Optical extinction combined with phase measurements for probing DNA-small-molecule interactions using an evanescent waveguide biosensor

Reusable chemiluminescent fiber optic aptasensor for the determination of 17β-estradiol in water samples

A reusable fiber optic chemiluminescent aptasensor (FOCA) is reported for the rapid and sensitive on-site detection of 17β-estradiol (E2), an endocrine-disrupting compound frequently found in water samples. The E2-ovalbumin conjugate (E2-OVA) was covalently immobilized onto the optical fiber as a biorecognition element as well as a transducer. The affinity constant of the E2/aptamer complex was determined to be 1.35 × 10⁶ M^-1 using the FOCA. An indirect competitive assay was then developed for E2 detection. A certain concentration of HRP-E2 aptamers pre-reacted with samples containing E2 in various concentrations. Part of HRP-E2 aptamers specially bound to the sensor surface after introduction of the mixture. This catalyzed the chemiluminescece reaction of a chemiluminescent system composed of luminol and H₂O₂. A higher concentration of E2 led to less HRP-E2 aptamer bound to the biosensor surface, thus resulting in less chemiluminescence. Highly sensitive detection of E2 was achieved under optimal conditions, and the limit of detection is 48 ng ·L^-1 (0.18 nM). The whole analytical process, including measurement and regeneration, can be performed in <15 min. The robustness of the biosensor allows its application to multiple assays with little activity loss. The selectivity, recovery, and accuracy of the sensor was demonstrated by evaluating its response to potentially interfering endocrine disruptors in spiked water samples. Graphical abstract Schematic diagram of the fiber optic chemiluminescent aptasensor system (A), detection mechanism of 17β-estradiol (B), and its application for detection of 17β-estradiol with rapidity and sensitivity (C and D).

Establishment of Logic Gates Based on Conformational Changes in a Multiple-Factor Biomolecule Interaction Process by Dual Polarization Interferometry

DNA-based logic gates stimulate the development of molecular scale computers and show enormous potential in nanotechnology, biotechnology, and medicine. However, the reported detectors to date usually require one to label appropriate signal probes, resulting in not only a high cost but also potentially tedious manipulation. For the first time, we established a label-free logic gate by regarding the structure-related signal as output. Dual polarization interferometry (DPI) was employed to reveal the detailed conformational transitions occurring in the multiple-factor biomolecule interactions and then was utilized as a detection tool of logic gate. As a vital merit of this system, the dependence of the density output signal on the interaction with multiple-factor input can mimic the function of signal communication in OR, INHIBIT, and IDENTITY logic gates and the INHIBIT-OR cascade circuit. Additionally, the DPI signal with logic stringency can unambiguously distinguish conformational polymorphisms and compare structural stability. This study provides a new way for the construction of a label-free logic gate, supplements information deficiency of reaction details, and extends the application of DPI in logic operation.

Real-time study of interactions between cytosine-cytosine pairs in DNA oligonucleotides and silver ions using dual polarization interferometry

The real-time conformational changes of cytosine (C)-rich ssDNA oligonucleotides upon binding with silver ions (Ag(+)) were studied using dual polarization interferometry (DPI). Upon the addition of Ag(+), Ag(+) selectively bound to cytosine-cytosine mismatches and formed C-Ag(+)-C complexes, inducing change of the structure of the C-rich ssDNA from random coil conformation to duplex conformation, whereas the control ssDNA without cytosine-cytosine mismatches had no such signal, which was consistent with circular dichroism (CD) characterization. The conformational change of DNA was reflected on the changes of the mass, thickness, and density values resolved by DPI. The calibration curves showed that as the concentration of Ag(+) increased from 10 nM to 8 μM, the thickness and mass values increased linearly while the density values decreased linearly. Other metal ions such as K(+), Ca(2+), Na(+), Mg(2+), Zn(2+), Mn(2+), Ni(2+), and Pb(2+) did not interfere with the interaction between Ag(+) and C-rich ssDNA, indicating that this method had a good selectivity. The practical application of this biosensor was also investigated in real samples such as drinking water. Besides, cysteine could specifically capture Ag(+) from C-Ag(+)-C complexes and transformed the structure of the C-rich DNA back from rigid double-stranded conformation to random coil conformation, which allowed cysteine to be detected selectively as well. It is expected that this biosensing strategy may be utilized to study the interaction of DNA with other molecules.

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.

Dual-polarization interferometry for quantification of small molecules using aptamers

An interferometry-based method was developed for detection of a small molecule, argininamide. The quantification of argininamide was demonstrated using aptamers immobilized on silicone oxynitride sensor surface via avidin-biotin binding. The aptamers formed a thin film over avidin layer corresponding to a thickness of 1.2 nm, consistent with a molecular positioning of multipoint attachment to the surface. The binding of argininamide did not cause any significant changes in the thickness of the aptamer film, suggesting that the specific binding did not affect the overall conformation of the aptamer molecules after adaptive rearrangement of aptamer molecules. However, the binding results in clearly detectable changes in mass calculated from multiple parameters determined by mass deposition and structural changes. The limit of detection of the developed sensor was determined to be 5 μM. The sensor can monitor real-time changes in argininamide concentrations with high reliability and sensitivity. The model system demonstrated that a combined measurement considering structural and mass changes through interferometry-based techniques can overcome one of the major problems associated with real-time monitoring of small mass analytes.

Biosensors in microfluidic chips

A biosensor is a sensing device that incorporates a biological sensing element and a transducer to produce electrochemical, optical, mass, or other signals in proportion to quantitative information about the analytes in the given samples. The microfluidic chip is an attractive miniaturized platform with valuable advantages, e.g., low cost analysis requiring low reagent consumption, reduced sample volume, and shortened processing time. Combination of biosensors and microfluidic chips enhances analytical capability so as to widen the scope of possible applications. This review provides an overview of recent research activities in the field of biosensors integrated on microfluidic chips, focusing on the working principles, characteristics, and applicability of the biosensors. Theoretical background and applications in chemical, biological, and clinical analysis are summarized and discussed.

Theory and applications of surface plasmon resonance, resonant mirror, resonant waveguide grating, and dual polarization interferometry biosensors

Biosensors have been used extensively in the scientific community for several purposes, most notably to determine association and dissociation kinetics, protein-ligand, protein-protein, or nucleic acid hybridization interactions. A number of different types of biosensors are available in the field, each with real or perceived benefits over the others. This review discusses the basic theory and operational arrangements of four commercially available types of optical biosensors: surface plasmon resonance, resonant mirror, resonance waveguide grating, and dual polarization interferometry. The different applications these techniques offer are discussed from experiments and results reported in recently published literature. Additionally, recent advancements or modifications to the current techniques are also discussed.