Facile fabrication of branched-chain carbohydrate chips for studying carbohydrate-protein interactions by QCM biosensor

A novel approach for fabricating branched-chain (BC) carbohydrate chips to study carbohydrate-protein interactions using quantz crystal microbalance (QCM) biosensor was developed. This approach utilizes functional alkynyl-branch molecule modified chip surfaces, which is functionalized with terminal alkynyl group for covalent linking of unprotected azide-carbohydrates via click chemistry.     

多壁碳纳米管修饰铂基片石英晶体微天平研究白细胞介素-6与其受体的相互作用

在pH 7.4、室温条件下,用多壁碳纳米管(MWCNTs)修饰石英晶体微天平(QCM) Pt基片,经过EDC/NHS活化后固定白细胞介素-6(IL-6),检测不同浓度可溶性白细胞介素-6受体(sIL-6R)与IL-6的结合所引起响应信号的变化,并用Origin软件对数据进行拟合分析,构建了一种高性能实时监测IL-6与s...     

An enzyme-free quartz crystal microbalance biosensor for sensitive glucose detection in biological fluids based on glucose/dextran displacement approach

A sensitive and facile quartz crystal microbalance (QCM) biosensor for glucose detection in biological fluids was developed by means of a displacement-type assay mode between glucose and its analogy dextran for concanavalin A (ConA) binding sites on a graphene-based sensing platform. To construct such a displacement-based sensor, phenoxy-derived dextran (DexP) molecules were initially assembled onto the surface of graphene-coated QCM probe via π-π stacking interaction, and ConA molecules were then immobilized on the dextran through the dextran-ConA interaction. Upon addition of glucose, the analyte competed with the dextran for the ConA, and displaced it from the QCM probe, leading to a change in the frequency. Under optimal conditions, the frequency change relative to the basic resonant frequency was proportional to glucose concentration, and exhibited a dynamic range from 0.01 to 7.5 mM with a low detection limit (LOD) of 5.0 μM glucose (at 3σ). The relative standard deviations (RSDs) were below 6.2% and 9.0% for the reproducibility and selectivity of the QCM glucose sensors, respectively. In addition, the assay system was evaluated with glucose spiking samples into the distilled water and blank cattle serum, receiving in excellent correlation with the referenced values.     

In situ growth of nanogold on quartz crystal microbalance and its application in the interaction between heparin and antithrombin III

A novel biosensor for detecting antithrombin III (AT III) was constructed based on in situ growth of nanogold on the gold electrode of quartz crystal microbalance (QCM). The growth process of nanogold was monitored by QCM in real time. Heparin was used as the affinity ligand and immobilized onto the nanogold modified gold electrode. A flow injection analysis-quartz crystal microbalance (FIA-QCM) system was used to investigate the relationship between nanogold growth and the AT III response. Along with the nanogold particle growth within initial 5 min, the amount of heparin immobilized onto the nanogold modified electrode increased quickly. Correspondingly, the frequency response to AT III binding increased rapidly at the same time. After that, both the immobilized amount of heparin and the sensor response to AT III decreased gradually. Compared with the directly immobilized large nanogold particles, the in situ grown particles with the same size occupy more sensor surface, resulting in higher frequency shifts to AT III in the interaction study between heparin and AT III. The obtained constants of AT III binding to immobilized heparin are k(ass)=(1.65+/-0.12)x10(3) L/mols, k diss=(2.63+/-0.18)x10(-2) 1/s and K(A)=(6.27+/-0.42)x10(4) L/mol.     

A Highly Sensitive and Selective Label-free Electrochemical Biosensor with a Wide Range of Applications for Bisphenol A Detection

A label-free DNA-based electrochemical biosensor owning high sensitivity and selectivity has been established for detecting bisphenol A in a wide range of applications. Coupling the high electrochemical performance of graphene oxide-thionine-Au nanomaterial with the specific binding capacity of the aptamers to BPA, the monitoring of trace amount of BPA was realized, the detection limit was 3.3 pg ⋅ mL⁻¹ with strong anti-interference. Besides, using molecular docking, it was found that BPA binds to the bases DC-49, DC-51, DG-52, DG-53 and DA-63 on the aptamer via hydrogen bonding and π-π stacking interactions. Finally, the biosensor had been successfully applied in different real samples.     

