Open and close curves

In this section, we compare the open and close curves from different samples, to ensure the good binding between the molecules and electrodes. We used pure buffer solution without DNA molecules, buffer solution with unmodified DNA samples and buffer solution with modified DNA samples. The last samples show a particular low resistance plateau because of the stable binding of DNA to the electrodes which lead to higher conductance. The resistance plateaus with the other two samples were very high (about 10 GΩ). In addition, the closing behavior with the modified DNA in solution is inspected in more detail. The obvious conductance enhancement at special positions is compared to a theoretical result.

4.2.4.1 The typical open and close curves

There are several features which can be clearly seen from the open-close curves in Figure 4.5:

The first one is the resistance difference. The conductance with the modified DNA sample (~100 MΩ) is ten times or hundreds of times higher than that of the control samples (1~10 GΩ). The mechanism of the charge migration in solution is not clear. Since there are counterions and water molecules around DNA samples, the electronic structure of DNA bases may not give rise to changes in the conductance measurement. However, since the bias voltage we applied was in the range of safe voltage, we can assume that the electrochemical effect is negligible in our case.

Second, we should mention that if the bonds are destroyed between the modified DNA molecules and the gold electrodes, the resistance will jump to the same value as in buffer, as shown in the red and black curves in Fig. 4.5. Finally, since in most cases the DNA has been stretched when the bridge was broken to electrodes, the closing curves show more information, since also the distance calibration for close curves is more reliable than for open curves.

100k 1M 10M 100M 1G 10G

close with um-DNA open with um-DNA

R[ Ω]

t[100s]

close with m-DNA2 open with m-DNA2 open without DNA close without DNA

open with m-DNA1 close with m-DNA1

Fig. 4.5: Typical open and close curves in buffer solution: Break until R ≥ 1 GΩ (~3 nm testing in solution), then close the electrode. The um-DNA is the dsDNA with its ends not modified. Both m-DNA1 and m-DNA2 are the dsDNA with both ends modified. However, curves with m-DNA1 sample were taken with the “over broken”

process as in Figure 4.3 and curves with m-DNA2 were taken with the “stable binding” process as in Figure 4.4.

4.2.4.2 Steps in open curves and conductance enhancement in close curves

In the open process, we can hardly get enough curves for statistical analysis since samples become unstable in a short time in solution, as we discussed in the former chapter. But, it is clear that some steps exist, as shown in Figure 4.6 a. The steps range from 500 kΩ to 10 MΩ. Furthermore, these steps occur at different resistance values in different curves. A possible explanation is that the number of molecules bond between the electrodes is different.

The most interesting phenomenon is seen in the close curves. Figure 4.6 b shows the typical close curves, which can be separated in two types. In type I, there is a trough of resistance (we call it conductance enhancement behavior) in the plateau region. The conductance enhancement behavior occurs at the distance from 0.7 nm to 1 nm. We can exclude the explanation that this phenomenon is caused by the change of binding between DNA and electrodes because the resistance rises back when the

been stretched when the electrode is opened. We therefore contribute the conductance enhancement to conformational changes of the stretched DNA during closing, which results in the enhancement of overlap of the conducting π-orbitals⁷.

10k

Figure 4.6: a, Typical open curves of modified DNA in solution. The steps indicate the presence of molecules in the junction, but the resistance values of the steps vary from curve to curve. b, Typical close curves of the modified DNA samples. The enhancement of the conductance around 1 nm might be due to rotation of neighboring stacks.

When a short DNA molecule is stretched by pulling its ends, the twist angle φ between consecutive base pairs reduces from its equilibrium value of 36^o. Smaller angles φ lead to an increased π-π overlap, resulting in larger charge transfer integrals.^6-8 On the other hand, the combined twist-stretch process leads increased inter-base distances d, effectively decreasing the values of the charge transfer integrals, therefore, antagonizing the effect of twist. This may lead to a complex behavior of electronic properties of DNA during the stretching process.

The change in overlap between neighboring bases, as a result of a changed DNA configuration during the stretching process, has been investigated theoretically by Maragakis et al. on a few geometry snapshots⁸. Song et al.⁷ investigated the conductance change of DNA along the conformation transition for the stretch-twist process in more detail. By merging density-functional-theory-based calculations and model-Hamiltonian approaches, they found that when the distance between two adjacent bases decreased from 0.6 nm to 0.4 nm, the conductance increases first and then decreases, forming a peak in conductance-distance curves, as shown in Figure

4.7, which is similar to the trough in our closing curve. In their theoretical work, dynamic aspects and the effects of the solvent are neglected, different to our case. But it can be expected that the average behavior is qualitatively the same. The solvent degrees of freedom lead to fluctuations in the onsite parameters, which is assumed to be not relevant to understand the qualitative picture. However, because the binding positions of DNA to electrodes are not controllable in our experiment, we cannot compare the absolute extension of DNA at the trough to their calculation.

A B

A B

Figure 4.7: A, The charge-transfer-integral t for the stretching-twisting process as a function of the distance between two GC pairs, d, and the angle f. The green dashed line represents the equilibrium position deq = 3.4 Å, φeq = 36^o. The blue dashed-dotted line represents the suppression point (d0 ≈ 4.45 Å, φ0 ≈ 24.6^o). The three horizontal shot-dashed gray lines are the references used for the intensity of the DNA coupling to the electrodes displayed in B. B, Current-distance relations along the three red (dash-dot) lines in figure 4 with same parameters. (a) Γ = 9.5 meV, (b) Γ = 3 meV, (c) Γ = 1 meV. The blue dash-dot lines are for the position (d = d0 , φ = φ0).

Figures are taken from reference ⁷ with permission.

4.2.5 Summary

In this section, the binding of the modified dsDNA molecules to the gold electrodes of MBCJ was monitored and investigated. The DNA conductance in aqueous solution was explored. The conductance enhancement in the closing curves were discussed together with the theoretical results by Song et al.⁷

4.3

Conductance characterization of dsDNA in ambient