Effects of Metal Ions on Conductivity and Structure of Single DNA Molecule in Different Environmental Conditions
© The Author(s) 2010
Received: 23 March 2010
Accepted: 19 May 2010
Published: 4 June 2010
We design a novel nano-gap electrode to measure the current of DNA molecule, by which the current–voltage characteristics of individual native DNA, Ag-DNA and Ni-DNA molecules are obtained, respectively. The results show that the voltage gap of Ag- and Ni-DNA is higher than that of native DNA, and the conductance is lower than native DNA in neutral environment. The structure transition from B- to Z-DNA is observed in the presence of high concentrations of nickel ions and Ag-DNA appears chaos state by STM image and U-V spectra characterization. But in alkaline environment, the conductance of Ni-DNA rises and the voltage gap decreases with the increasing of nickel ion concentration denotes that the conductive ability of Ni-DNA is higher than that of native DNA.
With the development of high-speed processing technology, more integrated silicon devices will be expected to reach a new level. Consequently, some new materials worked in nano-scale are strongly desired. In this aspect, DNA has received some attentions [1–3]. During the past few decades, DNA has taken center stage in biophysical chemistry research. The elucidation of the molecule structure 50 years ago and the translating of genetic code revolutionized the field of biotechnology. Biologically, the function of DNA is to code functional proteins that are the expressed form of hereditary information. But its unique double helix structure and nearly parallel base-pairs with overlapping π-electron systems make it a good candidate for long-distance and one-dimensional charge transport, which nature did not intend for this molecule. In recent years, charge transfer properties of DNA have attracted much attention among physicists, chemists and scientists in materials to exploit DNA in functional nanoelectronic devices [4–7]. Some reports consider that DNA may be a good linear conductor [5, 8], while other experimental measurements on DNA molecule showed that it seems to be an insulator , even a superconductor at low temperature .
To improve the electrical property of DNA, other approaches may be needed. Chemical doping is an effective way for improving the electrical properties of materials, as demonstrated in semiconductors  and electrically conductive polymers . There have been a few studies on the electrical property of chemically doped DNA [12–15], denotes that metal-DNA (M-DNA) could be formed by metal ions, such as Cu2+, Zn2+, Ni2+, binding into nucleobases, deoxyribose, or phosphodiester backbone and have provided potential applications to the areas of nanomaterials and biosensors. Some reports have showed that the conductive ability of M-DNA is better than that of native DNA [14, 16, 17], while other group reported the conductivity of M-DNA decreases . Therefore, a thorough understanding of the charge transfer properties of doped DNA is crucial in developing the future DNA-based nanoscale devices. At the same time, the effect of metal ions on the structure of DNA is not clear, and no topological structure has been reported by now. In this paper, we have reported the measurement results about the I-V characteristics and structures of native DNA, Ag-DNA and Ni-DNA, respectively, and have discussed the effects of metal ions on conductive ability of single DNA molecules in different environmental conditions.
Materials and Method
Calf thymus DNA in fiber and Tris were purchased from Sigma–Aldrich USA, and DNA was directly used without further purification. Silver nitrate (AR) and NiCl2 were from Zhengzhou Paini Chemical Reagent Factory (China). Millipore ultrapure water and gold target (99.999%) were also used in our experiment.
The Fabricating of Nanogap Metal Electrodes
The nanogap metal electrodes with a sandwich structure were fabricated by the technology of Laser Molecular-Beam Epitaxy 300 (LMBE-300) under 10−7 Pa high vacuum condition. It involved the successive deposition of Au (200 nm), Al2O3 and Au (200 nm) on the Si substrate, followed by cleaving the piece of Si to get nanogap (Al2O3) on the cleavage plane. The width of nanogap could be controlled by adjusting the thickness of Al2O3. No current was found between two electrodes when bias voltage was applied, denotes that nanogap is insulating.
