Unzipping of A-Form DNA-RNA, A-Form DNA-PNA, and B-Form DNA-DNA in the α-Hemolysin Nanopore

Biophysical Journal
Rukshan T PereraHenry S White

Abstract

Unzipping of double-stranded nucleic acids by an electric field applied across a wild-type α-hemolysin (αHL) nanopore provides structural information about different duplex forms. In this work, comparative studies on A-form DNA-RNA duplexes and B-form DNA-DNA duplexes with a single-stranded tail identified significant differences in the blockage current and the unzipping duration between the two helical forms. We observed that the B-form duplex blocks the channel 1.9 ± 0.2 pA more and unzips ∼15-fold more slowly than an A-form duplex at 120 mV. We developed a model to describe the dependence of duplex unzipping on structure. We demonstrate that the wider A-form duplex (d = 2.4 nm) is unable to enter the vestibule opening of αHL on the cis side, leading to unzipping outside of the nanopore with higher residual current and faster unzipping times. In contrast, the smaller B-form duplexes (d = 2.0 nm) enter the vestibule of αHL, resulting in decreased current blockages and slower unzipping. We investigated the effects of varying the length of the single-stranded overhang, and studied A-form DNA-PNA duplexes to provide additional support for the proposed model. This study identifies key differences between A- and B-form duplex unzip...Continue Reading

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Citations

Jul 28, 2017·Analytical Chemistry·Josip IvicaMaurits R R de Planque
Nov 28, 2018·Chemical Communications : Chem Comm·Liang WangXiyun Guan
Jun 22, 2019·Artificial Cells, Nanomedicine, and Biotechnology·Jiasheng XuZhenfang Xiong
Feb 23, 2020·Nucleic Acids Research·Taoli DingCheng Zhang
Jan 22, 2021·Analytical Chemistry·Dong-Hwa LeeMi-Kyung Lee
Apr 23, 2021·Nanoscale·Sotaro Takiguchi, Ryuji Kawano
Dec 17, 2021·Biomacromolecules·Sybil ObuobiNataša Škalko-Basnet

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