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

Total internal reflection microscopy: a powerful tool for exploring interactions and dynamics near interfaces

The occurrence of many micro/macrophenomena is closely related to interactions and dynamics near interfaces. Hence, developing powerful tools for characterizing near-interface interactions and dynamics has attached great importance among researchers. In this review, we introduce a noninvasive and ultrasensitive technique called total internal reflection microscopy (TIRM). The principles of TIRM are introduced first, demonstrating the characteristics of this technique. Then, typical measurements with TIRM and the recent development of the technique are reviewed in detail. At the end of the review, we highlight the great progress of TIRM during the past several decades and show its potential to be more influential in measuring interactions and dynamics near interfaces in various research fields.

The Role of Extracellular DNA in Microbial Attachment to Oxidized Silicon Surfaces in the Presence of Ca2+ and Na. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021;37:9838-9850. [PMID: 34347486 PMCID: PMC8397393 DOI: 10.1021/acs.langmuir.1c01410]

Attachment assays of a Pseudomonas isolate to fused silica slides showed that treatment with DNaseI significantly inhibited cellular adsorption, which was restored upon DNA treatment. These assays confirmed the important role of extracellular DNA (eDNA) adsorption to a surface. To investigate the eDNA adsorption mechanism, single-molecule force spectroscopy (SMFS) was used to measure the adsorption of eDNA to silicon surfaces in the presence of different concentrations of sodium and calcium ions. SMFS reveals that the work of adhesion required to remove calcium-bound eDNA from the silicon oxide surface is substantially greater than that for sodium. Molecular dynamics simulations were also performed, and here, it was shown that the energy gain in eDNA adsorption to a silicon oxide surface in the presence of calcium ions is small and much less than that in the presence of sodium. The simulations show that the length scales involved in eDNA adsorption are less in the presence of sodium ions than those in the presence of calcium. In the presence of calcium, eDNA is pushed above the surface cations, whereas in the presence of sodium ions, short-range interactions with the surface dominate. Moreover, SMFS data show that increasing [Ca2+] from 1 to 10 mM increases the adsorption of the cations to the silicon oxide surface and consequently enhances the Stern layer, which in turn increases the length scale associated with eDNA adsorption.

Artificial Taste Buds: Bioorthogonally Ligated Gustatory-Neuronal Multicellular Hybrids Enabling Intercellular Taste Signal Transmission

Heterogeneous tissue models require the assembly and co-culture of multiple types of cells. Our recent work demonstrated taste signal transmission from gustatory cells to neurons by grafting single-stranded DNA into the cell membrane to construct multicellular assemblies. However, the weak DNA linkage and low grafting density allowed the formation of large gustatory cell self-aggregates that cannot communicate with neurons efficiently. This article presents the construction of artificial taste buds exhibiting active intercellular taste signal transmission through the hybridization of gustatory-neuronal multicellular interfaces using bioorthogonal click chemistry. Hybrid cell clusters were formed by the self-assembly of neonatal gustatory cells displaying tetrazine with a precultured embryonic hippocampal neuronal network displaying trans-cyclooctene. A bitter taste signal transduction was provoked in gustatory cells using denatonium benzoate and transmitted to neurons as monitored by intracellular calcium ion sensing. In the multicellular hybrids, the average number of signal transmissions was five to six peaks per cell, and the signal transmission lasted for ∼5 min with a signal-to-signal gap time of 10-40 s. The frequent and extended intercellular signal transmission suggests that the cell surface modification by the bioorthogonal click chemistry is a promising approach to fabricating functional multicellular hybrid clusters potentially useful for cell-based biosensors, toxicity assays, and tissue regeneration.

Influence of the Electrolyte Salt Concentration on DNA Detection with Graphene Transistors

Liquid-gated Graphene Field-Effect Transistors (GFET) are ultrasensitive bio-detection platforms carrying out the graphene's exceptional intrinsic functionalities. Buffer and dilution factor are prevalent strategies towards the optimum performance of the GFETs. However, beyond the Debye length (λD), the role of the graphene-electrolytes' ionic species interactions on the DNA behavior at the nanoscale interface is complicated. We studied the characteristics of the GFETs under different ionic strength, pH, and electrolyte type, e.g., phosphate buffer (PB), and phosphate buffer saline (PBS), in an automatic portable built-in system. The electrostatic gating and charge transfer phenomena were inferred from the field-effect measurements of the Dirac point position in single-layer graphene (SLG) transistors transfer curves. Results denote that λ_D is not the main factor governing the effective nanoscale screening environment. We observed that the longer λ_D was not the determining characteristic for sensitivity increment and limit of detection (LoD) as demonstrated by different types and ionic strengths of measuring buffers. In the DNA hybridization study, our findings show the role of the additional salts present in PBS, as compared to PB, in increasing graphene electron mobility, electrostatic shielding, intermolecular forces and DNA adsorption kinetics leading to an improved sensitivity.

