Title
Probing Propeller-Like Loops of DNA G-quadruplexes with Looped-Out 2-Aminopurine for Label-Free Switchable Molecular Sensing
Author
Pai Peng, Yi Du, Yudie Sun, Shuangna Liu, Lan Mi, Tao Li
Year
2018
Journal
Analyst
Abstract
We report a new signal readout mechanism for DNA molecular sensing devices using ligand-free fluorogenic G-quadruplexes of which the propeller-like loops are distinguished from the diagonal and lateral ones with incorporated 2-aminopurine (2-AP, a fluorescent analogue of adenine). We study the fluorescence behaviors of looped-out 2-AP in duplexes and G-quadruplexes and demonstrate that it shows a better fluorescence property 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 dose 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 low to 25 μM K+. Upon addition of Pb2+, the folded FG9A converts into an antiparallel structure 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. Further, the ability to probing the propeller-like loops may allow 2-AP to identify the folding topologies of unknown G-quadruplexes in human gene regions.
Instrument
J-1500
Keywords
Circular dichroism, DNA structure, Chemical stability, Biochemistry, Materials, Sensors