In silico approach for Post-SELEX DNA aptamers: A mini-review

Nor Azlina Ahmad; Razauden Mohamed Zulkifli; Huszalina Hussin; Muhammad Helmi Nadri

doi:10.1016/j.jmgm.2021.107872

In silico approach for Post-SELEX DNA aptamers: A mini-review

J Mol Graph Model. 2021 Jun:105:107872. doi: 10.1016/j.jmgm.2021.107872. Epub 2021 Mar 2.

Authors

Nor Azlina Ahmad¹, Razauden Mohamed Zulkifli², Huszalina Hussin¹, Muhammad Helmi Nadri³

Affiliations

¹ Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor Bahru, Johor, Malaysia.
² Department of Biosciences, Faculty of Science, Universiti Teknologi Malaysia, 81310, Skudai, Johor Bahru, Johor, Malaysia; Centre of Research for Fiqh Science & Technology, Universiti Teknologi Malaysia, 81310, Skudai, Johor Bahru, Johor, Malaysia. Electronic address: razauden@fbb.utm.my.
³ Innovation Centre in Agritechnology for Advanced Bioprocessing, Universiti Teknologi Malaysia, 84600, Pagoh, Johor, Malaysia.

PMID: 33765525
DOI: 10.1016/j.jmgm.2021.107872

Abstract

Aptamers are short oligonucleotides that possess high specificity and affinity against their target. Generated via Systematic Evolution of Ligands by Exponential Enrichment, (SELEX) in vitro, they were screened and enriched. This review covering the study utilizing bioinformatics tools to analyze primary sequence, secondary and tertiary structure prediction, as well as docking simulation for various aptamers and their ligand interaction. Literature was pooled from Web of Science (WoS) and Scopus databases until December 18, 2020 using specific search string related to DNA aptamers, in silico, structure prediction, and docking simulation. Out of 330 published articles, 38 articles were assessed in the analysis based on the predefined inclusion and exclusion criteria. It was found that Mfold and RNA Composer web server is the most popular tool in secondary and tertiary structure prediction of DNA aptamers, respectively. Meanwhile, in docking simulation, ZDOCK and AutoDock are preferred to analyze binding interaction in the aptamer-ligand complex. This review reports a brief framework of recent developments of in silico approaches that provide predictive structural information of ssDNA aptamer.

Keywords: DNA aptamers; Docking simulation; In silico; Modelling; Structure prediction.

Publication types

Research Support, Non-U.S. Gov't
Review

MeSH terms

Aptamers, Nucleotide*
Computer Simulation
DNA, Single-Stranded
Ligands
SELEX Aptamer Technique*

Substances

Aptamers, Nucleotide
DNA, Single-Stranded
Ligands