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

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.