title: A computationally designed DNA aptamer template with specific binding to phosphatidylserine.
abstract: The phospholipid phosphatidylserine (PS) is an early marker exploited for detecting apoptosis (PS externalization in the cell membrane bilayer) and one factor that is associated with increased amyloid plaque deposition in transmissible spongiform encephalopathies (TSEs). PS can therefore be considered as a promising target for diagnosis or treatment of diseases. Aptamers (short nucleic acid sequences) are a particularly attractive class of materials among those currently considered for targeting PS. Here we applied an entropy based seed-and-grow strategy to design a DNA aptamer template to bind specifically to PS. The binding properties of designed aptamers were investigated computationally and experimentally. The studies identify the sequence, 5'-AAAGAC-3', as the preferred template for further modifications and studies toward its practical implementations.
authors.affiliation: 1 Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta , Edmonton, Alberta, Canada .
authors.forename: Md
authors.initials: M
authors.lastname: Ashrafuzzaman
authors.forename: Chih-Yuan
authors.initials: CY
authors.lastname: Tseng
authors.forename: Janice
authors.initials: J
authors.lastname: Kapty
authors.forename: John R
authors.initials: JR
authors.lastname: Mercer
authors.forename: Jack A
authors.initials: JA
authors.lastname: Tuszynski
mesh_terms: D017209:Apoptosis; D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001483:Base Sequence; D019277:Entropy; D008081:Liposomes / Q000737:chemistry; D062105:Molecular Docking Simulation; D009690:Nucleic Acid Conformation; D010718:Phosphatidylserines / Q000737:chemistry*; D013050:Spectrometry, Fluorescence
chemical_list: D052157:Aptamers, Nucleotide; D008081:Liposomes; D010718:Phosphatidylserines