Surface structure characterization of DNA oligomer on Cu„111… surface
using low temperature scanning tunneling microscopy
Chiho Hamai, Hiroyuki Tanaka, and Tomoji Kawaia)
The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka,
Ibaraki, Osaka 567-0047, Japan
共Received 7 January 1999; accepted 21 May 1999兲
The surface structures of DNA oligomers, pAAAAAAATTTTTTT, deposited on Cu共111兲 surface have
been characterized at liquid nitrogen temperature using a scanning tunneling microscope. Four
different types of adsorbed structures have been observed in DNA oligomers; 共i兲 an isolated whole
molecule, 共ii兲 a shortened molecule, 共iii兲 a cluster, and 共iv兲 a double helix. The internal structures of
the oligomers also have been resolved.
© 1999 American Vacuum Society.
关S0734-211X共99兲08104-4兴
I. INTRODUCTION
The scanning tunneling microscope 共STM兲 is an important tool for the study of biomolecules.1 A large number of
reports on the observations of DNA in air or water using
STM have been published.2–6 The invention of STM aroused
our interest in DNA base sequencing using STM, but sequencing using STM remains to be achieved.1 The resolution
of the images obtained in air or water seems not to be
enough to image the internal structure of DNA.2–6 For the
improvement in resolution, we have performed the observation at liquid nitrogen temperature in ultrahigh vacuum
共UHV兲.
Here, we report the STM observation of a DNA oligomer
adsorbed on Cu共111兲. By performing the observations at liquid nitrogen temperature in UHV, high resolution images
have been obtained. We have found that the oligomer forms
various structures on Cu共111兲 and the molecular internal
structures are also successfully resolved.
The observed DNA oligomer is pAAAAAAATTTTTTT 关abbreviated as A7T7兴. The 14-mer has 14 nucleotide units consisting of seven adenines and seven thymines attached to its
phosphate sugar backbone. Since the Watson–Crick basepairing forces DNA into the double helix structure, the 14mer is expected to form some interesting structures.
deposition of the DNA oligomer on the Cu surface, this
sample was subsequently transferred to the STM UHV
chamber (⬃10⫺10 Torr). And then surface structures of the
DNA were observed using STM at liquid nitrogen temperature 共⬃80 K兲. All images were obtained in constant current
mode at the bias voltage of 2 or 3 V. The atomic resolution
of Cu atoms13 cannot be obtained under the tunneling condition which is suitable for the imaging of DNA oligomers.
III. RESULTS AND DISCUSSION
Figure 1 shows a STM image of an A7T7 oligomer on the
clean Cu共111兲 surface. The size of the encircled bright object
is in agreement with that of one molecule in lateral dimensions. The various observed adsorbed structures can be classified into four different types: 共i兲 an isolated whole molecule
关Fig. 2共a兲兴, 共ii兲 a shortened molecule 关Fig. 2共b兲兴, 共iii兲 a cluster
which is constructed from two or more molecules 关Figs.
2共c兲–2共e兲兴, and 共iv兲 a double helix 关Figs. 2共f兲 and 2共g兲兴.
II. EXPERIMENT
A clean Cu共111兲 surface was prepared by several cycles
of annealing at 550 °C and sputtering with Ar⫹. 7,8 The A7T7
oligomer was deposited on the clean Cu共111兲 surface using
the pulse injection technique9 in order to prevent decomposition of the DNA oligomer because it was well known that
large molecules, such as DNA deposited using thermal
evaporation10 can be easily decomposed.11,12 A pulse valve
filled with a DNA aqueous solution was attached to the
preparation chamber in vacuum (⬃10⫺7 Torr). A clean
Cu共111兲 substrate was located just under the pulse valve.
The distance from the pulse valve to the substrate was 100
mm. The solution was injected toward the substrate at room
temperature when the valve was opened for 1.5 ms. After
a兲
Corresponding author; electronic mail: [email protected]
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J. Vac. Sci. Technol. B 17„4…, Jul/Aug 1999
FIG. 1. Image of A7T7 DNA oligomers on Cu共111兲 surface. The image was
taken in the constant current mode with I⫽4 pA and V t ⫽2.0 V for the area
of ⬃500 Å⫻⬃430 Å. The bright object encircled with a rectangular is an
isolated molecular image.
0734-211X/99/17„4…/1313/4/$15.00
©1999 American Vacuum Society
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Hamai, Tanaka, and Kawai: Surface structure characterization of DNA oligomer
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FIG. 2. STM images of A7T7 DNA oligomers adsorbed on Cu共111兲 surface. 共a兲 An image of two isolated whole molecules (⬃90 Å⫻90 Å). The topographic
heights of these molecular images are about 2Å. 共b兲 An image of a shortened molecule (⬃90 Å⫻90 Å). The chain length is about half of those measured for
the isolated molecules in 共a兲. 共c兲 An image of a cluster (⬃200 Å⫻200 Å). A pair of parallel two chains can be seen 共arrow兲. 共d兲 An image of a cluster
(300 Å⫻300 Å). A pair of parallel two chains is observed 共arrow兲. 共e兲 An image of clusters (220 Å⫻220 Å). A part of twisted chains can be seen 共arrow兲.
共f兲 An image of double helix (⬃130 Å⫻130 Å). White lines indicated by arrows show positions where the height of the molecule was measured. The
maximum topographic heights of cross sections 共a兲, 共b兲, 共c兲, 共d兲, and 共e兲 are 1.6, 2.9, 3.5, 2.6, and 2.2 Å, respectively. 共g兲 The perspective projection of 共f兲.
