Detection of SARS-CoV-2 RNA Using a DNA Aptamer Mimic of Green Fluorescent Protein.

TitleDetection of SARS-CoV-2 RNA Using a DNA Aptamer Mimic of Green Fluorescent Protein.
Publication TypeJournal Article
Year of Publication2022
AuthorsVarnBuhler BS, Moon J, Dey SKumar, Wu J, Jaffrey SR
JournalACS Chem Biol
Date Published2022 Apr 15
KeywordsAptamers, Nucleotide, COVID-19, DNA, Fluorescent Dyes, Green Fluorescent Proteins, Humans, RNA, RNA, Viral, SARS-CoV-2

RNA detection is important in diverse diagnostic and analytical applications. RNAs can be rapidly detected using molecular beacons, which fluoresce upon hybridizing to a target RNA but require oligonucleotides with complex fluorescent dye and quencher conjugations. Here, we describe a simplified method for rapid fluorescence detection of a target RNA using simple unmodified DNA oligonucleotides. To detect RNA, we developed Lettuce, a fluorogenic DNA aptamer that binds and activates the fluorescence of DFHBI-1T, an otherwise nonfluorescent molecule that resembles the chromophore found in green fluorescent protein. Lettuce was selected from a randomized DNA library based on binding to DFHBI-agarose. We further show that Lettuce can be split into two separate oligonucleotide components, which are nonfluorescent on their own but become fluorescent when their proximity is induced by a target RNA. We designed several pairs of split Lettuce fragments that contain an additional 15-20 nucleotides that are complementary to adjacent regions of the SARS-CoV-2 RNA, resulting in Lettuce fluorescence only in the presence of the viral RNA. Overall, these studies describe a simplified RNA detection approach using fully unmodified DNA oligonucleotides that reconstitute the Lettuce aptamer templated by RNA.

Alternate JournalACS Chem Biol
PubMed ID35341244
Grant ListR35 NS111631 / NS / NINDS NIH HHS / United States

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