title: Computational approach to analyze isolated ssDNA aptamers against angiotensin II.
abstract: Aptamers are oligonucleotides with highly structured molecules that can bind to their targets through specific 3-D conformation. Commonly, not all the nucleotides such as primer binding fixed region and some other sequences are vital for aptamers folding and interaction. Elimination of unnecessary regions needs trustworthy prediction tools to reduce experimental efforts and errors. Here we introduced a manipulated in-silico approach to predict the 3-D structure of aptamers and their target interactions. To design an approach for computational analysis of isolated ssDNA aptamers (FLC112, FLC125 and their truncated core region including CRC112 and CRC125), their secondary and tertiary structures were modeled by Mfold and RNA composer respectively. Output PDB files were modified from RNA to DNA in the discovery studio visualizer software. Using ZDOCK server, the aptamer-target interactions were predicted. Finally, the interaction scores were compared with the experimental results. In-silico interaction scores and the experimental outcomes were in the same descending arrangement of FLC112>CRC125>CRC112>FLC125 with similar intensity. The consistent results of innovative in-silico method with experimental outputs, affirmed that the present method may be a reliable approach. Also, it showed that the exact in-silico predictions can be utilized as a credible reference to find aptameric fragments binding potency.
authors.affiliation: Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
authors.forename: Mohammad
authors.initials: M
authors.lastname: Heiat
authors.affiliation: Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran. Electronic address: najafi74@bmsu.ac.ir.
authors.forename: Ali
authors.initials: A
authors.lastname: Najafi
authors.affiliation: Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
authors.forename: Reza
authors.initials: R
authors.lastname: Ranjbar
authors.affiliation: Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
authors.forename: Ali Mohammad
authors.initials: AM
authors.lastname: Latifi
authors.affiliation: Department of Clinical Biochemistry, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
authors.forename: Mohammad Javad
authors.initials: MJ
authors.lastname: Rasaee
mesh_terms: D000804:Angiotensin II / Q000737:chemistry* / Q000378:metabolism; D052157:Aptamers, Nucleotide / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology; D003198:Computer Simulation; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D052156:SELEX Aptamer Technique / Q000379:methods*
chemical_list: D052157:Aptamers, Nucleotide; D004277:DNA, Single-Stranded; D000804:Angiotensin II
keywords: Docking; In-silico analysis; SELEX; ssDNA aptamer