3D Structural Prediction of Catechin Specific Aptamer

Abstract

Catechin has been reported to possess many advantageous for practical application due to its distinctive antioxidant and anti-inflammatory performance. This paper reports the in-silico characterization of single stranded-DNA (ssDNA) aptamers, specific for catechin. 28 primary sequences from DNA-aptamers library screened via systemic evolution of ligands by exponential enrichment (SELEX) from previous research were predicted and constructed into 3D structural conformation using several bioinformatics tools. Blind docking was performed to all 28 aptamer candidates and resulted in 4 noticeable aptamer with highest binding energy, namely Aptamer 24, 18, 9 and 27 as catechin specific aptamer. Influence of environmental factors towards catechin specific aptamers also was taken in consideration. It was predicted that aptamer 24, 18, 9 and 27 were the most potential aptamer for catechin recognition tool at laboratory scale based on the docking result. However, further in vitro experimental study in laboratory needs to be done as validation.

Keywords

• 3D
• DNA aptamer
• catechin
• molecular docking

Project Number

This project was funded by Ministry of Higher Education (MOE), Malaysia and Innovation and Commercialization Centre (ICC), Universiti Teknologi Malaysia (UTM) [PRGS:ICC (PY/2020/03762)]

Thanks

We also would like to acknowledge Department of Bioscience, Faculty of Science, UTM for supporting this project

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