A study on the binding ability of truncated aptamers for the prostate specific antigen using both computational and experimental approaches

Hui Ting Lin, Wei Yang, Wen Yu Su, Chun Ju Chan, Wen Yih Chen, Jeffrey J.P. Tsai, Wen Pin Hu

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Prostate-specific antigen (PSA) test is a commonly used clinical examination to evaluate the risk of prostate cancer, with the antibodies used normally as the recognition molecules for measuring PSA levels in serum. Alternatively, aptamers that are able to bind target molecules with high affinity and specificity similar to antibodies could be generated much easier and cheaper than the production of antibodies. In this study, we used computaional and experimental approaches to select truncated PSA-binding aptamers generated from the sequence information of PSA-binding aptamers previously reported in a literature. Genetic algorithm, the analysis of secondary structure, and molecular simulation were utilized in the in silico analysis. The top 4 ranked sequecnes in silico analysis were evaluated through their PSA-binding ability on the quartz crystal microbalance (QCM) biosensor. Finally, We identified a truncated aptamer obtained from the selection showing a nearly 3.5-fold higher measured signal than the response produced by the best known DNA sequence in the QCM measurement.

Original languageEnglish
Title of host publicationFrontier Computing - Theory, Technologies and Applications FC 2017
EditorsNeil Y. Yen, Jason C. Hung, Lin Hui
PublisherSpringer Verlag
Pages46-55
Number of pages10
ISBN (Print)9789811073977
DOIs
StatePublished - 2018
Event6th International Conference on Frontier Computing, FC 2017 - Osaka, Japan
Duration: 12 Jul 201714 Jul 2017

Publication series

NameLecture Notes in Electrical Engineering
Volume464
ISSN (Print)1876-1100
ISSN (Electronic)1876-1119

Conference

Conference6th International Conference on Frontier Computing, FC 2017
Country/TerritoryJapan
CityOsaka
Period12/07/1714/07/17

Keywords

  • Aptamer
  • Molecular simulation
  • Prostate specific antigen (PSA)
  • Quartz crystal microbalance (QCM)

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