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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.

SUBMITTER: Shankla M

PROVIDER: S-EPMC4236004 | biostudies-literature | 2014 Oct

REPOSITORIES: biostudies-literature

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Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene.

Shankla Manish M Aksimentiev Aleksei A

Nature communications 20141009

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 r ...[more]

PMID: 25296960

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Project description:The ionic current rectification (ICR) is a non-linear current-voltage response upon switching the polarity of the potential across nanopore which is similar to the I-V response in the semiconductor diode. The ICR phenomenon finds several potential applications in micro/nano-fluidics (e.g., Bio-sensors and Lab-on-Chip applications). From a biological application viewpoint, most biological fluids (e.g., blood, saliva, mucus, etc.) exhibit non-Newtonian visco-elastic behavior; their rheological properties differ from Newtonian fluids. Therefore, the resultant flow-field should show an additional dependence on the rheological material properties of viscoelastic fluids such as fluid relaxation time [Formula: see text] and fluid extensibility [Formula: see text]. Despite numerous potential applications, the comprehensive investigation of the viscoelastic behavior of the fluid on ionic concentration profile and ICR phenomena has not been attempted. ICR phenomena occur when the length scale and Debye layer thickness approaches to the same order. Therefore, this work extensively investigates the effect of visco-elasticity on the flow and ionic mass transfer along with the ICR phenomena in a single conical nanopore. The Poisson-Nernst-Planck (P-N-P) model coupled with momentum equations have been solved for a wide range of conditions such as, Deborah number, [Formula: see text], Debye length parameter, [Formula: see text], fluid extensibility parameter, [Formula: see text], applied electric potential, [Formula: see text], and surface charge density [Formula: see text] and [Formula: see text]. Limited results for Newtonian fluid ([Formula: see text], and [Formula: see text]) have also been shown in order to demonstrate the effectiveness of non-Newtonian fluid behaviour over the Newtonian fluid behaviour. Four distinct novel characteristics of electro-osmotic flow (EOF) in a conical nanopore have been investigated here, namely (1) detailed structure of flow field and velocity distribution in viscoelastic fluids (2) influence of Deborah number and fluid extensibility parameter on ionic current rectification (ICR) (3) volumetric flow rate calculation as a function of Deborah number and fluid extensibility parameter (4) effect of viscoelastic parameters on concentration distribution of ions in the nanopore. At high applied voltage, both the extensibility parameter and Deborah number facilitate the ICR phenomena. In addition, the ICR phenomena are observed to be more pronounced at low values of [Formula: see text] than the high values of [Formula: see text]. This effect is due to the overlapping of the electric double layer at low values of [Formula: see text].

Dataset Information

Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene.

Publications

Conformational transitions and stop-and-go nanopore transport of single-stranded DNA on charged graphene.

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