2011 Annual Report - Center for Integrated Nanotechnologies - Los ...

Theory & Simulation of Nanoscale Phenomena Thrust
Electronic Fingerprints of DNA Bases on Graphene
Accomplishment: In this letter,
the use of graphene is proposed
as a deposition substrate for
macromolecular sequencing.
Both the Dirac linear dispersion
of electronic states in graphene
and its robust mechanical properties
serve to make it a superior
substrate compared to metals.
The authors have calculated the
tunneling conductance and local
density of states (LDOS) for
the specific case of single DNA
bases at various orientations
on the surface and have shown
that the different nucleotides
have significantly different LDOS
peaks (fingerprints), allowing
differentiation via local tunneling
conductance. The calculated
nitrogen atom LDOS for A, T,
C, and G bases show distinct
peaks that vary depending on
configuration. However, a planar
orientation of DNA bases with
respect to the graphene surface
is the most stable, since it favors
π−π stacking between the base
and aromatic carbons in graphene.
It is found that guanine
provides the largest peak at a
negative bias at −1.3 eV. Peaks
for the other bases at higher energies
have features at positive and negative scanning tunneling
microscopy (STM) bias and provide fingerprints that allow unique
identification. The calculated LDOS fingerprints can help guide
scanning tunneling spectroscopy (STS) as an approach to identify
DNA bases, and likely other biomolecules on graphene surfaces.
Challenge: The ability to sequence DNA quickly and affordably is
one of the great challenges in this era. The determination of the
precise sequence of the four nucleotides [adenine (A), cytosine
(C), guanine (G), and thymine (T)] in DNA molecules is an important
goal for both fundamental research interests as well as large
number of applications in biomedical research, biotechnology,
drug delivery, and biomaterial growth.
Significance: This work develops a detailed understanding of the
interactions and adsorption between graphene and biomolecules
using an approach goes beyond the structural analysis of such
hybrid systems. In this letter, the possibilities of using STM and
STS for the determination and sequencing of DNA on substrate
helps provide an opportunity for electronic identifications of all
bases via the tunneling conductance from a local probe.
(a) Molecular energy levels of each isolated DNA base molecule. (b) Upper panel
shows LDOS of carbon atom in pure graphene and lower panel shows nitrogen peak
LDOS in isolated DNA bases. (c) Integrated (−3.0 eV to EF = 0) partial charge
density of DNA bases on graphene plane. Base types are organized in columns and
angles between base-ring and graphene plane are varied along rows as indicated.
This simulation of STM topography is done using HIVE-STM code. (d) Molecular
orientations of DNA bases corresponding to the images in panel c are displayed.
Reference:
T. Ahmed, S. Kilina, T. Das, J. T. Haraldsen, J. J. Rehr, and A.
V. Balatsky, “Electronic Fingerprints of DNA Bases on Graphene,”
NanoLetters 12, 927 (2012).
CINT Contact: Sasha Balatsky
39