Open-tubular nanoelectrochromatography (OT-NEC): gel-free separation of single stranded DNAs (ssDNAs) in thermoplastic nanochannels

Electrophoresis or electrochromatography carried out in nanometer columns (width and depth) offers some attractive benefits compared to microscale columns. These advantages include unique separation mechanisms that are scale dependent, fast separation times, and simpler workflow due to the lack of a need for column packing and/or wall coatings to create a stationary phase. We report the use of thermoplastics, in this case PMMA, as the substrate for separating single-stranded DNAs (ssDNAs). Electrophoresis nanochannels were created in PMMA using nanoimprint lithography (NIL), which can produce devices at lower cost and in a higher production mode compared to the fabrication techniques required for glass devices. The nanochannel column in PMMA was successful in separating ssDNAs in free solution that was not possible using microchip electrophoresis in PMMA. The separation could be performed in <1 s with resolution >1.5 when carried out using at an electric field strength of 280 V/cm and an effective column length of 60 μm (100 nm × 100 nm, depth and width). The ssDNAs transport through the PMMA column was driven electrokinetically under the influence of an EOF. The results indicated that the separation was dominated by chromatographic effects using an open tubular nano-electrochromatography (OT-NEC) mode of separation. Interesting to these separations was that no column packing was required nor a wall coating to create the stationary phase; the separation was affected using the native polymer that was UV/O₃ activated and an aqueous buffer mobile phase.

Effect of Octadecylamine Surfactant on DNA Interactions with Graphene Surfaces

Understanding of how to integrate DNA molecules with graphene materials is important for the development of biosensors and biomolecular logic circuits. For some of these applications, controlling DNA structural conformation on the graphene substrate is critically important and can be achieved through the use of self-assembled monolayers. Here, we performed all-atom molecular dynamics simulations to understand how various 1-octadecylamine (ODA) coatings of the graphene surface affect the conformation of double-stranded DNA (dsDNA) on the surface. The simulation results demonstrated that dsDNA structures become more stable as ODA concentration increases due to the formation of DNA-ODA hydrogen bonds and reduction of DNA-surface interactions, which aid in retaining internal DNA interactions. Specifically, the interaction of ODA molecules with DNA prevents nucleobases from forming π-π stacking interactions with the surface. Some dsDNA conformations, such as sharp kinks or unwinding, can occur more frequently in DNA with A-T sequences due to weaker pairing interactions than with G-C sequences. Furthermore, our results conclude that both DNA sequence and ODA concentration play an essential role in experimentally observed conformational changes of DNA on the graphene surface.

A FRET-based dual-color evanescent wave optical fiber aptasensor for simultaneous fluorometric determination of aflatoxin M1 and ochratoxin A

A dual-color fluorescence resonance energy transfer (FRET) based aptasensor is described for simultaneous determination of the mycotoxins aflatoxin M1 (AFM1) and ochratoxin A (OTA). Aptamers against AFM1 and OTA were labeled with two fluorophores with different excitation wavelengths (Cy5.5; 675 nm; and Alexa 405; 401 nm), respectively. They were used as the signalling probes. A compact dual-color evanescent wave all-fiber detection system with two lasers (635 nm; red; and 405 nm; purple) was used for the simultaneous collection of two-wavelength fluorescence signals. The hybridization of labeled aptamers with complementary sequences (Q-cDNA) labeled with a dark quencher (BHQ₃ or dabcyl) causes fluorescence to be strongly reduced because of the fluorescence resonance energy transfer. In the presence of AFM1 and OTA, they bind to their respective aptamer and result in the dissociation of double stranded DNA, which induce fluorescence recovery. Under the optimum conditions, AFM1 and OTA can simultaneously and selectively be determined ranged from 1 ng·L^-1 to 1 mg·L^-1. The detection limits of AFM1 and OTA are 21 and 330 ng·L^-1, respectively (S/N = 3). The FRET-based dual-color detection scheme was applied to the simultaneous detection of AFM1 and OTA in milk with good recovery, precision, and accuracy. Graphical abstract Aptamers against AFM1 and OTA were labeled with two fluorophores with different excitation wavelengths (Cy5.5; 675 nm; and Alexa 405; 401 nm) and then used as signalling probes. A FRET-based aptasensor is described for simultaneous determination of AFM1 and OTA using dual-color evanescent wave system with two lasers (635 nm; red; and 405 nm).