Development of a thermal-stable structure-switching cocaine-binding aptamer
| dc.contributor.author | Shoara, Aron A | |
| dc.contributor.author | Reinstein, Oren | |
| dc.contributor.author | Borhani, Okty Abbasi | |
| dc.contributor.author | Martin, Taylor R | |
| dc.contributor.author | Slavkovic, Sladjana | |
| dc.contributor.author | Churcher, Zachary R | |
| dc.contributor.author | Johnson, Philip E | |
| dc.date.accessioned | 2023-05-10T16:22:11Z | |
| dc.date.available | 2023-05-10T16:22:11Z | |
| dc.date.issued | 2017-08-21 | |
| dc.description.abstract | We have developed a new cocaine-binding aptamer variant that has a significantly higher melt tem- perature when bound to a ligand than the currently used sequence. Retained in this new construct is the ligand-induced structure-switching binding mechanism that is important in biosensing applications of the cocaine-binding aptamer. Isothermal titration calorimetry methods show that the binding affinity of this new sequence is slightly tighter than the existing cocaine-binding aptamer. The improved thermal performance, a Tm increase of 4 C for the cocaine-bound aptamer and 9 C for the quinine-bound aptamer, was achieved by optimizing the DNA sequence in stem 2 of the aptamer to have the highest stability based on the nearest neighbor thermodynamic parameters and confirmed by UV and fluores- cence spectroscopy. The sequences in stem 1 and stem 3 were unchanged in order to retain the structure switching and ligand binding functions. The more favorable thermal stability characteristics of the OR3 aptamer should make it a useful construct for sensing applications employing the cocaine-binding aptamer system. | en_US |
| dc.identifier.citation | Biochimie 145 (2018): 137-144 | en_US |
| dc.identifier.uri | https://doi.org/10.1016/j.biochi.2017.08.010 | en_US |
| dc.identifier.uri | http://hdl.handle.net/10315/41134 | |
| dc.language.iso | en | en_US |
| dc.publisher | Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM) | en_US |
| dc.rights | Attribution-NonCommercial-NoDerivatives 4.0 International | * |
| dc.rights.uri | http://creativecommons.org/licenses/by-nc-nd/4.0/ | * |
| dc.subject | Aptamer design; DNA melts; NMR spectroscopy; Fluorescence spectroscopy; Isothermal titration calorimetry; DNA-Small molecule interactions | en_US |
| dc.title | Development of a thermal-stable structure-switching cocaine-binding aptamer | en_US |
| dc.type | Article | en_US |