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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Chem. | doi: 10.3389/fchem.2019.00528

Single Molecule Study of Hydrogen Bond Interactions between Single Oligonucleotide and Aerolysin Sensing Interface

Meng-Yin Li1, Ya-Qian Wang1, Yao Lu1,  Yi-Lun Ying1* and  Yitao Long1, 2*
  • 1East China University of Science and Technology, China
  • 2Nanjing University, China

The aerolysin nanopore displays charming sensing capability for single oligonucleotide discrimination. When reading from the electrochemical signal, the stronger interaction between the aerolysin nanopore and oligonucleotide represent as prolonged duration time, thereby amplifying the hidden but intrinsic signal thus improving the sensitivity. In order to further understand and optimize the performance of the aerolysin nanopore, we focus on the investigation of the hydrogen bond interaction between nanopore and analytes. Taking advantage of site mutagenesis, single residue is replaced. According to whole protein sequence screening, the region near K238 is one of the key sensing regions. Such positively charged amino acid is then mutagenized into cysteine and tyrosine denoted as K238C and K238Y. As (dA)4 traverses the pores, K238C produces dramatically six times longer duration time than the WT aerolysin nanopore at the voltage of +120 mV. However, K238Y shortens the dwell time which suggests the acceleration of the translocation causing poor sensitivity. Referring to our previous findings in K238G and K238F, our results suggest the hydrogen bond does not dominant the dynamic translocation process, but enhance the interaction between pore and analyte confined in such nanopore space. These insights give detailed information for rationally design of the sensing mechanism of the aerolysin nanopore, thereby providing further understanding for the weak interactions between biomolecules and the confined space for nanopore sensing.

Keywords: single-molecule interface, oligonucleotide, nanopore, hydrogen bond, electro confinement

Received: 12 Jun 2019; Accepted: 11 Jul 2019.

Edited by:

Binquan Luan, IBM Research (United States), United States

Reviewed by:

Hai-Chen Wu, University of Chinese Academy of Sciences, China
Xiyun Guan, Illinois Institute of Technology, United States  

Copyright: © 2019 Li, Wang, Lu, Ying and Long. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence:
Dr. Yi-Lun Ying, East China University of Science and Technology, Shanghai, 200237, Shanghai, China, yilunying@ecust.edu.cn
Prof. Yitao Long, East China University of Science and Technology, Shanghai, 200237, Shanghai, China, yitaolong@gmail.com