DNA aptamer selection in methanolic media: Adenine-aptamer as proof-of-concept

Methods : a Companion to Methods in Enzymology
Thinhinane ChaouLaurent Azéma

Abstract

The major objective of this study is to investigate the usefulness of aptamers as in situ detection tool in organic solvents, which are often used for environmental extraction. But two problems related to the use of methanol-containing buffers have to be addressed. Firstly, the folding of nucleic acids can be impaired, because of weaker hydrogen bonding interactions. Secondly, the affinity of aptamers selected in aqueous buffers can be altered by the presence of methanol. Thus, in order to improve hydrophobicity of the DNA pool, nucleotide with hydrophobic modification 5-(octa1,7-diynyl)-2'-deoxyuridine (ODT) has been chosen instead of thymidine. As a proof of concept, an adenine aptamer operating in presence 25% of methanol has been selected. We have shown that the modified nucleotide is essential for target binding in organic media, in addition to essential structural pattern as proposed through analysing truncated sequences analysis. The strategy described in this paper offers preliminary insight on the adaptability of the implementation of aptamers as key instrument for in situ detection. It could be broaden to identify other aptamers directed against other chemical species after alcoholic extraction or for monitoring by-pr...Continue Reading

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Citations

Mar 15, 2016·Methods : a Companion to Methods in Enzymology·Jean-Jacques ToulméFrédéric Ducongé
Aug 3, 2018·Angewandte Chemie·Rossella SvigeljM Jesús Lobo-Castañón
Dec 15, 2017·Current Protocols in Chemical Biology·Annamaria RuscitoMaria C DeRosa
May 1, 2021·Chembiochem : a European Journal of Chemical Biology·Tianjun ChangYingfu Li

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