Scanning Probe Microscopy Measurements
Results and Discussion
The Effects of Metal Ions on Conductive Ability and Structure of DNA in Neutral Environment
The Effects of Ni Ion on Conductivity of DNA
The Effects of Ag Ion on the Conductive Ability of DNA
In order to contrast the effects of other metal ions on the conductive ability in neutral solution, we measure I–V curves of DNA and Ag-DNA under nanogap of about 17 nm. First, DNA was dissolved in ultrapure water, and Ag-DNA was prepared by mixing 42 ng/μl DNA with 0.0005, 0.015, 0.15, 0.3, 0.75, 1.5, 15 mM AgNO3 according to 1:1 proportion for 15 min, respectively. Second, a drop of specimen was deposited between two electrodes. It can be found by AFM that the number of DNA molecule spread on Au electrode is about 1 molecule in every 4 μm. I–V curves of individual DNA and Ag-DNA molecules can be obtained and shown in Fig. 1b. It can be found that the voltage gap of native DNA is about 0.4 V and smaller than Ag-DNA. Ag-DNA presents insulating behavior when the concentration of Ag ions is under 0.0005 mM, indicated that the conductive ability of native DNA is better than that of Ag-DNA, and a small quantity of Ag ion could bind to site between base pair and destroy the π-stack, in agreement with the function of Ag ion sterilization . With the increasing of Ag+ concentration, the voltage gaps decreases, and the current increases, so that the conductive ability rises when Ag+ is in the range of 0.3–15 mM, denoted that a new conductive tunnel forms. This tunnel maybe results from the binding of Ag+ to phosphate group, so that the charge will mainly be transfer by phosphate backbone, instead of π-stack, as reported in Ref. . But the superfluous Ag can be found by AFM if Ag+ concentration increases further.
The Effects of Ag and Ni Ions on Structure of DNA
UV–Visible spectroscopy measurements
The STM images of native DNA, Ni-DNA and Ag-DNA
The analysis from STM images showed that the fall in conductance of DNA in high concentration of nickel ions maybe come from two reasons. (1) The backbone and base-pair were destroyed in some degree. (2) Great structure changes occurred after DNA underwent B-Z transition, such as obvious major and minor grooves, local unwinding and disordering region. Consequently, DNA molecules were in chaotic state so that few current passed through DNA molecules even high bias voltage was applied.
Figure 4c shows the STM images of Ag-DNA that is prepared by mixing 0.1 ng/μl DNA and 0.01 mM Ag+ according to 1:1 proportion. It can be found that a part of DNA strand is melting and appears chaos state, indicating that DNA structure is destroyed by silver ion, in agreement with the above result which the conductivity of Ag-DNA is less than native DNA.
The Effects of Ni2+ on the Conductive Ability of DNA in Alkaline Environment
The conductance of individual DNA at different Ni2+ concentrations in alkaline environmental condition
It can be found that the fitted curve shows a good agreement with the experimental data. The conducting mechanism of Ni-DNA in alkaline environment can be demonstrated as follows. When small amount of nickel ions was added to DNA solution (<0.01 mM), they firstly combine with the phosphate groups so that electron doping of DNA occurs  and the conductance remarkably increases. At the range of 0.01–0.05 mM, the nickel ions bonding to phosphate backbone are nearly saturated, meanwhile, few ions intercalate into base pairs so that the increase of conductance becomes slowly. And the conductance increase remarkably again when the concentration was above 0.05 mM, indicating that nickel ions intercalate into base pair and bind to N3 and N1 of Thymine and Guanine. Therefore, not only a π-stack but also an intercalated metal ion channel forms for Ni-DNA so that the conductance could be improved, in agreement with Ref. . But the conductance did not change when the concentration was above 0.1 mM, denotes that the combination between Ni2+ and DNA approaches to saturation.
In this work, we have obtained the I–V curves and topological structure of individual native DNA, Ni-DNA and Ag-DNA molecule at different environmental condition, respectively. The results showed that the conductive ability of native DNA is higher than that of Ag- and Ni-DNA in neutral environment. The conductance decreases, and the voltage gap increases with the increasing of Ni2+ concentration. Moreover, the structure transition from B- to Z-DNA occurs in high concentrations of nickel ions. The insulative behavior of Ag-DNA results from the appearance of chaos state. But Ni ion could enhance the conductive ability of DNA in alkaline environment. These results denoted that the effects of different metal ion on the conductive ability of DNA exist some distinction, and the conductivity of M-DNA has a close relation to the environmental condition.
This work was supported by the National Natural Science Foundation of China (Grant No. 60571062).
This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited.
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