212 research outputs found
Molecular Modelling Design of Artificial Receptors for the Detection of Dioxin in the Environment
No full text
Selection of thrombin-binding aptamers by using computational approach for aptasensor application
No full textThe 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.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.http://dx.doi.org/10.1016/j.bios.2011.04.053Copyright: Elsevierhttp://www.elsevier.com
Selection of Thrombin-binding aptamers by using computational approach for aptasensor application
No full textThe 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.[...
Screening Methodologies for Genetic Modified Organisms (GMOs)
No full textDescription of the bioanalytical approaches of GMOs detectio
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