactech blood glucose biosensor

Summary The Exactech blood glucose biosensor has been used successfully to measure glucose concentrations in fermentation broths. A highly sensitive linear calibration was obtained between the glucose concentration and the biosensor reading, which correlated well with a Reducing Sugar Assay.     

Development of a sandwich format, amperometric screen-printed uric acid biosensor for urine analysis

A screen-printed carbon electrode (SPCE) incorporating the electrocatalyst cobalt phthalocyanine (CoPC), fabricated using a water-based ink formulation, has been investigated as the base transducer for a uric acid biosensor. A sandwich biosensor was fabricated by first depositing cellulose acetate (CA) onto this transducer (CoPC-SPCE), followed by uricase (UOX) and finally a polycarbonate (PC) membrane; this device is designated PC-UOX-CA-CoPC-SPCE. This biosensor was used in conjunction with chronoamperometry to optimize the conditions for the analysis of urine: temperature, 35°C; buffer, pH 9.2; ionic strength, 50 mM; uricase, 0.6 U; incubation time, 180 s. The proposed biosensor was applied to urine from a healthy subject. The precision determined on unspiked urine (n=6) was 5.82%. Urine was fortified with 0.225 mM UA, and the resulting precision and recovery were 4.21 and 97.3%, respectively. The linear working range of the biosensor was found to be 0.015 to 0.25 mM (the former represents the detection limit), and the sensitivity was calculated to be 2.10 μA/mM.     

A sandwich enzyme-linked immunosorbent assay for human serum paraoxonase concentration

Serum paraoxonase (PON) is associated with plasma high density lipoproteins, and prevents the oxidative modification of low density lipoproteins. We have developed a sensitive sandwich enzyme-linked immunosorbent assay (ELISA), using two monoclonal antibodies against PON, to measure serum PON concentration. The concentration of PON in healthy Japanese subjects was 59.3 +/- 1.3 microgram/mL (mean +/- SEM; n = 87). Serum PON concentrations in relation to the PON 192 genetic polymorphism were: 69.5 +/- 2.9 microgram/mL in the QQ genotype; 63.0 +/- 1.9 microgram/mL in the QR genotype; and 52.8 +/- 1.7 microgram/mL in the RR genotype. Concentrations were significantly lower in the RR than in the QQ genotype (P < 0.01). Serum paraoxonase specific activity was higher in RR than in QQ subjects (18.6 +/- 0.40 vs. 2. 56 +/- 0.05 nmol/min/microgram, P < 0.01), but arylesterase specific activity was unrelated to genotype. PON concentration was positively associated (P < 0.001) with both serum arylesterase activity and, after adjusting for the effect of the position 192 polymorphism, with serum paraoxonase activity. Subjects with angiographically verified coronary heart disease had significantly lower PON concentrations than the healthy controls (52.0 +/- 2.3 microgram/mL; n = 35, P < 0.01). This association was independent of the position 192 genotype. Our new ELISA should be of value for epidemiologic and clinical studies of serum PON concentration. immunosorbent assay for human serum paraoxonase concentration.     

A nanoparticle-based solution DNA sandwich assay using ICP-AES for readout

We report herein a nanoparticle-based methodology for detecting DNA in solution using inductively coupled plasma atomic emission spectrometry (ICP-AES) as a readout tool. This represents the first homogeneous solution assay of biologically significant targets by employing ICP-related techniques. Two types of particles are employed: silica nanoparticles or gold nanoparticles functionalized with oligonucleotides that are capable of hybridizing with half of the target DNA sequence as signal readout components, and magnetic microparticles functionalized with oligonucleotides that are capable of hybridizing with the other half of the sequence as capture components. In the presence of target DNA, three components form typical sandwich structures, and the application of a magnetic field could effectively separate them from the rest of the solution. Subsequent application of ICP-AES effectively provides an inorganic elemental readout for the diagnosis of target DNA.