Accurate high-throughput identification of parallel G-quadruplex topology by a new tetraaryl-substituted imidazole.
G-quadruplex nucleic acids are four-stranded DNA or RNA secondary structures that are formed in guanine-rich sequences. These structures exhibit extensive structural polymorphism and play a pivotal role in the control of a variety of cellular processes. To date, diverse approaches for high-throughput identification of G-quadruplex structures have been successfully developed, but high-throughput methods for further characterization of their topologies are still lacking. In this study, we report a new tetra-arylimidazole probe psIZCM-1, which was found to display significant and distinctive changes in both the absorption and the fluorescence spectra in the presence of parallel G-quadruplexes but show insignificant changes upon interactions with anti-parallel G-quadruplexes or other non-quadruplex oligonucleotides. In view of this dual-output feature, we used psIZCM-1 to identify the parallel G-quadruplexes from a large set of 314 oligonucleotides (including 300 G-quadruplex-forming oligonucleotides and 14 non-quadruplex oligonucleotides) via a microplate reader and accordingly established a high-throughput method for the characterization of parallel G-quadruplex topologies. The accuracy of this method was greater than 95%, which was much higher than that of the commercial probe NMM. To make the approach more practical, we further combined psIZCM-1 with another G-quadruplex probe IZCM-7 to realize the high-throughput classification of parallel, anti-parallel G-quadruplexes and non-quadruplex structures.
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Ming-Hao
MH
Hu
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Shuo-Bin
SB
Chen
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Yu-Qing
YQ
Wang
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
You-Mei
YM
Zeng
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Tian-Miao
TM
Ou
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Ding
D
Li
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Lian-Quan
LQ
Gu
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China.
Zhi-Shu
ZS
Huang
School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China. Electronic address: tanjiah@mail.sysu.edu.cn.
Jia-Heng
JH
Tan
D015374:Biosensing Techniques / Q000379:methods*; D003124:Colorimetry / Q000379:methods; D004247:DNA / Q000737:chemistry; D005456:Fluorescent Dyes / Q000737:chemistry*; D054856:G-Quadruplexes; D057166:High-Throughput Screening Assays / Q000379:methods; D007093:Imidazoles / Q000737:chemistry*; D013050:Spectrometry, Fluorescence / Q000379:methods
D005456:Fluorescent Dyes; D007093:Imidazoles; D004247:DNA
Colorimetric probe; Fluorescent probe; G-quadruplex; High-throughput; Topology