Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study
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. Al...
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| Veröffentlicht in: | Analytical and bioanalytical chemistry 2021-08, Vol.413 (19), p.4739-4750 |
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| creator | Dillen, Annelies Vandezande, Wouter Daems, Devin Lammertyn, Jeroen |
| description | 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.
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| doi_str_mv | 10.1007/s00216-021-03444-y |
| format | Article |
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Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>MEDLINE - Academic</collection><jtitle>Analytical and bioanalytical chemistry</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Dillen, Annelies</au><au>Vandezande, Wouter</au><au>Daems, Devin</au><au>Lammertyn, Jeroen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study</atitle><jtitle>Analytical and bioanalytical chemistry</jtitle><stitle>Anal Bioanal Chem</stitle><date>2021-08-01</date><risdate>2021</risdate><volume>413</volume><issue>19</issue><spage>4739</spage><epage>4750</epage><pages>4739-4750</pages><issn>1618-2642</issn><eissn>1618-2650</eissn><abstract>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.
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| subjects | Analysis Analytical Chemistry Aptamers Binding Biochemistry Biosensors Case studies Characterization and Evaluation of Materials Chemistry Chemistry and Materials Science Equilibrium Food Science Identification and classification Laboratory Medicine Monitoring/Environmental Analysis Oligonucleotides Paper in Forefront Potassium Properties Software Thermal denaturation Thermodynamic models Thermodynamics Thrombin |
| title | Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study |
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