Recording of DNA Knots Formation and Their Splitting by TOPII with Solid-state Nanopore Devices

doi:10.1007/s40242-026-6140-y

Chemical Research in Chinese Universities ›› 2026, Vol. 42 ›› Issue (5): 1497-1503.doi: 10.1007/s40242-026-6140-y

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Recording of DNA Knots Formation and Their Splitting by TOPII with Solid-state Nanopore Devices

REN Meili¹, WENG Ting², XIANG Limin², CHEN Xun², LIANG Liyuan², ZENG Chunyu^1,2,3,4

1. Department of Cardiology, The First Affiliated Hospital of Kunming Medical University, Kunming 650032, P. R. China;
2. Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, P. R. China;
3. Department of Cardiology, Daping Hospital, the Third Military Medical University, Chongqing 400042, P. R. China;
4. Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education, Chongqing Key Laboratory for Hypertension Research, Cardiovascular Clinical Research Center, Chongqing Institute of Cardiology, Chongqing 400042, P. R. China

Received:2026-06-14 Accepted:2026-07-27 Online:2026-10-01 Published:2026-09-24
Supported by:
This work was supported by the National Natural Science Foundation of China (No. 81930008), the Fund of the Key Laboratory of Geriatric Cardiovascular and Cerebrovascular Disease Research, Ministry of Education of China (No. KFKT202505), the Project of the Youth Innovation Promotion Association, Chinese Academy of Sciences (No. 2023401), and the Program of the University of the Chinese Academy of Sciences.

Abstract

Abstract: DNA knots represent critical topological structures arising during DNA replication, recombination, and repair, of which the aberrant accumulation threatens genomic stability. Helicases and topoisomerases act cooperatively to maintain genomic integrity by specifically recognizing DNA knots and progressively unwinding them or relieving topological stress through transient DNA strand cleavage. This study employs solid-state nanopore (SSN) technology to achieve high-resolution detection of λ-DNA knots under optimized conditions. Our work demonstrates that DNA knot translocation generates multistage signals of ionic current blockade, with blockage current amplitude positively correlating with topological complexity. Furthermore, the capture frequency of DNA knots increases significantly with applied bias voltages, while translocation duration decreases with reduced channel length (referring to the thickness of silicon nitride). Notably, topoisomerase II (TOPII) exhibits moderate resolving activity toward DNA knots, manifested by an increased proportion of linear DNA signals and shortened blockade durations. The splitting efficiency of TOPII is influenced by the supercoiling status of DNA and the concentration of enzyme; the underlying molecular mechanism needs further investigation with combined single-molecule fluorescence techniques. This study innovatively applies solid-state nanopore technology to explore DNA topology and DNA-TOPII interaction, providing a new research strategy for related fields.

Key words: DNA knot, Single-molecule conformation, Topoisomerase II (TOPII), DNA-protein interaction, Solid-state nanopore

REN Meili, WENG Ting, XIANG Limin, CHEN Xun, LIANG Liyuan, ZENG Chunyu. Recording of DNA Knots Formation and Their Splitting by TOPII with Solid-state Nanopore Devices[J]. Chemical Research in Chinese Universities, 2026, 42(5): 1497-1503.

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Recording of DNA Knots Formation and Their Splitting by TOPII with Solid-state Nanopore Devices

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