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Journal ArticleDOI

DNA imaged on a HOPG electrode surface by AFM with controlled potential.

01 Apr 2005-Bioelectrochemistry (Elsevier)-Vol. 66, Iss: 66, pp 117-124

Abstract: Single-molecule AFM imaging of single-stranded and double-stranded DNA molecules self-assembled from solution onto a HOPG electrode surface is reported. The interaction of DNA with the hydrophobic surface induced DNA aggregation, overlapping, intra- and intermolecular interactions. Controlling the electrode potential and using the phase images as a control method, to confirm the correct topographical characterization, offers the possibility to enlarge the capability of AFM imaging of DNA immobilized onto conducting substrates, such as HOPG. The application of a potential of +300 mV (versus AgQRE) to the HOPG enhanced the robustness and stability of the adsorbed DNA molecules, increasing the electrostatic interaction between the positively charged electrode surface and the negatively charged DNA sugar-phosphate backbone.
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DNA imaged on a HOPG electrode surface by AFM
with controlled potential
Ana Maria Oliveira Brett
*
, Ana-Maria Chiorcea Paquim
Departamento de Quı´mica, Faculdade de Cieˆncias e Tecnologia, Universidade de Coimbra, 3004-535 Coimbra, Portugal
Received 12 December 2003; received in revised form 27 April 2004; accepted 5 May 2004
Available online 26 August 2004
Abstract
Single-molecule AFM imaging of single-stranded and double-stranded DNA molecules self-assembled from solution onto a HOPG
electrode surface is reported. The interaction of DNA with the hydrophobic surface induced DNA aggregation, overlapping, intra- and
intermolecular interactions. Controlling the electrode potential and using the phase images as a control method, to confirm the correct
topographical characterization, offers the possibility to enlarge the capability of AFM imaging of DNA immobilized onto conducting
substrates, such as HOPG. The application of a potential of +300 mV (versus AgQRE) to the HOPG enhanced the robustness and stability of
the adsorbed DNA molecules, increasing the electrostatic interaction between the positively charged electrode surface and the negatively
charged DNA sugar-phosphate backbone.
D 2004 Elsevier B.V. All rights reserved.
Keywords: DNA; Adsorption; HOPG; Atomic force microscope; AFM
1. Introduction
DNA is an important biomacromolecule with remarkable
chemical and biophysical properties [1–3]. The adsorption
of single-stranded and double-stranded DNA at the solid
electrodes surface plays a vital role in a variety of
biotechnological, medical and nanoscience application s
and enables the chemical and structural modification of
the sensor surface [4], being very important for under-
standing many physiological processes. Different structures
and conformations that DNA molecules can adopt at the
electrode surface lead to different interactions with other
molecules, such as modifications of the accessibility of
different drugs to the DNA grooves and modifications in
DNA hybridization efficiency.
Atomic force microscopy (AFM) has proved to be a
powerful tool for obtaining high-resolution images of DNA
in air and in solution. Images of DNA conformations,
unusual structures and DNA–protein complexes have been
obtained almost exclusively on mica or silicon [5–8], but
rarely on conducting materials. Effectively, the DNA
molecules do not bind strongly enough to conducting
substrates and the AFM tip tends to sweep away the
adsorbed macromolecules. AFM imaging onto conducting
substrates has been limited to gold substrates [9]. However,
the oxidation of the gold electrodes occurs at potentials of
approximately +0.8 V, [10,11] and the gold surface becomes
covered with gold oxides. Electrochemical oxidation of
nucleic acids on carbon electrodes showed that, with the
exception of guanine base, which has an oxidation peak at
approximately +0.8 V, depending on the experimental
conditions and electrodes used, all the other nucleic acid
bases and nucleosides are oxidized at higher electrode
potentials [12,13]. Consequently, the gold surface is not a
good choice for electrochemical studies of DNA due to its
limited potential range. A major challenge in the area of
direct visualization of DNA molecules is to extend the
capability of AFM imaging to other conducting substrates
required in electrochemical applications.
1567-5394/$ - see front matter D 2004 Elsevier B.V. All rights reserved.
doi:10.1016/j.bioelechem.2004.05.009
* Corresponding author. Tel./fax: +351 239 835295.
E-mail address: brett@ci.uc.pt (A.M. Oliveira Brett).
Bioelectrochemistry 66 (2005) 117 124
www.elsevier.com/locate/bioelechem

