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Computational approach to analyze isolated ssDNA aptamers against angiotensin II

Paper ID Volume ID Publish Year Pages File Format Full-Text
22643 43368 2016 6 PDF Available
Title
Computational approach to analyze isolated ssDNA aptamers against angiotensin II
Abstract

•Here we introduced a manipulated in-silico approach to predict the 3-D structure of ssDNA aptamers and their interaction with target.•Results obtained from innovative in-silico method were in agreement with the experimental outputs.•The structural and sequential homology between aptamers can be considered as a sign of similar characteristics.•Analog aptameric structures with different sequences, cannot completely exhibit the same characteristics.

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.

Keywords
Docking; In-silico analysis; SELEX; ssDNA aptamer
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Computational approach to analyze isolated ssDNA aptamers against angiotensin II
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 230, 20 July 2016, Pages 34–39
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us