A study of glycoprotein-lectin interactions using quartz crystal microbalance

A study of biospecific interactions between lectins and glycoproteins using a quartz crystal microbalance biosensor with dissipation monitoring (QCM-D) was reported. Four lectins were covalently immobilised on the thiol-modified gold electrode of the QCM chips in order to obtain sensing surfaces. The frequency shift served as analytical signal and the dissipation shift provided additional information about the viscoelastic properties of the glycoprotein-lectin complex formed on the surface of the QCM chip. The working conditions of the assay were optimised. The interaction between different lectins and glycoproteins was characterised by specific frequency shifts and each glycoprotein displayed its own unique lectin-binding pattern. This lectin pattern can serve as a finger print for the discrimination between various glycoproteins. The biosensor enabled quantitative determination of glycoproteins in the concentration range of 50 μg mL⁻¹ to 1 mg mL⁻¹ with good linearity and R.S.D. of less than 6.0%. An additional advantage of the proposed biosensor was the possibility to re-use the same lectin surfaces during a long period of time (2 month) without changes in analytical response. This was experimentally achieved by the application of a proper regeneration solution (10 mM glycine-HCl, pH 2.5). The lectin-based quartz crystal microbalance technique is suitable both for rapid screening and for quantitative assay of serum glycoproteins.     

Kinetic discrimination of sequence-specific DNA-drug binding measured by surface plasmon resonance imaging and comparison to solution-phase measurements

We demonstrate the use of surface plasmon resonance (SPR) imaging for direct detection of small-molecule binding to surface-bound DNA probes. Using a carefully designed array surface, we quantitatively discriminate between the interactions of a model drug with different immobilized DNA binding sites. Specifically, we measure the association and dissociation intercalation rates of actinomycin-D (ACTD) to and from double-stranded 5'-TGCT-3' and 5'-GGCA-3' binding sites. The rates measured provide mechanistic information about the DNA-ACTD interaction; ACTD initially binds nonspecifically to DNA but exerts its activity by dissociating slowly from strong affinity sites. We observe a slow dissociation time of kd-1 = 3300 +/- 100 s for ACTD bound to the strong affinity site 5'-TGCT-3' and a much faster dissociation time (210 +/- 15 s) for ACTD bound weakly to the site 5'-GGCA-3'. These dissociation rates, which differ by an order of magnitude, determine the binding affinity for each site (8.8 x 10(6) and 1.0 x 10(6) M(-1), respectively). We assess the effect the surface environment has on these biosensor measurements by determining kinetic and thermodynamic constants for the same DNA-ACTD interactions in solution. The surface suppresses binding affinities approximately 4-fold for both binding sites. This suppression suggests a barrier to DNA-drug association; ACTD binding to duplex DNA is approximately 100 times slower on the surface than in solution.     

QCM DNA biosensor for the diagnosis of a fish pathogenic virus VHSV

Viral haemorrhagic septicaemia (VHS) is one of the most serious viral diseases damaging both fresh and marine fish species. VHS caused by VHSV and diagnosis of VHSV has been dependent on the conventional methods, such as cell culture and RT-PCR, which takes a few days or several hours. This study demonstrates a rapid and sensitive QCM biosensor for diagnosis of VHSV infection in fish. The QCM biosensor was developed to detect a main viral RNA encoding G protein in VHSV using the specific DNA probe. To maximize the sensitivity of the biosensor, we prepared three different DNA probes which modified 3′ end of DNA by thiol, amine, or biotin and compared three different immobilisation methods on quartz surface coated with gold: immobilisation of thiol labelled probe DNA on naked gold surface, immobilisation of amino labelled probe DNA on gold surface prepared as carboxyl chip using MPA followed by EDC/NHS activation, and immobilisation of biotin labelled probe DNA on gold surface after immobilising avidin on carboxyl chip prior to biotin. As a result, immobilisation method using avidin-biotin interaction was most efficient to immobilise probe DNA and to detect target DNA. The QCM biosensor system using biotinylated probe DNA was stable enough to withstand 32 times of repeated regenerations and the detection limit was 0.0016 μM. Diagnosis using the QCM biosensor system was more sensitive and much faster than a conventional RT-PCR analysis in detecting the viral RNA.     