共a兲, 共b兲, 共c兲, and 共f兲 The extracted images from Fig. 1. 共e兲 Extracted from Fig. 3. 共d兲 A region picked out in an image which is not presented here. 共d兲 A
constant current image taken with I⫽5 pA and V t ⫽3.0 V.
The topographic heights of isolated molecules 关Fig. 2共a兲兴
are about 2 Å. Figure 2共b兲 is a STM image of the shortened
molecule, whose chain length is approximately half of that of
the isolated molecule shown in Fig. 2共a兲. Figures 2共c兲–2共e兲
show STM images of ‘‘clusters.’’ Parallel chains 关Figs. 2共c兲
and 2共d兲兴 and a twisted chain 关Fig. 2共e兲兴 are seen. A ‘‘double
helix’’ structure has been found as shown in Figs. 2共f兲 and
2共g兲. The value of lateral dimension indicates that the
J. Vac. Sci. Technol. B, Vol. 17, No. 4, Jul/Aug 1999
‘‘double helix’’ is formed from two oligomers. White lines
indicated by arrows in Fig. 2共f兲 show positions where the
height of molecule was measured. The maximum heights of
cross sections 共a兲, 共b兲, 共c兲, 共d兲, and 共e兲 of Fig. 2共f兲 are 1.6,
2.9, 3.5, 2.6, and 2.2 Å, respectively. Since the heights of
cross sections 共b兲 and 共c兲 of Fig. 2共f兲 are larger than those of
cross sections 共a兲, 共d兲, and 共e兲, 共b兲 and 共c兲 are the positions
where the two strands cross. The ‘‘double helix’’ is therefore
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Hamai, Tanaka, and Kawai: Surface structure characterization of DNA oligomer
FIG. 3. 共a兲 Image of A7T7 DNA oligomers on Cu共111兲 surface. The internal
structures of the oligomers are resolved in this image. The image was taken
in the constant current mode with I⫽5 pA and V t ⫽3.0 V for the region of
480 Å⫻320 Å. The bright object enclosed with a square is an isolated molecule. 共b兲 The inset is the expanded image of the isolated molecular image
enclosed with a square in 共a兲. The molecular model is for the isolated molecule of the inset. The model and the molecular image are in agreement in
lateral dimensions.
one and a half turned double helix. A double strand DNA in
a crystal or solution has about ten base pairs per turn.14 If the
double helix is constructed from two A7T7 oligomers, then
it ideally has one and a half turns. The number of turns
present in the ‘‘double helix’’ image is the same as that of
the helix structure existing in a crystal or solution. However
the topographic heights of the helix image are considerably
smaller than the diameter of a DNA double helix in a solid or
a solution 共⬃20 Å兲.14 This difference may be attributed to
the imaging mechanism or the molecule–surface interaction
which transforms the conformation without changing the
number of helix turns, but only shortening the height.
In addition to the imaging of four adsorbed structural
types, the internal structure of A7T7 has been resolved 关Fig.
3共a兲兴. The bright object enclosed with a square in Fig. 3共a兲
corresponds to an isolated molecule. Its topographic height is
about 2 Å. All molecular images consist of small bright
maxima that are about 7–10 Å in diameter. The length of
one oligomer in STM images is approximately equal to 14
times of the bright maximum diameter 共7–10 Å兲, therefore
JVST B - Microelectronics and Nanometer Structures
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each bright maximum is considered to be one nucleotide
unit. A molecular model whose base planes were parallel to
the Cu surface was constructed for an isolated molecular
image as shown in Fig. 3共b兲. The inset of Fig. 3共b兲 is the
expanded image of the isolated molecule enclosed with a
square in Fig. 3共a兲. The model is in agreement with the isolated molecular image shown in the inset in lateral dimensions.
The height of the isolated molecular image 共2 Å兲 in Figs.
2共a兲 and 3共a兲, and the diameter of the bright maximum 共7–10
Å兲 in Fig. 3共a兲 suggest that the small bright maximum observed in Fig. 3共a兲 corresponds to one base. It has been
shown that DNA base molecules adsorbed flat on Cu共111兲
surfaces are imaged with the height of 1–2 Å.15 The value of
1–2 Å is relatively consistent with the height of the isolated
oligomers 共2 Å兲. And the diameter of the bright maximum
共7–10 Å兲 is a typical value for the lateral size of DNA base
molecules lying flat on metal surfaces.15–17 The discrimination between A and T was not achieved in this experiment.
Improving the resolution and optimizing the tunneling condition 共such as bias voltage or tunneling current兲 can lead to
identification of DNA bases. However, we cannot assert that
only bases are imaged, because we have not measured anything but constant current images.
The STM images depend on two factors, namely local
density of state 共LDOS兲 and barrier height. If the LDOS
contributes more to the imaging of DNA oligomers compared with the barrier height, then the small bright maximum
observed in this study corresponds to one base. This is because the ␲ orbitals of the base exists at the highest energy
level of all orbitals of DNA and the flat plane of the base
could result in a sufficient interaction with the Cu surface.
On the other hand, if the barrier height contributes more to
the imaging compared with the LDOS, then it is not possible
to infer which part of DNA is imaged most brightly. In order
to clarify the imaging mechanism, we would need further
investigations.
IV. CONCLUSIONS
DNA oligomers (A7T7) adsorbed on Cu共111兲 surface
have been observed with a low temperature STM in UHV.
We have found that A7T7 oligomers form various adsorbed
structures on Cu共111兲 surfaces. These adsorbed structures are
classified into four types: isolated molecule type, cut molecule type, cluster type, and double helix type. The internal
structures of A7T7 oligomers have also been resolved.
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