In silico evaluation of potential murine M49 DNA aptamer on ORF7a of SARS-COV-2: A similar target

Abstract

DNA aptamers are short nucleotides with a high affinity for their target. However, the process of isolating aptamers via the systematic evolution of ligands by exponential enrichment (SELEX) procedure is laborious. Therefore, an in silico approach is used to screen potential DNA aptamer candidates as a kickstart specifically for ORF7a of SARSCOV-2. By applying the TM-align program, the murine receptor (CD200R) protein was found to have structural similarities with ORF7a. Based on the literature, this CD200R protein is successfully bound by M49 DNA aptamers experimentally. Herein, the 3D structure of the M49 DNA aptamer was generated using Mfold, RNA Composer webserver, Discovery Studio Visualizer, and UCSF Chimera software, and the docking simulation was predicted using the HDOCK webserver. The binding energy scores for the M49-CD200R complex were slightly higher than those for the M49-ORF7a complex with-233.78 and-220.11, respectively. The molecular interaction in the complexes was contributed by the hydrogen bond. In conclusion, the M49 aptamer of CD200R protein can bind to the other similar target, the ORF7a protein of SARS-COV-2. Even though CD200R and ORF7a proteins share structural similarities, the binding sites of the individual complex are distinct. The current study shows that two different proteins with structural similarities may have a possibility to share the same DNA aptamer. This strategy may result in efficient aptamer discovery using an in silico method as a first step. © 2022 Marmara University Press.