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Unwinding process of DNA/RNA quadruplexes by proteins under label-free nanopore monitoring

解旋酶 核糖核酸 DNA 纳米孔 核酸 生物 端粒 G-四倍体 生物物理学 核酸结构 纳米孔测序 生物化学 细胞生物学 纳米技术 DNA测序 材料科学 基因
作者
Meili Ren,Ting Weng,Liyuan Liang,Xun Chen,Daixin Liu,Shaoxi Fang,Rong Tian,Wanyi Xie,Liang Wang,Deqiang Wang,Chunyu Zeng
出处
期刊:Nucleic Acids Research [Oxford University Press]
卷期号:53 (12)
标识
DOI:10.1093/nar/gkaf547
摘要

Abstract Noncanonical quadruplexes (G4s) in the nucleic acids represent specific secondary structures that correlate and participate in important biological processes, including telomeric propagation and tumor cell proliferation, and are close to the life span. The interaction of G4 with specific proteins and monitoring of the unfolding process are important to understand the development and evolution of some diseases and for further regulation of telomere and to disclose the mechanism of typical cancers. Different from the most reported single-molecule tweezers’ manipulation, this work provides a nanopore-based electric approach for label-free monitoring of the unfolding process of both DNA- and RNA-G4 under various conditions. Twenty nanomolar of hTel sequence could be mostly unfolded via incubation with 10 nM of both TEP1 that is associated with telomerase and helicase RTEL1 under weak acidic conditions for 1 h, and this process could be recorded in a single-molecule nanopore device with a pore diameter of 3.7 nm in 0.5 M CsCl buffered solution at 150 mV. TEP1 is proved to specifically interplay with hybrid G4 and nearly does not unfold parallel G4. The efficient and selective unfolding process of RNA-G4 originated from SARS-CoV by helicase nsp13 is also demonstrated at pH 5 in 2 M LiCl with a 3.6-nm pore; with 50% molar ratio of helicase nsp13, RNA-1574-G4 could be selectively and significantly unfolded in 1 h. This work presents the selective unfolding of both DNA- and RNA-G4 by specific proteins, which is a new approach to modulate and monitor the secondary structure of nucleic acids, and shed light on the understanding of the mechanism of the interaction between nucleic acids and proteins and the related kinetics.
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