Resonance energy-transfer studies of the conformational change on the adsorption of oligonucleotides to a silica interface

Revealing the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation

It has been recently demonstrated that free DNA tracers have the potential in tracing water flow and contaminant transport through the vadose zone. However, whether the free DNA tracer can be used in flood irrigation area to track water flow and solute/contaminant transport is still unclear. To reveal the infiltration process and retention mechanisms of surface applied free DNA tracer through soil under flood irrigation, we tested the fate and transport behavior of surface applied free DNA tracers through packed saturated sandy soil columns with a 10 cm water head mimicking flood irrigation. From the experimental breakthrough curves and by fitting a two-site kinetic sorption model (R2 = 0.83-0.91 and NSE = 0.79-0.89), adsorption/desorption rates could be obtained and tracer retention profiles could be simulated. Together these results revealed that 1) the adsorption of free DNA was dominantly to clay particles in the soil, which took up 1.96 % by volume, but took up >97.5 % by surface area and densely cover the surface of sand particles; and 2) at a pore water pH of 8.0, excluding the 4.9 % passing through and 3.1 % degradation amount, the main retention mechanisms in the experimental soil were ligand exchange (42.0 %), Van der Waals interactions (mainly hydrogen bonds), electrostatic forces and straining (together 44.7 %), and cation bridge (5.3 %). To our knowledge, this study is the first to quantify the contribution of each of the main retention mechanisms of free synthetic DNA tracers passing through soil. Our findings could facilitate the application of free DNA tracer to trace vadose zone water flow and solute/contaminant transport under flood irrigation and other infiltration conditions.

In-situ investigation of dye pollutant adsorption performance on graphitic carbon nitride surface: ATR spectroscopy experiment and MD simulation insight

The adsorption performances on graphitic carbon nitride (g-C₃N₄) surface were investigated for organic dye pollutants by both experimental and calculation methods. For experimental investigation, adsorption thermodynamics and kinetics results were in-situ obtained and evaluated. With [Formula: see text] by Langmuir modeling^, g-C₃N₄ showed superior adsorption spontaneity of MB⁺ >MO^-. With linear and exponential modeling, g^-C₃N₄ showed only adsorption process for MB⁺ but both diffusion and adsorption processes for MO^-. For simulation insight, all MB⁺ molecules but only parts of MO^- molecules were inclined to orient in parallel position at g-C₃N₄ surface after optimization during low concentration. And both MB⁺ and MO^- molecules were inclined to orient in perpendicular position at g-C₃N₄ surface after optimization during high concentration. Combined with experimental and calculation results, a molecular-orientation and force-dominance mechanism adsorption model are proposed to explain the surface interaction processes between dyes and g-C₃N₄. Electrostatic interaction and π-π stacking interaction were revealed to dominate for MB⁺ adsorption, and π-π stacking interaction and van der Waals force were revealed to dominate for MO^- adsorption. This work obtained 'localized' interfacial information and elucidated in-situ intermolecular interactions at g-C₃N₄ interface, which can provide fundamental basis for operation removal of organic dye pollutants by g-C₃N₄.

Insight into the Adsorption-Interaction Mechanism of Cr(VI) at the Silica Adsorbent Surface by Evanescent Wave Measurement

The investigation of adsorption performance at the adsorbent surface can help to reveal the treatment mechanism and improve the treatment efficiency of adsorption technology for heavy metal ions (HMIs). This work developed a methodology to investigate the adsorption behavior of HMI Cr(VI) at the silica surface by confined near-field evanescent wave (CNFEW) measurement. A silica optical fiber (SOF) was used as the adsorption substrate and light waveguide element to integrate both Cr(VI) adsorption and CNFEW production on its surface. According to the sensitive CNFEW response, the adsorption behavior of Cr(VI) was in situ monitored and real-time evaluated. The thermodynamic information of adsorption equilibrium constant (K_ads) and adsorption free energy (ΔG) and dynamic information of the apparent adsorption rate (v_ads) and adsorption time (t_ads) were obtained through Langmuir isotherm and kinetic fitting, respectively. Different reaction performances between Cr(VI) and adsorption sites were successfully differentiated, evaluated, and characterized. A site-decided-mechanism was therefore presented to describe the surface interaction process for Cr(VI), which including fast adsorption on type I Si-O^- site through electrostatic attraction with [Formula: see text] and slow adsorption on type II Si-OH site through coordinative interaction with ΔG_SiOH-Cr(VI)^II = -26.18 kJ mol^-1. The adsorption mechanism of Cr(VI) at the SOF silica surface was furthermore verified by zeta potential analysis, Fourier transform infrared investigation, and fluorescence imaging. Unlike conventional ex situ or in bulk detection, the present CNFEW-based approach targets the "localized" adsorption of Cr(VI) adsorbed to the solid adsorbent surface. Consequently, our work favorably constructs a surface platform and provides new insights on understanding the adsorption mechanism for HMIs.

