Concentric DNA Amplifier That Streamlines In-Solution Biorecognition and On-Particle Biocatalysis.

Colloidal nanoparticle biosensors capable of on-particle biocatalysis are powerful tools for amplified detection of biomolecules. The development and practical uses of such concentric amplifiers can be complicated because of the on-particle biorecognition that involves varying interfacial factors at the biomolecule-nanoparticle interfaces. Herein, we reason that a nanoparticle biosensor equipped with an in-solution biorecognition element may be better fabricated, predicted, controlled, and performed.

Probing and Controlling Dynamic Interactions at Biomolecule-Nanoparticle Interfaces Using Stochastic DNA Walkers.

Herein, we report a bottom-up approach to assemble a series of stochastic DNA walkers capable of probing dynamic interactions occurring at the bio-nano interface. We systematically investigated the impact of varying interfacial factors, including intramolecular interactions, orientation, cooperativity, steric effect, multivalence, and binding hindrance on enzymatic behaviors at the interfaces of spherical nucleic acids. Our mechanistic study has revealed critical roles of various interfacial factors that significantly alter molecular binding and enzymatic behaviors from bulk solutions.

Simulation-guided engineering of an enzyme-powered three dimensional DNA nanomachine for discriminating single nucleotide variants.

Single nucleotide variants (SNVs) are important both clinically and biologically because of their profound biological consequences. Herein, we engineered a nicking endonuclease-powered three dimensional (3D) DNA nanomachine for discriminating SNVs with high sensitivity and specificity. Particularly, we performed a simulation-guided tuning of sequence designs to achieve the optimal trade-off between device efficiency and specificity.

Comparison of soil analytical methods for estimating wheat potassium fertilizer requirements in response to contrasting plant K demand in the glasshouse.

The traditional soil potassium (K) testing methods fail to accurately predict K requirement by plants. The Diffusive Gradients in Thin-films (DGT) method is promising, but the relationship between the DGT-measured K pool and plant available K is not clear. Wheat (Triticum aestivum L.

Diffusive gradients in thin films measurement of sulfur stable isotope variations in labile soil sulfate.

A diffusive gradient in thin films (DGT) technique, based on a strongly basic anion exchange resin (Amberlite IRA-400), was successfully tested for S/S analysis in labile soil sulfate. Separation of matrix elements (Na, K, and Ca) that potentially cause non-spectral interferences in S/S analysis by MC ICP-MS (multi-collector inductively coupled plasma-mass spectrometry) during sampling of sulfate was demonstrated. No isotopic fractionation caused by diffusion or elution of sulfate was observed below a resin gel disc loading of ≤79 μg S.

Novel diffusive gradients in thin films technique to assess labile sulfate in soil.

A novel diffusive gradients in thin films (DGT) technique for sampling labile soil sulfate was developed, based on a strong basic anion exchange resin (Amberlite IRA-400) for sulfate immobilization on the binding gel. For reducing the sulfate background on the resin gels, photopolymerization was applied instead of ammonium persulfate-induced polymerization. Agarose cross-linked polyacrylamide (APA) hydrogels were used as diffusive layer.

Enzyme-Powered Three-Dimensional DNA Nanomachine for DNA Walking, Payload Release, and Biosensing.

Herein, we report a DNA nanomachine, built from a DNA-functionalized gold nanoparticle (DNA-AuNP), which moves a DNA walker along a three-dimensional (3-D) DNA-AuNP track and executes the task of releasing payloads. The movement of the DNA walker is powered by a nicking endonuclease that cleaves specific DNA substrates on the track. During the movement, each DNA walker cleaves multiple substrates, resulting in the rapid release of payloads (predesigned DNA sequences and their conjugates).

Application of the diffusive gradients in thin films technique for available potassium measurement in agricultural soils: effects of competing cations on potassium uptake by the resin gel.

The utilization of Amberlite (IRP-69 ion-exchange resin, 100-500 wet mesh) as the binding phase in the diffusive gradients in thin films (DGT) technique has shown potential to improve the assessment of plant-available K in soils. The binding phase has recently been optimized by using a mixed Amberlite and ferrihydrite (MAF) gel which results in linear K uptake over extended deployment periods and in solutions with higher K concentrations. As restriction of K uptake by Ca on the Amberlite based resin gel has been previously proposed, potential competing effects of Ca(2+), Mg(2+) and NH(4+) on K uptake by the MAF gel were investigated.

Optimization of the diffusive gradients in thin films (DGT) method for simultaneous assay of potassium and plant-available phosphorus in soils.

Potassium (K) and phosphorus (P) are two important macronutrients for crops, and are usually applied to soils as granular fertilizer before seeding. Therefore, accurate soil tests prior to planting to predict crop response to fertilizers are important in optimizing crop yields. Traditional methods used for testing both available K and P in soils, which are based on chemical extraction procedures, are to be soil-type dependent, and the predictive relationships across a broad range of soils are generally poor.

Investigating chemical constraints to the measurement of phosphorus in soils using diffusive gradients in thin films (DGT) and resin methods.

The effect of potential chemical constraints on the performance of two relatively new soil P testing methods, anion exchange membrane (AEM) and diffusive gradients in thin films (DGT), were evaluated. Exposures to ranges of anion (Cl(-), NO(3)(-), SO(4)(2-) and HCO(3)(-)) concentrations relevant to agricultural soils had minimal effect on P recoveries using DGT. It has also been shown previously that DGT P recoveries are unaffected by varying pH (3-9).

Performance of a mixed binding layer for measuring anions and cations in a single assay using the diffusive gradients in thin films technique.

The performance of a mixed binding layer (MBL) for use in diffusive gradients in thin films (DGT) was investigated. The MBL consisted of ferrihydrite and Chelex-100 cation-exchange resin combined together in a binding gel in an attempt to allow measurement of anions and cations in a single assay. Results from the MBL were compared to experiments performed using individual Chelex gels and ferrihydrite gels that have been shown to work successfully for DGT methodology.

Biochemical characterization of the active heterodimer form of human heparanase (Hpa1) protein expressed in insect cells.

The mammalian endoglycosidase heparanase (Hpa1) is primarily responsible for cleaving heparan sulphate proteoglycans (HSPGs) present on the basement membrane of cells and its potential for remodelling the extracellular matrix (ECM) could be important in embryonic development and tumour metastasis. Elevated expression of this enzyme has been implicated in various pathological processes including tumour cell proliferation, metastasis, inflammation and angiogenesis. The enzyme therefore represents a potential therapeutic target.

Self-assembly of proteins and their nucleic acids.

We have developed an artificial protein scaffold, herewith called a protein vector, which allows linking of an in-vitro synthesised protein to the nucleic acid which encodes it through the process of self-assembly. This protein vector enables the direct physical linkage between a functional protein and its genetic code. The principle is demonstrated using a streptavidin-based protein vector (SAPV) as both a nucleic acid binding pocket and a protein display system.

Chemical speciation of Zn, Cd, Cu, and Pb in pore waters of agricultural and contaminated soils using Donnan dialysis.

Knowledge of trace metal speciation in soil pore waters is important in addressing metal bioavailability and risk assessment of contaminated soils. Numerous analytical methods have been utilized for determining trace metal speciation in aqueous environmental matrixes; however, most of these methods suffer from significant interferences. The Donnan dialysis membrane technique minimizes these interferences and has been used in this study to determine free Zn2+, Cd2+, Cu2+, and Pb2+ activities in pore waters from 15 agricultural and 12 long-term contaminated soils.