Carbon electrodes such as glassy carbon, carbon fibres,
graphite or carbon black have a wide useful potential range,
particularly in the positive direction, which enables the
detection of damage caused to DNA by following the
oxidation peaks of the purine bases [12–14].
Highly oriented pyrolytic graphite (HOPG) has been
used to study single DNA molecules by STM. However, the
geometry of the grain boundary, the step edge texture and
surface defects of the freshly cleaved HOPG surface
produce STM images that mimic both single-stranded and
double-stranded DNA molecules, interfering with the ability
to d istinguish between the true biological features and the
features related with the clean HOPG steps [15–17]. The
problems encount ered in STM imaging of the molecules
adsorbed onto HOPG steps also limited the use of HOPG in
AFM studies of single-DNA molecules. AFM has been has
been limited to studying the formation of DNA networked
films assembled from high and very high DNA solution
concentrations [18–20], which enabled the formatio n of
thick and stable DNA lattices, completely covering the
HOPG boundary defects. Nevertheless, the nature of the
single DNA–surface interaction and the morphology adop-
ted by isolated DNA molecules when small solution
concentrations are used is still not yet well understood.
Magnetic AC mode AFM (MAC Mode AFM) permits
the visualization of the molecules weakly bound to the
substrate mat erial and it can be very helpful in the
investigation of single-molecules loosely attached to the
conducting surface of electrochemical transducers. AFM is
not as sensitive as STM to unusual electronic structures on
the surface, the AFM images being less affected by artefacts
than STM [5].
In this context, this paper explores the possibility of
using MAC Mode AFM to image single-stranded DNA
(ssDNA) and double-stranded DNA (dsDNA) from calf-
thymus immobi lized by free adsorption and by applying a
potential of +300 mV vs. AgQRE to the HOPG electrode
surface immersed in solutions of low DNA concentration.
Calf-thymus DNA is a large molecule that is easily
commercially available and has already been used for
biosensor construction [13,14].
2. Materials and methods
2.1. Materials
Calf-thymus double-stranded DNA (sodium salt, type I)
and single-stranded DNA were purchased from Sigma-
Aldrich Quı´mica, Spain and were used without further
purification. The electrolyte used was pH 7.0 0.1 M
phosphate buffer solution and was prepared using analytical
grade reagents and purified water from a Millipore Milli-Q
system (conductivity b0.1 AScm
1
). Solutions of different
concentrations were obtained by direct dilution of the
appropriate volume in phosphate buffer.
Highly oriented pyroly tic graphite (HOPG), grade
ZYH, of rectangular shape with 15
15
2 mm dimen-
sions, from Advanced Ceramics, UK, was used through-
out this study as a substrate. The HOPG was freshly
cleaved with adhesive tape prior to each experiment and
was imaged by Contact Mode AFM in order to establish
its cleanliness.
Voltammetric experiments were carried out in a one-
compartment Teflon cell of approximately 12.5 mm internal
diameter holding the HOPG sample—the working elec-
trode—on the base. A Pt wire counter electrode and a silver
wire as quasi-reference (AgQRE) electrode were placed in
the cell, dipping approximately 5 mm into the solution. The
electrochemical control was done wi th a PalmSens poten-
tiostat, running with PalmScan version 1.11 software, from
Palm Instruments, The Netherlands.
2.2. DNA sample preparation
For DNA samples prepared by free adsorption, 100 Alof
DNA solutions were adsorbed onto freshly cleaved HOPG
surface and incubated for 3 min. The excess of DNA was
gently cleaned with a jet of Milli Q water and the HOPG
with adsorbed DNA was then dried with nitrogen, which is a
typical procedure used for imaging dry nucleic acid
molecules in air [6].
For DNA samples prepared by electrochemically assisted
adsorption 500 Al of the desired DNA solution were placed
in the electrochemical cell holding the HOPG working
electrode on the base. A positive potential of 300 mV (vs.
AgQRE) was applied to the electrode during 3 min. The
HOPG with adsorbed DNA was rinsed with a jet of Milli -Q
water and dried with nitrogen.
2.3. Atomic force microscopy
AFM was performed with a Pico SPM controlled by a
MAC Mode (Magnetic AC Mode) module and interfaced
with a PicoScan controller from Molecular Imaging, USA.
All the AFM experiments were performed with a CS AFM S
scanner with the scan range 6 Aminxy and 2 Aminz,
Molecular Imaging Corporation. Silicon type II MAClevers
225 Am length, 2.8 N/m spring constant and 60–90 kHz
resonant frequencies (Molecular Imaging) were used in
MAC Mode AFM. Silicon nitride NanoProbes TM V-
shaped cantilevers, 100 Am length, 0.58 N/m spring
constant were used for contact AFM in air.
All images (256 samples/line
256 lines) were taken at
room temperature, scan rates 1.0–1.3 lines s
1
. The images
were processed by first order flattening in order to remove
the background slope and the contrast and brightness were
adjusted. All images were visualized in three-dimensions
using the Scanning Probe Image Processor, SPIP version
2.3011, Image Metrology ApS. Section analysis over DNA
molecules and films was performed with PicoScan software
version 6.0, Molecular Imaging.
A.M. Oliveira Brett, A.-M. Chiorcea Paquim / Bioelectrochemistry 66 (2005) 117–124118