Characterization and differentiation of the adsorption behavior of crystal violet and methylene blue at the silica/water interface using near field evanescent wave

Different molecular structures lead to different adsorption performances. In this work, the adsorption behavior of two organic dyes, namely, crystal violet (CV, triphenylmethane dye of symmetric structure) and methylene blue (MB, azo dye of linear structure), were investigated, characterized and differentiated at the silica/water interface using the total internal reflection induced near field evanescent wave (TIR-NFEW) platform. According to the change in the evanescent wave intensity and following Beer's law, the adsorption behaviors of CV and MB can be monitored real time and sensitively. On one hand, the Langmuir adsorption model was applied to obtain the related thermodynamic data (including adsorption equilibrium constant (Kads) and adsorption free energy (ΔG)). With ΔG(MB) = -25.7 ± 1.7 kJ mol-1 < ΔG(CV) = -21.5 ± 0.6 kJ mol-1 < 0, the linear MB showed a higher spontaneous adsorption ability than the symmetric CV at the silica/water interface. On the other hand, a two-step adsorption kinetic model was applied to obtain the dynamics data including the linear adsorption rate constant (k1) and the exponential adsorption rate constant (k2). With k1(CV) < k1(MB) and k2(CV) ≈ k2(MB), MB diffused faster than CV at the first diffusion step but had nearly the same interaction speed as CV in the second adsorption step. A molecular-aligned-mechanism was successfully proposed to describe the interfacial interaction process for both CV and MB that includes molecular reactions involving electrostatic attraction of type I SiO- and H-bonds of type II SiOH. This work provides new insights into the molecular-level interpretation of the adsorption of the azo and triphenylmethane dyes at the silica-water interface.

Real-time measurement of the crystal violet adsorption behavior and interaction process at the silica-aqueous interface by near-field evanescent wave

The interfacial adsorption and interaction of crystal violet (CV) at the silica-water interface was real-time measured based on a total-internal-reflection-induced near-field evanescent wave (TIR-NFEW). A silica optical fiber (SOF) was employed as a charged substrate for CV adsorption and as a light transmission waveguide for evanescent wave production for the investigation system. According to the change of evanescent wave intensity, the CV adsorption behavior could be real-time monitored at the silica-aqueous interface. The Langmuir adsorption model and two kinetic models were applied to obtain the related thermodynamic and kinetic data, including the adsorption equilibrium constant (Kads) of (5.9 ± 1.5) × 104 M-1 and adsorption free energy (ΔG) of -21.6 ± 0.6 kJ mol-1. Meanwhile, this method was shown to be able to isolate the elementary processes of adsorption and desorption under steady-state conditions, and gave an adsorption rate constant (ka) and desorption rate constant (kd) of 2089 ± 6.96 M min-1 and 0.35 ± 0.0012 min-1 for a 15 rpm flow rate. The surface interaction process was revealed and the adsorption mechanism proposed by a molecular orientation adsorption model with three-stage-concentration, indicating that CV first adsorbed on Si-O- sites through electrostatic attraction, then on Si-OH sites through hydrogen bonding, and lastly on the surface through van der Waals forces with different CV concentrations. This study can provide a molecular-level interpretation of CV adsorption and provides important insights into how CV adsorption can be controlled at the silica-water interface.

Real-Time Monitoring of Azo Dye Interfacial Adsorption at Silica-Water Interface by Total Internal Reflection-Induced Surface Evanescent Wave

An interface research method based on total internal reflection induced evanescent wave (TIR-EW) is developed to monitor the adsorption behavior of azo dye at the silica-water interface. The monitoring system is constructed by employing silica optical fiber (SOF) as both charged substrate for dye adsorption and light transmission waveguide for evanescent wave production. According to the change of evanescent wave intensity and followed by Beer's law, the methylene blue (MB) adsorption behavior can be real-time monitored at the silica-water interface. Langmuir adsorption model and pseudo-first-order model are applied to obtain the related thermodynamic and kinetic data. The adsorption equilibrium constant ( K_ads) and adsorption free energy (Δ G) of MB at the silica-water interface are determined to be (3.3 ± 0.5) × 10⁴ M^-1 and -25.7 ± 1.7 kJ mol^-1. Meanwhile, this method is highlighted to isolate elementary processes of adsorption and desorption under steady-state conditions, and gives adsorption rate constant ( k_a) and desorption rate constant ( k_d) of 8585 ± 19.8 min^-1 and 0.26 ± 0.0006 min^-1 for 15 r/min flow rate. The surface interaction process is revealed and adsorption mechanism is proposed, indicating MB first adsorbed on Si-O^- sites through electrostatic attraction and then on Si-OH sites through hydrogen bond with increasing MB concentrations. Our findings from this study provided molecular-level interpretation of azo dye adsorption at silica-water interface, and the results provide important insight into how MB adsorption can be controlled at the interface.

