Our work - Review of experimental investigations of DNA conductance

Chapter 1 Background on DNA conductance

1.3 Review of experimental investigations of DNA conductance

1.4.2 Our work

The challenge to improve measured conductance of DNA can be overcome in two ways, either to improve its bonds to electrodes or to improve its intrinsic conductance. In this thesis, we develop two strategies to achieve these goals.

We improve the attachment of DNA molecule to the gold electrodes by changing the position of thiol-group on terminal bases. In the former work by Kang et al. in our group, measurements of the conductance through a single or a small number of DNA molecules was carried out using mechanically controllable break-junctions (MCBJs).

The DNA molecules were terminated with thiol end-groups attached to the 5’end of the terminal bases. This chemical adsorption ensures good mechanical coupling of the molecules to the gold electrodes, and thus mechanical stretching of the molecule is possible before the molecule–metal bond breaks. However, by this method, the electrons from gold electrodes are coupled to the sugar backbone of DNA, instead directly coupled to the nucleotide bases in which the π-π stacking occurs. We solve this problem by synthesizing new nucleotides with a thiol-end group attached to the 5-position of terminal thymine bases. Synthesis of this new nucleotide and DNA samples are conducted by Bornemann et al. in chemistry department of our university.

We verify its adsorption on a gold surface by fluorescence microscopy and AFM. The conductance behavior is characterized with MCBJ in water, ambient and vacuum.

Detailed results and discussion about this part of work are shown in chapter 4.

To improve its intrinsic conductance, we employed DNA G-quadruple instead of the double-stranded structure. Such constructions can offer an improved stiffness and electronic overlap that may enhance the conductivity of the molecules. Details about G-quadruplex and its conductance measurement are shown in chapter 5.

Before going into the measurement of dsDNA and G-quadruplex, in chapter 2 the methods to fabricate the MCBJ and synthesis of all DNA samples are introduced.

Moreover, test of the MCBJ in water and buffer solution is presented in chapter 3. The results provide a fundamental and solid background to use MCBJ for conductance

measurement of various DNA molecules.

We end this thesis by a conclusion of DNA conductance based on our experiments and a prospect for further studies.

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Group DNA sample Electrodes Method Ions Environment Results

Yielded no observable current up to 10 V The resistance >10¹³Ω

Ohmic behavior IVs, sustained up to 40 mV The resistance in the MΩ range

3 Porath et al. (2000) Single

nA range current was observed beyond a threshold voltage of 0.5-1V

At RT and ambient: 600 nm length yields a resistance about 100 MΩ and 16 μm length yields a about 10 GΩ

The overall temperature dependence suggested two contributions to the transport, a weakly temperature dependent response at low temperature and a strongly temperature dependent contribution at high temperatures.

The magnitude of the conductivity at room temperature and above depends on the chemical surroundings of the double helix with a buffer environment leading to larger conductivity

5 de Pablo et al.

Length 70 nm mica Ambient The resistance is about 200 MΩ

L=100 nm linear ohmic IV behavior.

The resistance is about 10 GΩ at 4 V

Clear length-dependent conductivity that was about an order of magnitude larger for the Poly(G)-Poly(C) than Poly(A)-Poly(T).

7 Rakitin et al. (2001) λ-DNA /M-DNA Length 16 μm

Au Free hanging Na⁺ RT vacuum

Metallic like conduction through M-DNA (The resistance is about 200MΩ) in contrast, measurements on λ-DNA (The

resistance is about 1 GΩ at 2 V) give evidence of semi- conducting behavior with a few hundred meV band gap.

8 Storm et al. (2001) Single/small

The resistance is about 10TΩ at 10V.

9 Yoo et al. (2001) Super-coiled

Linear Ohmic behavior with resistance about 1.5 MΩ for the Poly(G)-Ploy(C), much smaller than Poly(A)-Poly(T)

Low T

Semiconductor behavior with Poly(G)-Poly(C) exhibits p-type semiconducting behaviors, while Poly(A)-Poly(T) does n-type ones

10 Kasumov Few λ-DNAs Re/C On mica Mg²⁺ T< 1K Induced superconductivity

( 2001) Length 500 nm.

The current dropped form 2 nA (resistance is about 1GΩ) bout 2 nm to less than 0.1 nA in the length rang of 6-20 nm at 2V

Insulating behavior with R >> 10 TΩ at 20 V

13 Hartzell and McCord

The repaired DNA a close-to-linear IV characteristic.

In contrast, the nicked DNA shows pronouncedly nonlinear and rectifying behavior, with a conductivity gap of ∼3 eV.

14 B. McCord et al.

For either the disulfide groups were attached to the opposite DNA strands, or only one strand is attached, current–voltage characteristics are linear and do not reveal significant differences Resistance is about 1 GΩ at 20 V

Resistance of DNA Poly(A)-Poly(T) and Poly(A)-Poly(T) in air was found to be 1 to5 MΩ.

