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BioMed Research International
Volume 2017, Article ID 5041683, 11 pages
https://doi.org/10.1155/2017/5041683
Research Article

The Combination of Computational and Biosensing Technologies for Selecting Aptamer against Prostate Specific Antigen

1Department of Bioinformatics and Medical Engineering, Asia University, Taichung City 41354, Taiwan
2Department of Physical Therapy, I-Shou University, Kaohsiung City 82445, Taiwan
3Department of Chemical and Materials Engineering, National Central University, Jhongli 32001, Taiwan
4Department of Medical Laboratory Science and Biotechnology, China Medical University, Taichung City 40402, Taiwan

Correspondence should be addressed to Wen-Pin Hu; wt.ude.aisa@uhnipnew

Received 24 November 2016; Revised 10 March 2017; Accepted 19 March 2017; Published 28 March 2017

Academic Editor: Hicham Fenniri

Copyright © 2017 Pi-Chou Hsieh et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Herein, we report a method of combining bioinformatics and biosensing technologies to select aptamers against prostate specific antigen (PSA). The main objective of this study is to select DNA aptamers with higher binding affinity for PSA by using the proposed method. Based on the five known sequences of PSA-binding aptamers, we adopted the functions of reproduction and crossover in the genetic algorithm to produce next-generation sequences for the computational and experimental analysis. RNAfold web server was utilized to analyze the secondary structures, and the 3-dimensional molecular models of aptamer sequences were generated by using RNAComposer web server. ZRANK scoring function was used to rerank the docking predictions from ZDOCK. The biosensors, the quartz crystal microbalance (QCM) and a surface plasmon resonance (SPR) instrument, were used to verify the binding ability of selected aptamer for PSA. By carrying out the simulations and experiments after two generations, we obtain one aptamer that can have the highest binding affinity with PSA, which generates almost 2-fold and 3-fold greater measured signals than the responses produced by the best known DNA sequence in the QCM and SPR experiments, respectively.