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Selection of thrombin-binding aptamers by using computational approach for aptasensor application
University of Florence.
University of Teramo.
University of Florence.
Linköping University, Department of Physics, Chemistry and Biology, Biosensors and Bioelectronics. Linköping University, The Institute of Technology.ORCID iD: 0000-0002-1815-9699
2011 (English)In: Biosensors & bioelectronics, ISSN 0956-5663, E-ISSN 1873-4235, Vol. 26, no 11, 4411-4416 p.Article in journal (Refereed) Published
Abstract [en]

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 mMTrisHC1pH 7.4, 140 mM NaCl, 1 mM MgCl(2), 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 (R(2)) and reproducibility (CVav %). The experimental results were in agreement with the simulation findings.

Place, publisher, year, edition, pages
Elsevier , 2011. Vol. 26, no 11, 4411-4416 p.
Keyword [en]
Molecular dynamics, Thrombin, Aptamers, Binding score, Surface plasmon resonance biosensor
National Category
Engineering and Technology
URN: urn:nbn:se:liu:diva-70110DOI: 10.1016/j.bios.2011.04.053ISI: 000293104100025OAI: diva2:435543
Original Publication: Alessandra Bini, Marcello Mascini, Marco Mascini and Anthony Turner, Selection of thrombin-binding aptamers by using computational approach for aptasensor application, 2011, Biosensors & bioelectronics, (26), 11, 4411-4416. Copyright: Elsevier Available from: 2011-08-19 Created: 2011-08-19 Last updated: 2013-10-04

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