文献类型：期刊文献

英文题名：Identification of Essential Sensitive Regions of the Aerolysin Nanopore for Single Oligonucleotide Analysis

作者：Wang, Ya-Qian[1,2];Li, Meng-Yin[1,2];Qiu, Hu[3];Cao, Chan[1,2];Wang, Ming-Bo[4];Wu, Xue-Yuan[1,2];Huang, Jin[4];Ying, Yi-Lun[1,2];Long, Yi-Tao[1,2]

机构：[1]East China Univ Sci & Technol, Key Lab Adv Mat, Shanghai 200237, Peoples R China;[2]East China Univ Sci & Technol, Sch Chem & Mol Engn, Shanghai 200237, Peoples R China;[3]Nanjing Univ Aeronaut & Astronaut, State Key Lab Mech & Control Mech Struct, Nanjing 210016, Jiangsu, Peoples R China;[4]East China Univ Sci & Technol, Sch Pharm, Shanghai 200237, Peoples R China

年份：2018

卷号：90

期号：13

起止页码：7790

外文期刊名：ANALYTICAL CHEMISTRY

收录：;EI(收录号：20182505352788);WOS:【SCI-EXPANDED(收录号:WOS:000438008600002)】；

基金：This research was supported by the National Key R&D Program of China (Grant 2017YFC0906500), the National Natural Science Foundation of China (Grants 21421004, 21327807, and 11772152), Yi-Lun Ying is sponsored by the "Chen Guang" project supported by Shanghai Municipal Education Commission and Shanghai Education Development Foundation (Grant 17CG27), Innovation Program of Shanghai Municipal Education Commission (Grant 2017-01-07-00-02-E00023), the Fundamental Research Funds for the Central Universities (Grants 222201718001 and 222201717003), and the Jiangsu Province NSF (Grant SBK2018030099).

语种：英文

外文关键词：Molecular dynamics - Amino acids - Electrostatics - Nucleic acids - Oligonucleotides - Bioinformatics

摘要：The aerolysin nanopore channel is one of the confined spaces for single molecule analysis which displays high spatial and temporal resolution for the discrimination of single nucleotides, identification of DNA base modification, and analyzing the structural transition of DNAs. However, to overcome the challenge of achieving the ultimate goal of the widespread real analytical application, it is urgent to probe the sensing regions of the aerolysin to further improve the sensitivity. In this paper, we explore the sensing regions of the aerolysin nanopore by a series of well-designed mutant nanopore experiments combined with molecular dynamics simulations-based electrostatic analysis. The positively charged lumen-exposed Lys-238, identified as one of the key sensing sites due to the presence of a deep valley in the electrostatic potentials, was replaced by different charged and sized amino acids. The results show that the translocation time of oligonucleotides through the nanopore can be readily modulated by the choice of the target amino acid at the 238 site. In particular, a 7-fold slower translocation at a voltage bias of +120 mV is observed with respect to the wild-type aerolysin, which provides a high resolution for methylated cytosine discrimination. We further determine that both the electrostatic properties and geometrical structure of the aerolysin nanopore are crucial to its sensing ability. These insights open ways for rationally designing the sensing mechanism of the aerolysin nanopore, thus providing a novel paradigm for nanopore sensing.