A Structure Based Study of Selective Inhibition of Factor IXa over Factor Xa

Blood coagulation is an essential physiological process for hemostasis; however, abnormal coagulation can lead to various potentially fatal disorders, generally known as thromboembolic disorders, which are a major cause of mortality in the modern world. Recently, the FDA has approved several anticoagulant drugs for Factor Xa (FXa) which work via the common pathway of the coagulation cascade. A main side effect of these drugs is the potential risk for bleeding in patients. Coagulation Factor IXa (FIXa) has recently emerged as the strategic target to ease these risks as it selectively regulates the intrinsic pathway. These aforementioned coagulation factors are highly similar in structure, functional architecture, and inhibitor binding mode. Therefore, it remains a challenge to design a selective inhibitor which may affect only FIXa. With the availability of a number of X-ray co-crystal structures of these two coagulation factors as protein–ligand complexes, structural alignment, molecular docking, and pharmacophore modeling were employed to derive the relevant criteria for selective inhibition of FIXa over FXa. In this study, six ligands (three potent, two selective, and one inactive) were selected for FIXa inhibition and six potent ligands (four FDA approved drugs) were considered for FXa. The pharmacophore hypotheses provide the distribution patterns for the principal interactions that take place in the binding site. None of the pharmacophoric patterns of the FXa inhibitors matched with any of the patterns of FIXa inhibitors. Based on pharmacophore analysis, a selectivity of a ligand for FIXa over FXa may be defined quantitatively as a docking score of lower than −8.0 kcal/mol in the FIXa-grids and higher than −7.5 kcal/mol in the FXa-grids.     

A kinetic study of protein binding to ecabet sodium using quartz-crystal microbalance.

To define the mechanism of the protection by ecabet sodium of the gastric mucosa, the characteristics of protein binding of this drug were investigated using a quartz-crystal microbalance (QCM) method. The binding rate constants (kb) and the binding amounts (delta m) were obtained from time courses of the frequency decrease (mass increase) of the QCM. The binding constants to proteins of two ecabet analogues (G1, ecabet type and G2, non-ionic ecabet type) were dependent on the pH, leading to large kb values at the acidic region. Furthermore, the kb values of G1 with the addition of bovine serum albumin (BSA) and bovine serum fibrinogen (BSF) at the acid region were larger than those of G2. The difference in kb values between G1 and G2 for porcine gastric mucin (PGM) is hardly discernible. Ecabet seems to be more heavily distributed in the ulcerous areas than in the intact mucosa, judging from the large binding constants of this drug to BSA and BSF compared with those to PGM. It is suggested that ecabet is bound to proteins by hydrophobic interaction, moreover, the electrostatic interaction between this drug and proteins (BSA and BSF) occurs at acidic pH region. On account of these interactions, ecabet sodium seems to have a more protective effect on an ulcer at intraluminal acidity than sucralfate. Finally, QCM was found to be a useful technique for detecting quantitatively the time course of binding proteins with drug.     

Probing BSA binding to citrate-coated gold nanoparticles and surfaces

The interaction of bovine serum albumin (BSA) with gold colloids and surfaces was studied using zeta-potential and quartz crystal microbalance (QCM) measurements, respectively, to determine the surface charge and coverage. The combination of these two measurements suggests that BSA binding to gold nanoparticles and gold surfaces occurs by an electrostatic mechanism when citrate is present. The binding of BSA to bare gold is nearly two times greater than the binding of BSA to a citrate-coated gold surface, suggesting that protein spreading (denaturation) on the surface may occur followed by secondary protein binding. On the other hand, binding to citrate-coated gold surfaces can be fit to a Langmuir isotherm model to obtain a maximum surface coverage of (3.7 +/- 0.2) x 10(12) molecules/cm(2) and a binding constant of 1.0 +/- 0.3 microM(-1). The zeta-potential measurements show that the stabilization of colloids by BSA has a significant contribution from a steric mechanism because the colloids are stable, even at their isoelectric point (pI approximately 4.6). To be consistent with the observed phenomena, the electrostatic interactions between BSA and citrate must consist of salt-bridges, for example, of the carboxylate-ammonium type, between the citrate and the lysine on the protein surface. The data support the role of strong electrostatic binding but do not exclude contributions from steric or hydrophobic interactions with the surface adlayer.     

