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Probing the propeller-like loops of DNA G-quadruplexes with looped-out 2-aminopurine for label-free switchable molecular sensing

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Abstract

We report a new signal readout mechanism for DNA molecular sensing devices using ligand-free fluorogenic G-quadruplexes in which the propeller-like loops are distinguished from the diagonal and lateral loops with incorporated 2-aminopurine (2-AP, a fluorescent analogue of adenine). We study the fluorescence behavior of looped-out 2-AP in duplexes and G-quadruplexes and demonstrate that it shows better fluorescence properties in shorter loops. In particular, 2-AP in the propeller-like loops of parallel or hybrid G-quadruplexes displays a perfect fluorescence emission whereas that in the diagonal and lateral loops does not. This loop-environment-sensitive feature allows 2-AP to probe the propeller-like loops of G-quadruplexes, illustrated by an ion-tuned allosteric G-quadruplex FG9A and a (3 + 1) hybrid human telomeric DNA. In the presence of K+, FG9A folds into a parallel structure where 2-AP is in the propeller-like loops and shows a high fluorescence signal, which can probe K+ concentrations down to 25 μM. Upon addition of Pb2+, the folded FG9A converts into an antiparallel structure which is revealed by a sharp decrease in 2-AP fluorescence, which can easily be reset with EDTA. This process is utilized to reversibly sense Pb2+ with a detection limit of 100 nM. Furthermore, its ability to probe the propeller-like loops may allow 2-AP to identify the folding topologies of unknown G-quadruplexes in human gene regions.

Graphical abstract: Probing the propeller-like loops of DNA G-quadruplexes with looped-out 2-aminopurine for label-free switchable molecular sensing

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Publication details

The article was received on 17 May 2018, accepted on 21 Jun 2018 and first published on 22 Jun 2018


Article type: Paper
DOI: 10.1039/C8AN00914G
Citation: Analyst, 2018, Advance Article
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    Probing the propeller-like loops of DNA G-quadruplexes with looped-out 2-aminopurine for label-free switchable molecular sensing

    P. Peng, Y. Du, Y. Sun, S. Liu, L. Mi and T. Li, Analyst, 2018, Advance Article , DOI: 10.1039/C8AN00914G

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