Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study.

Publisher: Springer-Verlag Country of Publication: Germany NLM ID: 101134327 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1618-2650 (Electronic) Linking ISSN: 16182642 NLM ISO Abbreviation: Anal Bioanal Chem Subsets: MEDLINE

Original Publication: Heidelberg : Springer-Verlag, 2002-

Aptamers, Nucleotide* ; Thermodynamics*; Single Molecule Imaging/*methods ; Thrombin/*chemistry; Biosensing Techniques ; Models, Chemical ; Protein Binding

Duplexed aptamers (DAs) are widespread aptasensor formats that simultaneously recognize and signal the concentration of target molecules. They are composed of an aptamer and aptamer complementary element (ACE) which consists of a short oligonucleotide that partially inhibits the aptamer sequence. Although the design principles to engineer DAs are straightforward, the tailored development of DAs for a particular target is currently based on trial and error due to limited knowledge of how the ACE sequence affects the final performance of DA biosensors. Therefore, we have established a thermodynamic model describing the influence of the ACE on the performance of DAs applied in equilibrium assays and demonstrated that this relationship can be described by the binding strength between the aptamer and ACE. To validate our theoretical findings, the model was applied to the 29-mer anti-thrombin aptamer as a case study, and an experimental relation between the aptamer-ACE binding strength and performance of DAs was established. The obtained results indicated that our proposed model could accurately describe the effect of the ACE sequence on the performance of the established DAs for thrombin detection, applied for equilibrium assays. Furthermore, to characterize the binding strength between the aptamer and ACEs evaluated in this work, a set of fitting equations was derived which enables thermodynamic characterization of DNA-based interactions through thermal denaturation experiments, thereby overcoming the limitations of current predictive software and chemical denaturation experiments. Altogether, this work encourages the development, characterization, and use of DAs in the field of biosensing.
(© 2021. Springer-Verlag GmbH Germany, part of Springer Nature.)

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FWO SB/1SC8519N Fonds Wetenschappelijk Onderzoek

Keywords: Aptamer; DNA nanosensor; DNA nanotechnology; Duplexed aptamer; Modeling; Thermal denaturation

0 (Aptamers, Nucleotide)
EC 3.4.21.5 (Thrombin)

Date Created: 20210610 Date Completed: 20211019 Latest Revision: 20211019

20231215

10.1007/s00216-021-03444-y

34109445