Physical adsorption of protamine for heparin assay using a quartz crystal microbalance and electrochemical impedance spectroscopy

This study attempted to determine absolute heparin concentration in phosphate buffer solution (PBS, pH 7.4) by using quartz crystal microbalance (QCM) as an affinity biosensor. Electrochemical impedance spectroscopy (EIS) was also used to investigate immobilization of protamine and heparin assay. In addition, the effectiveness of physical adsorption in immobilizing protamine was confirmed by examining the preparation conditions, including the incubation time and protamine concentration. It induced maximum decrease (ca. −100 Hz) in oscillating frequency of QCM by applying 20 mg/ml protamine and 20 min for incubation in PBS. Heparin adsorption onto protamine-modified electrode in PBS revealed an exponential-like binding curve and long duration for reaching the steady state in frequency response of QCM. Moreover, two linear calibration curves were obtained judging from the initial slope (df/dt) and the frequency change (Δf) of QCM obtained after a binding interval (600 s) for heparin concentrations from 0 to 3.0 and 7.0 U/ml, respectively. In EIS analysis, calibration curves with linear concentration range of 0-3.0 U/ml were obtained for heparin in PBS when ferrocyanide was used as an electroactive marker.     

表面等离子体共振法检测人血清白蛋白抗体活性

表面等离子体共振法是研究生物大分子间相互作用的有效方法之一,和非直接方法（如酶联免疫）相比,具有实时、快速和免标记等特点。我们在甲羧基化葡聚糖修饰的传感片表面直接交联固一人血清白蛋白（ＨＳＡ）,用于ａｎｔｉ－ＨＳＡ抗体活性的检测,并用Ｈ３ＰＯ４（０．１ｍｏｌ／Ｌ）溶液再生。结果表明表面等离子体共振（ＳＰＲ）生物传感器能快速实时检测ａｎｔｉ－ＨＳＡ抗体的活性,且传感片能够重复使用１００次以上。     

Quartz crystal microbalance biosensor for recombinant human interferon-beta detection based on antisense peptide approach

Quartz crystal microbalance (QCM) biosensors for recombinant human interferon-β (rhIFN-β) were constructed by utilizing antisense peptides adhering to the QCM gold surfaces. Two antisense peptides, both corresponding to the N-terminal fragment 1-14 of rhIFN-β, were used in this study. Antisense peptide AS-1 was the original antisense peptide and AS-2 was the modified antisense peptide based on the antisense peptide degeneracy. Both antisense peptides were immobilized on the gold electrodes of piezoelectric crystals, respectively, via a self-assembling monolayer of 1,2-ethanedithiol. The binding affinity between rhIFN-β and each immobilized antisense peptide in solution was evaluated using a quartz crystal microbalance-flow injection analysis (QCM-FIA) system. The dissociation constant of rhIFN-β on the antisense peptide AS-1 and AS-2 biosensor was (1.89 ± 0.101) × 10⁻⁴ and (1.22 ± 0.0479) ×10⁻⁵ mol L⁻¹, respectively. The results suggested that AS-2 had a higher binding affinity to rhIFN-β than AS-1. The detection for rhIFN-β using each biosensor was precise and reproducible. The linear response ranges of rhIFN-β binding to both biosensors were same with a concentration range of 0.12-0.96 mg mL⁻¹. The results demonstrated the successful construction of highly selective QCM biosensors using antisense peptide approach, and also confirmed the feasibility of increasing antisense peptide binding affinity by appropriate sequence modification.     

Molecular dynamics modeling the synthetic and biological polymers interactions pre-studied via docking

