The possibility of introducing a computationally assisted method to study aptamer–protein interactionwas evaluated with the aim of streamlining the screening and selection of new aptamers. Starting frominformation on the 15-mer (5-GGTTGGTGTGGTTGG-3) thrombin binding aptamer (TBA), a library ofmutated DNA sequences (994 elements) was generated and screened using shapegauss a shape-basedscoring function from openeye software to generate computationally derived binding scores. The TBA andthree 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 (bindingbuffer, 50 mM TrisHCl pH 7.4, 140 mM NaCl, 1 mM MgCl2, diluted 1:50) in order to match the simulatedcondition, the analytical performances of the four oligonucleotide sequences were compared using signalamplitude, sensitivity (slope), linearity (R2) and reproducibility (CVav %). The experimental results werein agreement with the simulation findings.[...]

Selection of Thrombin-binding aptamers by using computational approach for aptasensor application

MASCINI, Marcello;
2011

Abstract

The possibility of introducing a computationally assisted method to study aptamer–protein interactionwas evaluated with the aim of streamlining the screening and selection of new aptamers. Starting frominformation on the 15-mer (5-GGTTGGTGTGGTTGG-3) thrombin binding aptamer (TBA), a library ofmutated DNA sequences (994 elements) was generated and screened using shapegauss a shape-basedscoring function from openeye software to generate computationally derived binding scores. The TBA andthree 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 (bindingbuffer, 50 mM TrisHCl pH 7.4, 140 mM NaCl, 1 mM MgCl2, diluted 1:50) in order to match the simulatedcondition, the analytical performances of the four oligonucleotide sequences were compared using signalamplitude, sensitivity (slope), linearity (R2) and reproducibility (CVav %). The experimental results werein agreement with the simulation findings.[...]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11575/10945
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