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Aptamer-based detection of thrombin by acoustic method using DNA tetrahedrons as immobilisation platform

Alexandra Poturnayová, Maja Šnejdárková, Gabriela Castillo, Peter Rybár, Michael Leitner, Andreas Ebner, and Tibor Hianik

Institute of Biochemistry and Animal Genetics, Slovak Academy of Sciences, Moyzesova 61, 900 28 Ivanka pri Dunaji, Slovakia

 

E-mail: Tibor.Hianik@fmph.uniba.sk

Abstract: The thickness shear mode acoustic method was used to study the binding of thrombin to DNA aptamers immobilised on the gold surface covered by DNA tetrahedrons. The binding of thrombin to conventional aptamers sensitive to fibrinogen (FBT) and heparin (HPT) exosites as well as to HPT in a loop configuration (HPTloop) made it possible to determine the constant of dissociation (KD) and the limit of detection (LOD). The sensing system composed of a HPTloop was characterised by KD = (66.7 ± 22.7) nM, which was almost twice as low as that of FBT and HPT. For this biosensor, a lower LOD of 5.2 nM compared with 17 nM for conventional HPT aptamers was also obtained. Less sensitive sensors based on FBT aptamers revealed an LOD of 30 nM which is in agreement with the lower affinity of these aptamers to thrombin in comparison with that of HPT. The surface concentration of DNA tetrahedrons was determined by the electrochemical method using [Ru(NH3)6]3+ as a redox probe. These experiments confirmed that the “step by step” method of forming the sensing layer, consisting first in chemisorption of DNA tetrahedrons onto a gold surface and then in hybridisation of the aptamer-supporting part with complementary oligos at the top of the tetrahedron, is preferable. In addition, atomic force microscopy was applied to analyse the topography of the gold layers modified stepwise by DNA tetrahedrons, DNA aptamers and thrombin. The height profiles of the layers were in reasonable agreement with the dimensions of the adsorbed molecules. The results indicate that DNA tetrahedrons represent an efficient platform for immobilisation of aptamers.

Keywords: aptamers – DNA tetrahedrons – thrombin – thickness shear mode

Full paper is available at www.springerlink.com.

DOI: 10.1515/chempap-2015-0044

 

Chemical Papers 69 (1) 211–226 (2015)

Monday, November 28, 2022

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