In previous works we reported the design, synthesis and in vitro evaluations of synthetic anionic polymers modified by alicyclic pendant groups (hydrophobic anchors), as a novel class of inhibitors of the human immunodeficiency virus type 1 (HIV-1) entry into human cells. Recently, these synthetic polymers interactions with key mediator of HIV-1 entry-fusion, the tri-helix core of the first heptad repeat regions [HR1]₃ of viral envelope protein gp41, were pre-studied via docking in terms of newly formulated algorithm for stepwise approximation from fragments of polymeric backbone and side-group models toward real polymeric chains. In the present article the docking results were verified under molecular dynamics (MD) modeling. In contrast with limited capabilities of the docking, the MD allowed of using much more large models of the polymeric ligands, considering flexibility of both ligand and target simultaneously. Among the synthesized polymers the dinorbornen anchors containing alternating copolymers of maleic acid were selected as the most representative ligands (possessing the top anti-HIV activity in vitro in correlation with the highest binding energy in the docking). To verify the probability of binding of the polymers with the [HR1]₃ in the sites defined via docking, various starting positions of polymer chains were tried. The MD simulations confirmed the main docking-predicted priority for binding sites, and possibilities for axial and belting modes of the ligands–target interactions. Some newly MD-discovered aspects of the ligand’s backbone and anchor units dynamic cooperation in binding the viral target clarify mechanisms of the synthetic polymers anti-HIV activity and drug resistance prevention.     

L-苯丙氨酸衍生物的一锅法合成及其抗/促凝活性

氨基酸及其衍生物在止血/抗凝活性方面有一定的应用。以L-苯丙氨酸为起始原料,经磺化引入磺酸基,再与甲醇、乙醇、丙醇、异丙醇和正丁醇脱水酯化,一锅法合成了6种未见报道的L-苯丙氨酸的磺酸酯类衍生物(L1~L6),以期获得具有的较强血液生理活性的潜在药物。实验中采用了质谱、核磁共振进行结构表征。该合成方法产率高(78%~95%),后处理简单,不失为合成该类衍生物的好方法。衍生物的凝血四项实验表明:抗促凝效果是内源性和外源性凝血途径共同作用的结果。血浆复钙实验表明:衍生物均具有一定的抗凝活性,其抗凝效果随浓度变化而变化,但是随R链的长度增加,抗凝效果并未见规律性。衍生物的抗凝活性主要受磺酸基及酯基的影响,因此在设计合成抗血栓化合物时可以考虑引入磺酸基及酯类基团。     

Computational binding study of cardiac troponin I antibody towards cardiac versus skeletal troponin I

A computational study of the interaction of cardiac troponin I (cTnI) with its specific antibody and of that antibody with skeletal troponin I (sTnI), the principal interferon of cTnI, is carried out. Computational and simulation tools such as FTSite, FTMap, FTDock and pyDock are used to determine the binding sites of these molecules and to study their interactions and molecular docking performance, allowing us to obtain relevant information related with the antigen-antibody interaction for each of the targets. In the context of the development of immunosensing platforms, this type of computational analysis allows performing a preliminary in-silico affinity study of the available bioreceptors for a better selection when moving to the experimental stage, with the subsequent saving in cost and time.     

Determination of acetamiprid partial-intercalative binding to DNA by use of spectroscopic, chemometrics, and molecular docking techniques

Acetamiprid (ACT) is an insecticide widely used for controlling a variety of insect pests. The binding mode associated with calf thymus DNA (ctDNA) upon interaction with ACT was determined using spectroscopic, chemometrics, and molecular docking techniques to clarify the interaction mechanism at the molecular level. Fluorescence titration suggested that the fluorescence quenching of ACT by ctDNA is a static procedure. The binding constants between ACT and ctDNA at different temperatures were calculated to be of the order 10³?10⁴ L mol^?1. The positive values of enthalpy and entropy change suggested that the binding process is primarily driven by hydrophobic interactions. Multivariate curve resolution?alternating least squares (MCR?ALS), a chemometrics approach, was used to resolve the expanded UV–visible spectral data matrix. The concentration profiles and the spectra for the three reaction components (ACT, ctDNA, and ACT?ctDNA complex) of the system, which formed a highly overlapping composite response, were then successfully obtained and used to evaluate the progress of ACT interacting with ctDNA. The results of the single-stranded ctDNA and iodide quenching experiments, ctDNA-melting investigations, and viscosity measurements indicated that ACT binds to ctDNA by means of a partial intercalation. Molecular docking studies showed that the specific binding site is mainly located between the ACT and G–C base pairs of ctDNA. This docking prediction was confirmed by use of Fourier-transform infrared (FT-IR) spectral analysis. Results from circular dichroism (CD) spectroscopy revealed that ACT induced a conformational change from the B–ctDNA form to the A–ctDNA form.