3. Results and discussion
3.1. Free adsorption of ssDNA and dsDNA on HOPG
DNA is a highly charged, hydrophilic molecule, whereas
HOPG has a hydrophobic surface. These characteristics
reduce the spontaneous interaction of DNA with the HOPG
surface. Despite the fact that MAC mode AFM is a gentle
technique, with a view to minimizing as much as possible
any damage to the biological films by the AFM tip, it
represents one of the most significant problems when
imaging single DNA molecules. In order to improve the
stability of the molecules on the surface, the DNA samples
have been dried and imaged in air before being observed by
AFM. This adsorption procedure, used in the AFM studies,
is similar to the real procedure of preparation and storage of
DNA-modified electrodes.
The AFM results indicate that both ssD NA and dsDNA
adsorb freely at the HOPG surface and the adsorption is fast.
The MAC Mode AFM topographical images of ssDNA
adsorbed onto HOPG, from a 1 Ag/ml ssDNA solution in pH
7.0 0.1 M phosphate buffer electrolyte, showed that the
ssDNA molecules condensed at the surface in very large,
coiled and twisted featureless aggregates, Fig. 1A. ssDNA
has the bases exposed, which facilitates interaction with the
substrate. The long ssDNA molecules exist in solution in
flexible polymeric-like configurations with some hybrid-
ization of randomly complementary zones. The conforma-
tion of the molecules is inevitably modified by the transition
from three dimensions in solution to two dim ensions on the
surface. The ssDNA molecules are stabilized on the HOPG
surface by hydroph obic interactions between the hydro-
phobic aromatic rings of the bases and the hydrophobic
carbon surface.
Scanning probe microscopy visualization of DNA as
such small concentrations of molecules of 1 Ag/ml requires a
careful analysis of the geometry related with the HOPG
domain walls, since the molecules are isolated and not
actually form uniform films, not covering completely the
HOPG surface. As demonstrated by STM studies, difficulty
arise in distinguish between an HOPG step and an adsorbed
molecule [15,16].
In MAC Mode AFM, the parameters of AFM cantilever
oscillations (amplitude, frequency, phase) change when the
cantilever contacts the sample surface. A significant advant-
age of MAC Mode AFM, compared with contact mode AFM,
is the possibility of using the changes in phase angle of the
AFM cantilever probe to produce a second image, the phase
image. As well as the amplitude image (feedback error),
which is the equivalent of the deflectio n ima ge in contact
mode AFM, the phase image is recorded simultaneously with
the topographical image of the surface, and represents the
difference between the oscillating magnetic field driving
the cantilever and its true response at surface contact. The
reference phase is considered the free oscillation phase of
the AFM cantilever, far away from the surface. During
scanning of the sample, the changes in phase contrast depend
not only on topography changes, but also on the adhesion,
elasticity and viscoelastic properties of the surface. The
modifications in the phase angle are correlated with different
damping produced by different areas of the sample surface.
Frequently, the phase images show an improved contrast
compared with the corresponding DNA topographical
image [21], and can give a second opinion about the
doubtful features in the HOPG sample and about th e
presence of DNA molecules.
In Fig. 1 are presented the amplitude image (feedback
error), Fig. 1B, and the phase image, Fig. 1C, recorded
simultaneously with the topographic image from Fig. 1A.
The big ssDNA aggregate observed is marked by (1) in the
images and an HOPG edge step between two graphite
terraces is marked by (2). As can be observed in topo-
graphical and amplitude images, it is difficult to distinguish
between the soft biological molecules and the HOPG
border. However, DNA is much more viscous than the bare
HOPG surface leading to a more pronounced difference in
phase angle as the AFM tip passes over, Fig. 1C. Using the
phase image, it is very easy to ident ify the real DNA
molecules with an improved contrast and to distinguish
them from the unusual HOPG structures, overcoming in this
Fig. 1. (A) MAC Mode AFM topographical image in air of ssDNA prepared onto HOPG by 3 min free adsorption from 1 Ag/ml ssDNA solution in pH 7.0 0.1
M phosphate buffer electrolyte. (B) Amplitude image (feedback error) and (C) phase image recorded simultaneously with the topographic image A. Inside the
images (1) marks an ssDNA aggregate and (2) marks an HOPG step.
A.M. Oliveira Brett, A.-M. Chiorcea Paquim / Bioelectrochemistry 66 (2005) 117–124 119