Adsorption Kinetics of Single-Stranded DNA on Functional Silica Surfaces and Its Influence Factors: An Evanescent-Wave Biosensor Study

Thorough understandings on the real-time kinetics involved in DNA adsorption on a solid surface is essential in various fields, such as in DNA hybridization studies, DNA extraction and purification, DNA-based biosensing, and gene-based medicine discovery. Herein, the real-time properties of single-stranded DNA (ssDNA) adsorption onto functional silica surfaces under various conditions were investigated using an evanescent wave optical biosensing platform. Results demonstrated that the driving force and adsorption mechanism of DNA were closely related to the kind of functional groups on the silica surfaces. The main driving forces of DNA adsorption onto hydroxyl- and protein-modified solid surfaces were the hydrophobic interaction, hydrogen bonding, and the interaction between DNA phosphate and functional groups on the silica surface, which strengthened with increased ionic strength. However, the electrostatic attraction between the negative charge of DNA and positive charge of the amino silica surface was likely the most important factor influencing DNA adsorption onto the amino surface. This influence can be reduced by increasing the ionic strength. Although low-ionic-strength Mg²⁺ provided a greater adsorption efficiency than high-ionic-strength Na⁺, the balance of ssDNA adsorption onto hydroxyl- and ovalbumin (OVA)-modified silica surfaces was achieved faster in the presence of Na⁺ than in the presence of Mg²⁺. DNA adsorption was also influenced significantly by pH, and the hydroxyl- and OVA-modified surfaces exhibited the strongest adsorption at pH 3.0, whereas DNA adsorption onto the amino surface increased with increased pH. DNA adsorption onto various functional surfaces could be perfectly fitted by second-order Langmuir models, indicating that the process was a single-molecular-layer adsorption.

Steady-state acceptor fluorescence anisotropy imaging under evanescent excitation for visualisation of FRET at the plasma membrane

We present a novel imaging system combining total internal reflection fluorescence (TIRF) microscopy with measurement of steady-state acceptor fluorescence anisotropy in order to perform live cell Förster Resonance Energy Transfer (FRET) imaging at the plasma membrane. We compare directly the imaging performance of fluorescence anisotropy resolved TIRF with epifluorescence illumination. The use of high numerical aperture objective for TIRF required correction for induced depolarization factors. This arrangement enabled visualisation of conformational changes of a Raichu-Cdc42 FRET biosensor by measurement of intramolecular FRET between eGFP and mRFP1. Higher activity of the probe was found at the cell plasma membrane compared to intracellularly. Imaging fluorescence anisotropy in TIRF allowed clear differentiation of the Raichu-Cdc42 biosensor from negative control mutants. Finally, inhibition of Cdc42 was imaged dynamically in live cells, where we show temporal changes of the activity of the Raichu-Cdc42 biosensor.

DNA adsorption to and elution from silica surfaces: influence of amino acid buffers

Solid phase extraction and purification of DNA from complex samples typically requires chaotropic salts that can inhibit downstream polymerase amplification if carried into the elution buffer. Amino acid buffers may serve as a more compatible alternative for modulating the interaction between DNA and silica surfaces. We characterized DNA binding to silica surfaces, facilitated by representative amino acid buffers, and the subsequent elution of DNA from the silica surfaces. Through bulk depletion experiments, we found that more DNA adsorbs to silica particles out of positively compared to negatively charged amino acid buffers. Additionally, the type of the silica surface greatly influences the amount of DNA adsorbed and the final elution yield. Quartz crystal microbalance experiments with dissipation monitoring (QCM-D) revealed multiphasic DNA adsorption out of stronger adsorbing conditions such as arginine, glycine, and glutamine, with DNA more rigidly bound during the early stages of the adsorption process. The DNA film adsorbed out of glutamate was more flexible and uniform throughout the adsorption process. QCM-D characterization of DNA elution from the silica surface indicates an uptake in water mass during the initial stage of DNA elution for the stronger adsorbing conditions, which suggests that for these conditions the DNA film is partly dehydrated during the prior adsorption process. Overall, several positively charged and polar neutral amino acid buffers show promise as an alternative to methods based on chaotropic salts for solid phase DNA extraction.

Multiphasic DNA adsorption to silica surfaces under varying buffer, pH, and ionic strength conditions

Reversible interactions between DNA and silica are utilized in the solid phase extraction and purification of DNA from complex samples. Chaotropic salts commonly drive DNA binding to silica but inhibit DNA polymerase amplification. We studied DNA adsorption to silica using conditions with or without chaotropic salts through bulk depletion and quartz crystal microbalance (QCM) experiments. While more DNA adsorbed to silica using chaotropic salts, certain buffer conditions without chaotropic salts yielded a similar amount of eluted DNA. QCM results indicate that under stronger adsorbing conditions the adsorbed DNA layer is initially rigid but becomes viscoelastic within minutes. These results qualitatively agreed with a mathematical model for a multiphasic adsorption process. Buffer conditions that do not require chaotropic salts can simplify protocols for nucleic acid sample preparation. Understanding how DNA adsorbs to silica can help optimize nucleic acid sample preparation for clinical diagnostic and research applications.