In vacuum, the resistance of Poly(A)-Poly(T) was found to be 0.1to 0.5GΩ

The measured conductance depends on the DNA sequence and length. For (GC)n sequences, the conductance is inversely proportional to the length. When inserting (A:T)m into GC-rich domains, it decreases exponentially with the length of A:T base pairs (m)

Resistance of 8 base pairs is about 10 MΩ Linear IV behavior below 0.5 V

17 Kasumov et al. Few λ-DNAs Pt On NH₃⁺ from 0.1K to RT Strongly deformed DNA molecules deposited on a substrate,

(2004) Length 3 μm Functionaliz ed mica or un-functional

ized mica substrate

vacuum whose thickness is less than half the native thickness of the molecule, are insulating, whereas molecules keeping their native thickness are conducting (the resistance is about 100 kΩ ) down to very low temperature with a non-ohmic behavior

18 Xu et al. (2005) HS-DNA

the resistance is about 10G Ω

the dsDNA molecules behave as an insulator at low bias, and that they can transport charge carriers beyond the threshold voltage 2V

Under dry conditions 0% humidity, no difference was observed for the electrical current both of the DNA network and mica surface, whereas the electrical current along the DNA network was larger than that of the mica surface by 20 pA (resistance is about 200GΩ at a bias voltage of 5 V under high humidity conditions of 60%.

Before and after a temperature ramp from 300 to 400 K a dramatic decrease in conductance was observed.

the dc resistance of dry DNA strands of the same length decreases with increasing guanine-cytosine content in the sequence with values ranging from 10M Ω to 2 G Ω.

21 Cohen et al. (2005) Hs-DNA

S-shaped current–voltage curves that show I >220 nA ( resistance is less than 10MΩ) at 2 V.

22 Wierzibinsiki et al. Hs-DNA a gold STM Free hanging RT Wide distribution of currents independent of the ds-DNA length.

(2006) Poly(G)-Ploy(C)

The lower currents are also observed for ds-DNA molecules containing a single CA base mismatch.

Resistance is from 100MΩ to 1GΩ at 100mV

23 Zalinge et al. (2006) HS-

The G-C sequence gives a higher conductance than the equivalent length A-T sequence.

Temperature-independent.

Resistance is around 2GΩ 24 Hong et al. (2008) Few DNAs

The samples of DNA are excellent insulators; however,

their impedances show strong frequency dependence in the range of 10 Hz–7.5 MHz.

Favorable response in the gold electrodes is attributed to the higher ability of DNA molecules to bridge the narrower gold electrode gaps in contrast to that in the wider platinum junctions 25 Roy et al. ( 2008) Single DNA.

ssDNA/dsDNA 80 base pairs complex base

sequences

SWNTs Free hanging Gate voltage

Ambient /High

vacuum

dsDNA has about a 25-40 pA current (resistance is around 10GΩ, at 1 V), acting as a p-type channel,

with initial increase in current value (from 25 to 40^oC)

at the device temperature (50-70⁰C), diminishing current signal at a given voltage.

Above the melting temperature of the DNA molecule (75.6^oC), detectable signal

ssDNA carries current of about 1 pA or less.

Resistance is higher in vacuum than in ambient.

Chapter 2 Experimental Methods

2.1 Introduction to the mechanically controllable break junction (MCBJ) technique and our DNA samples

We carried out the measurements of the conductance through a single or a small number of DNA molecules using mechanically controllable breakjunctions (MCBJs).

This technique has been used to characterize atom-sized metallic contacts¹ as well as current transport through single organic molecules². The main advantage of this technique in the current context is its possibility of adjusting the separation of the metallic contacts at a precision of fractions of 1 Å. With MBCJs setup, one can change the length of the contacted molecule in a very controlled way and measure the conductance of the same molecule simultaneously. The details of the conductance measurement with MBCJs setup are introduced in the second section.

In the other part of this chapter, we focus on the preparation of our DNA samples.

The thiol end-groups for binding DNA to the electrodes have been firstly connected directly to the π electron systems of dsDNA and protected by a trimethylsilyl (TMS) group from oxidation. The methods to prove that this modification and protection work effectively for the stable binding between gold substrate and DNA molecule were carried out by fluorescence microscope and atomic force microscopy (AFM).

Methods for preparing G-quadruplex samples are also described.

At the end of this chapter, we discuss the setup for depositing the DNA onto the MBCJs.

2.2 Conductance measurement system with MCBJs

The pioneering work for exploring atomic sized contacts came with the invention

of the Scanning Tunneling Microscope (STM) by Binnig and Rohrer in 1983. At the same time Moreland et al. invented a “Squeezable electron tunneling junction”³ which resulted in the birth of break junctions after further development⁴. In 1992, Moreland’s breakjunction technique was improved further by Muller et al. in order to obtain clean and stable contacts ⁵. The technique was then named Mechanically Controllable Break Junction (MCBJ). In the following years many experiments were realized to study the interplay between quantized conductance and atomic structure

6-10. In 1997 MCBJs were applied for the first time in the context of molecular electronics ¹¹. Break junctions were employed to contact molecules because they allow a relatively simple fabrication of clean metallic contacts at the molecular size.