way the problems of image artefacts encountered in STM
imaging of single DNA molecules.
MAC Mode AFM images in air of dsDNA self-assembled
on HOPG, from 1 Ag/ml dsDNA solution in pH 7.0 0.1 M
phosphate buffer electrolyte, also revealed coiled and twisted
structures but the dsDNA molecules appeared more extended
on the HOPG surface, Fig. 2A. Sporadically, sections of
straight dsDNA could be observed as shown in Fig. 2C. The
phase images, Fig. 2B and D, represent a control method to
certify that the topographical characterization is correct and it
is really the DNA that is seen in the images.
The measured full width at half-maximum height (fwhm)
of isolated dsDNA was approximately 10–25 nm, being
overestimated due to the convolution effect of the tip radius.
The height measurements were not limited by the tip radius
and give a better representation of the dsDNA diameter.
Therefore, the straight portions of dsDNA offe r the
possibility of evaluating the true height of the dsD NA
molecules. The average height measured by section analysis
over parts of single dsDNA molecules in the images, Fig.
2F, was 0.7F0.2 nm. It is expected that isolated dsDNA
adopts the A-for m due to strong dehy dration of th e
molecules leading to a double-helix diameter of approx-
imately 2.6 nm. In AFM studies in air, the reported heights
for dsDNA confined on a solid support vary from 0.5 to
1.9 nm [6], usually much smaller than the helix diameter,
which probably due to elastic deformations of dsDNA
caused by the AFM tip [6]. The large fwhm of dsDNA may
Fig. 2. (A, C) MAC Mode AFM topographical images in air of dsDNA prepared onto HOPG by 3 min free adsorption from 1 Ag/ml dsDNA solution in pH 7.0
0.1 M phosphate buffer electrolyte. (B, D) Phase images recorded simultaneously with the topographic images A and C. Inside the images A and B (1) marks
an dsDNA aggregate and (2) marks an HOPG step. (E) Three-dimensional representation of image C. (F) Cross-section profiles through white lines 1 and 2 in
the image C.
A.M. Oliveira Brett, A.-M. Chiorcea Paquim / Bioelectrochemistry 66 (2005) 117–124120

