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Title: Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/ h -BN nanopore

Abstract

The feasibility of synthesizing unnatural DNA/RNA has recently been demonstrated, giving rise to new perspectives and challenges in the emerging field of synthetic biology, DNA data storage, and even the search for extraterrestrial life in the universe. In line with this outstanding potential, solid-state nanopores have been extensively explored as promising candidates to pave the way for the next generation of label-free, fast, and low-cost DNA sequencing. In this work, we explore the sensitivity and selectivity of a graphene/h-BN based nanopore architecture towards detection and distinction of synthetic Hachimoji nucleobases. The study is based on a combination of density functional theory and the non-equilibrium Green's function formalism. Our findings show that the artificial nucleobases are weakly binding to the device, indicating a short residence time in the nanopore during translocation. Significant changes in the electron transmission properties of the device are noted depending on which artificial nucleobase resides in the nanopore, leading to a sensitivity in distinction of up to 80%. Our results thus indicate that the proposed nanopore device setup can qualitatively discriminate synthetic nucleobases, thereby opening up the feasibility of sequencing even unnatural DNA/RNA.

Authors:
ORCiD logo [1]; ORCiD logo [2]; ORCiD logo [3]; ORCiD logo [4]; ORCiD logo [5]; ORCiD logo [6]
+ Show Author Affiliations
  1. Federal Institute of Education, Science and Technology of Espírito Santo, Ibatiba/ES, Brazil
  2. Argonne Leadership Computing Facility, Argonne National Laboratory, Lemont, USA, Data Science and Learning Division
  3. Institute for Computational Physics, Universität Stuttgart, Stuttgart, Germany
  4. Division of Materials Theory, Department of Physics and Astronomy, Uppsala University, Sweden
  5. Departamento de Física, Universidade Federal do Espírito Santo-UFES, Vitória/ES, Brazil
  6. Departamento de Física, ICEx, Universidade Federal Fluminense – UFF, Volta Redonda/RJ, Brazil
Publication Date:
Research Org.:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org.:
USDOE Office of Science (SC); Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq); Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior
OSTI Identifier:
1651235
Alternate Identifier(s):
OSTI ID: 1756892
Grant/Contract Number:  
AC02-06CH11357; 2017-04627; 301648/2017-4; 421227/2018-4; 2535/2017-1; 437182/2018-5; E-26/010.101126/2018; 26/202.699/2019
Resource Type:
Published Article
Journal Name:
Nanoscale
Additional Journal Information:
Journal Name: Nanoscale; Journal ID: ISSN 2040-3364
Publisher:
Royal Society of Chemistry
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES

Citation Formats

de Souza, Fábio A. L., Sivaraman, Ganesh, Fyta, Maria, Scheicher, Ralph H., Scopel, Wanderlã L., and Amorim, Rodrigo G. Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/ h -BN nanopore. United Kingdom: N. p., 2020. Web. doi:10.1039/D0NR04363J.
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de Souza, Fábio A. L., Sivaraman, Ganesh, Fyta, Maria, Scheicher, Ralph H., Scopel, Wanderlã L., & Amorim, Rodrigo G. Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/ h -BN nanopore. United Kingdom. https://doi.org/10.1039/D0NR04363J
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de Souza, Fábio A. L., Sivaraman, Ganesh, Fyta, Maria, Scheicher, Ralph H., Scopel, Wanderlã L., and Amorim, Rodrigo G. Wed . "Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/ h -BN nanopore". United Kingdom. https://doi.org/10.1039/D0NR04363J.
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@article{osti_1651235,
title = {Electrically sensing Hachimoji DNA nucleotides through a hybrid graphene/ h -BN nanopore},
author = {de Souza, Fábio A. L. and Sivaraman, Ganesh and Fyta, Maria and Scheicher, Ralph H. and Scopel, Wanderlã L. and Amorim, Rodrigo G.},
abstractNote = {The feasibility of synthesizing unnatural DNA/RNA has recently been demonstrated, giving rise to new perspectives and challenges in the emerging field of synthetic biology, DNA data storage, and even the search for extraterrestrial life in the universe. In line with this outstanding potential, solid-state nanopores have been extensively explored as promising candidates to pave the way for the next generation of label-free, fast, and low-cost DNA sequencing. In this work, we explore the sensitivity and selectivity of a graphene/h-BN based nanopore architecture towards detection and distinction of synthetic Hachimoji nucleobases. The study is based on a combination of density functional theory and the non-equilibrium Green's function formalism. Our findings show that the artificial nucleobases are weakly binding to the device, indicating a short residence time in the nanopore during translocation. Significant changes in the electron transmission properties of the device are noted depending on which artificial nucleobase resides in the nanopore, leading to a sensitivity in distinction of up to 80%. Our results thus indicate that the proposed nanopore device setup can qualitatively discriminate synthetic nucleobases, thereby opening up the feasibility of sequencing even unnatural DNA/RNA.},
doi = {10.1039/D0NR04363J},
journal = {Nanoscale},
number = ,
volume = ,
place = {United Kingdom},
year = {2020},
month = {1}
}
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https://doi.org/10.1039/D0NR04363J
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