title: DNA aptamer selection in methanolic media: Adenine-aptamer as proof-of-concept.
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-product traces in drugs production.
authors.affiliation: Univ. Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France; INSERM, U869, ARNA Laboratory, F-33000 Bordeaux, France.
authors.forename: Thinhinane
authors.initials: T
authors.lastname: Chaou
authors.affiliation: Univ. Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France; INSERM, U869, ARNA Laboratory, F-33000 Bordeaux, France.
authors.forename: Brune
authors.initials: B
authors.lastname: Vialet
authors.affiliation: Univ. Bordeaux, ARNA Laboratory, F-33000 Bordeaux, France; INSERM, U869, ARNA Laboratory, F-33000 Bordeaux, France. Electronic address: laurent.azema@u-bordeaux.fr.
authors.forename: Laurent
authors.initials: L
authors.lastname: Azéma
mesh_terms: D000225:Adenine / Q000737:chemistry*; D052157:Aptamers, Nucleotide / Q000737:chemistry; D002021:Buffers; D006801:Humans; D055029:Inverted Repeat Sequences; D000432:Methanol / Q000737:chemistry; D052156:SELEX Aptamer Technique; D012996:Solutions; D012997:Solvents / Q000737:chemistry
chemical_list: D052157:Aptamers, Nucleotide; D002021:Buffers; D012996:Solutions; D012997:Solvents; D000225:Adenine; D000432:Methanol
keywords: Adenine; Aptamer; Modified nucleotide; Organic buffer