be not only to an artefact caused by the size and shape of the
tip, but also a broadening of dsDNA itself as a consequence
of dsDNA deformation by the tip.
In the case of dsDNA, the aggregation phenomena were
less critical than in the case of ssDNA, due to larger
electrostatic repulsion between the negatively charged
sugar-phosphate backb one of the molecule stra nds. How-
ever, it was noticed that the dsDNA displayed spherical
aggregates along its length with sizes between 1 and 2.5 nm,
the 150
150 nm scan size image. The presence of salt in the
buffer electrolyte can induce spontaneous condensation of
dsDNA due to lateral aggregation of the molecule [1]. Also,
the hydrophobic HOPG surface may induce aggregation of
long dsD NA, even in the absence of buffer solution . At the
solid–liquid interface, the dsDNA environment is drastically
different from that in bulk solution since DNA is forced to
pass from the solution 3D conformation to the adsorbed 2D
conformation. The drying procedu re does not modify the
adsorbed double- or single-stranded DNA on the HOPG
surface but the aggregates of the dehydrated 2D conforma-
tion are less high.
Adsorption and aggregation at other hydrophobic poly-
meric surfaces [22,23] was observed. In the double-helical
structure, a continuous dissociation–association of the bases
of dsDNA occurs at the ends as well as at single-stranded
overhangs (bsticky endsQ) [1–3]. The stabilization of dsDNA
at the surface may occur through interaction between the
hydrophobic HOPG surface and several hydrophobic bases
at the dsDNA ends. The interaction of dsDNA with the
HOPG surface can induce overlapping and superposition of
the molecules, sticky-ended cohesion and c onformation
changes, leading to DNA–DNA interactions and to for-
mation of alternative DNA structures [2,3,23].
3.2. Adsorption of ssDNA and dsDNA on HOPG under an
applied potential
The immobiliz ation of ssDNA and dsDNA by free
adsorption onto HOPG is very quick and easy to perform.
The main disadvantage of this method is that the nucleic
acids cluster into very large aggregates, especially in the
case of ssDNA.
Nucleic acid self-assembly involves a large number of
weak interactions and the DNA molecules do not bind
strongly enough to the conducting HOPG substrate. Con-
sequently, the DNA molecules are rather unstable on the
surface and may be desorbed. The friction caused by the
AFM tip during scanning the surface is frequently superior
to the adhesion to the surface and the AFM tip easily sweeps
away and drags the DNA molecules adsorbed on the HOPG
surface. It was observed during the experiments that the
AFM tip could easily move fragments of DNA molecules
condensed by free adsorption . Fig. 3 shows an example of
how the AFM tip causes the dislocation and movement of
ssDNA fragments along the HOPG surface; this image was
recorded immediately after the images from Fig. 1. In all
three images (topography Fig. 1A, amplitude Fig. 1B, phase
Fig. 1C), traces of the trajectories of these fragments clearly
appear.
During free adsorption, the single DNA molecules are
preferentially attached near the step edges of the HOPG
surface, Figs. 1A and 2A. A clean, atomically flat surface is
produced by peeling the top layer of the HOPG basal
cleavage plane. This process induces the formation of
different structures on graphite, e.g., grain boundaries,
dislocations, cleavage steps and point defects [17]. The
non-bound carbon atoms existing on these defects may form
bonds with hydrogen, hydroxyl and carboxyl groups [24].
These functional groups formed at the HOPG steps as well
as breaks in the surface may contribute to the predisposition
of nucleic acid molecules to accumulate at these sites.
In order to overcome all these problems, a stronger and
controlled adsorption of DNA onto the HOPG surface is
required. A better immobilization was obtained by applying
a positive potential to the surface during adsorption. The
positively charged HOPG substrat e exerts electrostatic
attraction on the nucleic acid molecules. The potential
chosen was +300 mV, versus AgQRE, during 3 min,
because this potential is not positive enough to irreversibly
oxidize the DNA bases inside the molecules [12] and was
AB
300nm 300nm
300nm
C
Fig. 3. (A) MAC Mode AFM topographical image in air of ssDNA prepared onto HOPG by 3 min free adsorption from 1 Ag/ml ssDNA solution in pH 7.0 0.1
M phosphate buffer electrolyte. (B) Amplitude image (feedback error) and (C) phase image recorded simultaneously with the topographic image C. Inside the
images, the arrows mark the trajectory traces of ssDNA fragments moved by the AFM tip.
A.M. Oliveira Brett, A.-M. Chiorcea Paquim / Bioelectrochemistry 66 (2005) 117–124 121

