title: Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene.
abstract: Control over interactions with biomolecules holds the key to applications of graphene in biotechnology. One such application is nanopore sequencing, where a DNA molecule is electrophoretically driven through a graphene nanopore. Here we investigate how interactions of single-stranded DNA and a graphene membrane can be controlled by electrically biasing the membrane. The results of our molecular dynamics simulations suggest that electric charge on graphene can force a DNA homopolymer to adopt a range of strikingly different conformations. The conformational response is sensitive to even very subtle nucleotide modifications, such as DNA methylation. The speed of DNA motion through a graphene nanopore is strongly affected by the graphene charge: a positive charge accelerates the motion, whereas a negative charge arrests it. As a possible application of the effect, we demonstrate stop-and-go transport of DNA controlled by the charge of graphene. Such on-demand transport of DNA is essential for realizing nanopore sequencing.
authors.affiliation: Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, 1110W. Green Street, Urbana, Illinois 61801, USA.
authors.forename: Manish
authors.initials: M
authors.lastname: Shankla
authors.affiliation: Department of Physics, University of Illinois at Urbana-Champaign, 1110W. Green Street, Urbana, Illinois 61801, USA.
authors.forename: Aleksei
authors.initials: A
authors.lastname: Aksimentiev
mesh_terms: D001692:Biological Transport; D019175:DNA Methylation; D004277:DNA, Single-Stranded / Q000378:metabolism*; D004586:Electrophoresis; D006108:Graphite / Q000378:metabolism*; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D058608:Nanopores; D011108:Polymers
chemical_list: D004277:DNA, Single-Stranded; D011108:Polymers; D006108:Graphite