Additionally the distance between the electrodes is adjustable and the system offers a high mechanical stability. These advantages lead to manifold use of the breakjunction for single-molecule measurements^12-15. The principle of MCBJs setup will be introduced in this section followed by the fabrication methods of MCBJ electrodes.

δx

Figure 2.1: a, Principle of the mechanically controllable breakjunction, with substrate thickness t, distance between counter supports L, free suspended length u, elongation of the free suspended lengthδx, and movement of the pushing rod ∂z. b, Colored scanning electron microscope image of the bridge. c, Sketch of the breaking mechanism: 1 electrode substrate, 2 differential screws, 3 guiding rod, 4 counter bearing, 5 pushing rod.

2.2.1 MCBJ

The principle of the breakjunction is rather simple. A metal wire with a constriction is fixed on top of an elastic substrate. Bending the substrate causes an expansion of the top surface. The metal wire can break at the constriction if the expansion is big enough. This results in two electrodes. Relaxing the force on the substrate, the electrodes can be brought back into contact.

A picture of the entire installation of MCBJ is shown in Figure 2.1. In experiments, the metal bridge does not only need to be opened, but the distance between the bridge-ends needs to be adjusted with sub-nanometer precision. This can be accomplished with a purely mechanical setup as shown in Figure 2.1a. A sketch of a sample (an elastic substrate with metal on the top of it) in the center of the breaking mechanism is shown in Figure 2.1 b. In principle, a pushing rod at center bends the sample, which is held in place by counter supports at the ends. The bending transfers the vertical movement of the pushing rodδzinto a lateral stretching of the metal bridge according toδu=rδz, where the factorris given by

6₂

r= ut (2.1)

Where, u is the free suspended length of the metal bridge, t is the substrate thickness, and L is the distance between the counter supports. Typical values for r range from 10^-4to 10^-5.

The MCBJ setup contains two copper plates, as shown in Figure 2.1c. The sample is held in the upper copper plate. The pushing rod is fixed onto the lower copper plate. This plate is connected to the upper one by three smooth guiding rods and one differential screw. The lower copper plate contains a thread nut with a pitch of 0.35 mm, while the thread nut in the upper copper plate is cut with a pitch of 0.25 mm. The threads of the differential screw are cut accordingly. Rotating the screw by one full turn therefore only raises the lower plate by the difference of the two pitches α = 100 μm. The differential screw is driven by a DC motor (Faulhaber MiniMotor) using gears with a reduction ratio Rmotor = 1 : 5490. The MiniMotor is controlled by a Faulhaber Motion Controller, Series MCDC2805. The Motion Controller is driven using a LabView program and can be positioned at exactly one thousand steps per turn. The continuous elongation δu finally causes the bridge to tear apart, resulting in a gap of width Δs. The relation between the electrodes distance Δs and the

motor-step counts can therefore be finally written as 1000

counts R

r s= α _motor

Δ (2.2)

2.2.2 Electrode fabrication

Here we introduce the fabrication of electrodes for MBCJ by nano-lithography.

The fabrication of the electrodes started from polishing a bronze or steel wafer. The polished wafer is then coated by a layer of polyimide by spin-coating. Polyimide does not only serve as an electrical insulator and a smoothing layer, but also serves as a

‘sacrificial layer’ in the subsequent etching process. On top of polyimide, two layers of electron beam resists, methyl-methacrylate-co-methacrylacid (MMA-MAA) and poly(methyl-methacrylate) (PMMA), are coated. These two resists differ in resolution and sensitivity when rinsed in suitable solvents, which are crucial during the

‘developing’ step. Figure 2.2 a shows the stacked layers on the wafer.

gold PMMA MMA-MAA Polyimide Substrate

a

d

b c

e f

gold PMMA MMA-MAA Polyimide Substrate

a

d

b c

e f

Figure 2.2: Steps to fabricate electrodes. a, three layers on the substrate; b, electron beam lithography; c, development of the electron beam resists; d, evaporation of the gold; e, lift-off of the remaining resist and the metal on the top; f, after etching with reactive ion plasma.

The patterns for electrodes are fabricated with lithography (Figure 2.2b) and a development step (Figure 2.2 c). With a scanning electron microscope (SEM), an electron beam illuminates predefined areas on the sample (Figure 2.3). The area contains two big squares (0.5 mm×0.5 mm) connected with a 50-μm-narrow bar. In the center of the pattern, there is a slim part as narrow as 100 nm, which is continuously increased to the width of the electrode (50 μm). The electron beam causes a breaking of chemical bonds of the resists, which can then be dissolved with

Im Dokument Conductance of individual DNA molecules measured with adjustable break junctions (Seite 34-0)