Bioinformatical Prediction of G-quadruplex Aptamer for Detection of a Ligand in Practice

Considering the introduction of aptamers as a new generation of analyte identifiers, this class of materials can be used in diagnostic systems because aptamers are easier to produce, more sensitive, higher accuracy, less sensitive to environmental factors, easier to handle and can be used. A special type of aptamer that has sequence rich in guanine base can create a special nanostructure called G-quadraplex. The creation of this structure gives the aptamer an enzyme property so that it can act like an enzyme in the vicinity of it, oxidize a chromogenic substrate and produce a colored signal. The main way to produce aptamers is a laboratory technique called SELEX (Systematic evolution of ligands by exponential enrichment), in which a mixture of different oligo libraries in the vicinity of the target analyte creates aptamers in several consecutive cycles. The aim of this study was the introduction a novel approach for obtaining DNA aptamers for detection a ligand such as aflatoxin M1 in bioinformatically manner in replacing to SELEX for obtaining the specific oligoaptamers against aflatoxin M1. For this purpose, the structure of the selected oligoaptamers were predicted using some molecular simulators and bioinformatically techniques. The results of these molecular simulations suggested G-quadruplex aptamers with suitable affinity for binding to aflatoxin M1 in colorimetric assays

Ultrastructural characterizations of DNA nanotubes using scanning tunneling and atomic force microscopes

AbstractThe potential applications of scanning tunneling microscopy and atomic force microscopy for the characterizations of DNA nanotubes in nanoscale have been described here. The nanotubes were designed using the Cadnano software according to M13mp18 DNA as a scaffold. DNA nanotubes were fabricated using the origami technique assisted with ligase treatment subsequently. Transmission electron microscopy confirmed the morphology of DNA nanotubes. For the topographic characterization of DNA nanotubes, an atomic force microscope was used in comparison to a scanning tunneling microscope. The scanning tunneling microscopy results revealed a high-resolution topography of DNA nanotubes in the constant-current mode; however, more details of the self-assembly in DNA strands in nanotubes were explored by atomic force microscopy with contact mode (or constant height). Our findings suggested that those two microscopes could be candidates for ultrastructural characterizations of DNA nanotubes for obtaining two- and three-dimensional micrograph

Stabilization of antioxidant thyme-leaves extract (Thymus vulgaris) within biopolymers and its application in functional bread formulation

The aim of this study was to stabilize the antioxidant compounds of thyme (Thymus vulgaris) extract by spray-drying process and MD, WPC and MD-WPC carriers at different temperatures (120 and 150°С). Then, the optimal encapsulated sample was used in different ratios (1, 2, 3 and 5% w/w) to fortify pan-breads. The highest production yield (∼68 %) was obtained in the extract encapsulated with MD-WPC at 150°С. The values of moisture (3.2–4.1 %) and water activity (0.28–0.33) indicated the microbial stability of the powders. The functional characteristics of the particles (solubility and wettability) were affected by the composition and nature of the carriers. Also, the use of WPC led to an increase in physical stability, encapsulation efficiency (∼84 %), TPC (4.4 mgGAE/g) and antioxidant activity (∼77 %). The results of SEM and staining of the samples respectively indicated the effect of the process parameters on the morphology and the placement of the phenolic compounds within carrier's matrix. The physicochemical, textural characteristics, color indices (crumb and crust) and antioxidant activity of fortified breads were affected by the ratio of added free and spray-dried extract. The evaluation of sensory indices (color, texture, chewiness, taste and overall acceptance) indicated the ability to fortify bread with 3 % spray-dried extract