Research Article: Competing Interactions in DNA Assembly on Graphene

Date Published: April 12, 2011

Publisher: Public Library of Science

Author(s): Saliha Akca, Ashkan Foroughi, Daniel Frochtzwajg, Henk W. Ch. Postma, Maxim Antopolsky.

Abstract: We study the patterns that short strands of single-stranded DNA form on the top
graphene surface of graphite. We find that the DNA assembles into two distinct
patterns, small spherical particles and elongated networks. Known interaction
models based on DNA-graphene binding, hydrophobic interactions, or models based
on the purine/pyrimidine nature of the bases do not explain our observed
crossover in pattern formation. We argue that the observed assembly behavior is
caused by a crossover in the competition between base-base pi stacking and
base-graphene pi stacking and we infer a critical crossover energy of
eV. The experiments therefore provide a projective
measurement of the base-base interaction strength.

Partial Text: A thorough understanding of DNA binding to graphene is at the heart of interpreting
DNA interactions with graphene-like substances. This is relevant to efforts of using
DNA to sort carbon nanotubes, which may be thought of as folded up sheets of
graphene [1]–[3], DNA sequencing using graphene [4], and DNA sensing with carbon
nanotubes [5], [6],
chemically-converted graphene [7], and graphene [8]–[10]. Here, we elucidate a crossover
mechanism in interaction strengths between base-base binding and base-graphene

Images of the assembled DNA on graphite are presented in figure 1. The line scans indicate that the
control experiment shows a rather flat surface with a root mean square (RMS) height
of nm with a handful of scattered particles, while the poly-A
and C are more rough with an RMS height of nm. In contrast, the
line scans of the poly-T and G show a flat surface with a similar roughness as the
control, interrupted by high and wide features. The narrow peak in the histogram
corresponding to the image of the control is indicative of the natural corrugation
of graphene, combined with a small layer of contamination from the buffer and
deionized water, and environmetal and instrument fluctuations. The wider tail of the
histogram on the right side of the control’s histogram peak is caused by the
small number of larger contamination particles that are visible in the image. In
contrast, the wider peaks in the histograms for poly-A and C have no such wider tail
and are symmetric. These histograms are indicative of the clustering of DNA into
small tightly-packed spherical particles. Finally, the histograms for poly-T and G
show two peaks, the lower of which corresponds to the graphene surface and the
higher corresponds to the DNA.

It is clear that the DNA assembles in two distinct manners on the graphene surface.
The poly-A and C have formed spherical particles, while the poly-T and G have formed
a network on the surface. Several mechanisms have been suggested to play a role in
DNA-graphene interaction, e.g. hydrogen bonding, base stacking, electrostatic, van
der Waals, and hydrophobic interactions [13]. Note that in the experiments
reported here, we have not applied any potential to facilitate adsorption, so the
main mechanism is free adsorption [13]–[16]. Here, we first discuss candidate mechanisms for these
two distinct assembly types and since they do not explain our observations, we
propose a new model based on competing pi stacking interactions. The candidate
mechanisms are summarized in table

Square highly-oriented pyrolytic graphite (HOPG) was used as a substrate (grade ZYH,
Veeco, USA). The graphite was freshly cleaved with adhesive tape prior to each
deposition to ensure a clean and atomically flat surface and was not further
modified [23],
Single-stranded DNA (ssDNA) was purchased from Integrated DNA Technologies Inc, USA.
The poly-A,T, and C strands were 30 bases long, while the poly-G was 20 bases long.
A 1x TAE buffer solution was prepared with 40 mM Tris-HCl, 19 mM Acetic Acid, 1 mM
ethylenediaminetetraacetic acid (EDTA), and 12.5 mM
Mg. A 10 l, 0.5 mM ssDNA
solution was incubated with 10 l TAE buffer and 10
l Ni Acetate solution on the freshly-cleaved surface for 3
minutes [13]. After
incubation, samples were washed with 18 M de-ionized water and
dried. The graphite cleaving, ssDNA deposition, incubation, and rinsing were done at
room temperature in a class 100 hood in a clean room to limit contamination of the
surface. Images of the deposited DNA samples were then acquired in Close-Contact
Mode with an Atomic Force Microscope (Dual-Scan AFM, Pacific Nanotechnology, USA).
Control experiments were performed, in which a buffer solution without DNA was
deposited and incubated on graphite, rinsed, dried, and imaged. We have used
single-stranded poly DNA here to exclude the effects of hybridization.