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"DNA imaged on a HOPG electrode surf..." refers background in this paper

  • ...In the double-helical structure, a continuous dissociation–association of the bases of dsDNA occurs at the ends as well as at single-stranded overhangs (bsticky endsQ) [1–3]....

    [...]

  • ...DNA is an important biomacromolecule with remarkable chemical and biophysical properties [1–3]....

    [...]

  • ...The interaction of dsDNA with the HOPG surface can induce overlapping and superposition of the molecules, sticky-ended cohesion and conformation changes, leading to DNA–DNA interactions and to formation of alternative DNA structures [2,3,23]....

    [...]


Journal ArticleDOI
B.E. Conway1Institutions (1)
Abstract: The mechanisms of electrochemical oxide film formation at noble metals are described and exemplified by the cases of Pt and Au, especially in the light of recent experimentation by means of cyclic voltammetry, ellipsometry and vacuum surface-science studies using LEED and AES. Unlike the mechanisms of base-metal oxidation, e.g., in corrosion processes, anodic oxide film formation at noble metals proceeds by surface chemical processes involving, initially, sub-monolayer, through monolayer, formation of 2-dimensional OH O arrays. During such 2-d processes, place-exchange between electrosorbed OH or O species on the surface, and Pt or Au atoms within the surface lattice, takes place leading to a quasi-2-d compact film which then grows ultimately to a multilayer hydrous oxide film, probably by continuing injection of ions of the substrate metal and their migration through the growing film under the influence of the field. The initial, sub-monolayer stage of electrosorption of OH involves competitive chemisorption by anions, e.g. HSO4−, ClO4−, Cl−, which inhibits onset of the first stage of surface oxidation. These processes are demonstrable in experiments on single-crystal surfaces. The combination of such anion effects with place-exchange during the extension of the film, leads to a general mechanism of noble metal oxide film formation. The formation of the oxide films can be examined in detail by recording the distinguishable stages in the film's electrochemical reduction in linear-sweep voltammetry which is sensitive down to OH O fractional coverages as low as 0.5% and over time-scales down to 50μs in experiments on time-evolution and transformation of the states of the oxide films. By means of LEED, AES and STM or AFM experiments, the reconstructions and perturbations (e.g. generation of stepped terraces) which oxide films cause on singlecrystal surfaces can be followed.

519 citations


"DNA imaged on a HOPG electrode surf..." refers background in this paper

  • ...8 V, [10,11] and the gold surface becomes covered with gold oxides....

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Journal ArticleDOI
Helen G. Hansma1, James Vesenka2, C. Siegerist2, G.L. Kelderman1  +5 moreInstitutions (2)
22 May 1992-Science
TL;DR: Reproducible images of uncoated DNA in the atomic force microscope (AFM) have been obtained by imaging plasmid DNA on mica in n-propanol by increasing the force applied by the AFM tip at selected locations.
Abstract: Reproducible images of uncoated DNA in the atomic force microscope (AFM) have been obtained by imaging plasmid DNA on mica in n-propanol. Specially sharpened AFM tips give images with reproducible features several nanometers in size along the DNA. Plasmids can be dissected in propanol by increasing the force applied by the AFM tip at selected locations.

473 citations


"DNA imaged on a HOPG electrode surf..." refers background in this paper

  • ...unusual structures and DNA–protein complexes have been obtained almost exclusively on mica or silicon [5–8], but rarely on conducting materials....

    [...]

  • ...AFM is not as sensitive as STM to unusual electronic structures on the surface, the AFM images being less affected by artefacts than STM [5]....

    [...]


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