title: Selection of thrombin-binding aptamers by using computational approach for aptasensor application.
abstract: The possibility of introducing a computationally assisted method to study aptamer-protein interaction was evaluated with the aim of streamlining the screening and selection of new aptamers. Starting from information on the 15-mer (5'-GGTTGGTGTGGTTGG-3') thrombin binding aptamer (TBA), a library of mutated DNA sequences (994 elements) was generated and screened using shapegauss a shape-based scoring function from openeye software to generate computationally derived binding scores. The TBA and three other mutated oligonucleotides, selected on the basis of their binding score (best, medium, worst), were incorporated into surface plasmon resonance (SPR) biosensors. By reducing the ionic strength (binding buffer, 50 mM TrisHCl pH 7.4, 140 mM NaCl, 1mM MgCl₂, diluted 1:50) in order to match the simulated condition, the analytical performances of the four oligonucleotide sequences were compared using signal amplitude, sensitivity (slope), linearity (R²) and reproducibility (CVav %). The experimental results were in agreement with the simulation findings.
authors.affiliation: Dipartimento di Chimica, Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy.
authors.forename: Alessandra
authors.initials: A
authors.lastname: Bini
authors.forename: Marcello
authors.initials: M
authors.lastname: Mascini
authors.forename: Marco
authors.initials: M
authors.lastname: Mascini
authors.forename: Anthony P F
authors.initials: AP
authors.lastname: Turner
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics; D001483:Base Sequence; D001665:Binding Sites; D015374:Biosensing Techniques / Q000379:methods* / Q000706:statistics & numerical data; D019295:Computational Biology; D015723:Gene Library; D009025:Morpholines; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D011487:Protein Conformation; D052156:SELEX Aptamer Technique / Q000706:statistics & numerical data; D020349:Surface Plasmon Resonance; D013917:Thrombin / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D009025:Morpholines; C081676:thrombin aptamer; C038974:amorolfine; D013917:Thrombin