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

Abstract

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.

Keywords

• g-quadraplex nanostructure
• aptamers
• bioinformatics
• aflatoxin m1
• molecular docking