International Journal of Life Sciences and Biotech
3D Structural Prediction of Catechin Specific Aptamer
3D Structural Prediction of Catechin Specific Aptamer
Authors: Nor Azlina Ahmad, Arinaasna Mat Tamidi, Razauden Mohamed Zulkifli, Huszalina Hussin, Muhammad Helmi Nadri
Abstract: Catechin has been reported to possess many advantageous for practical application due to its distinctive antioxidant and anti-inflammatory activities. This paper reports the insilico 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 simulation was performed to all 28 aptamer candidates and resulted in 4 noticeable aptamers with highest binding energy arrangement from Aptamer 24, 18, 9 and 27. Influence of external factors towards catechin specific aptamers also was taken in consideration. It was predicted that these aptamers 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: DNA aptamer, 3D, catechin, molecular docking
3D Structural Prediction of Catechin Specific Aptamer
3D Structural Prediction of Catechin Specific Aptamer
Authors: Nor Azlina Ahmad, Arinaasna Mat Tamidi, Razauden Mohamed Zulkifli, Huszalina Hussin, Muhammad Helmi Nadri
Abstract: Catechin has been reported to possess many advantageous for practical application due to its distinctive antioxidant and anti-inflammatory activities. This paper reports the insilico 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 simulation was performed to all 28 aptamer candidates and resulted in 4 noticeable aptamers with highest binding energy arrangement from Aptamer 24, 18, 9 and 27. Influence of external factors towards catechin specific aptamers also was taken in consideration. It was predicted that these aptamers 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: DNA aptamer, 3D, catechin, molecular docking