Probing nanotube-nanopore interactions

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Original entry by Andrew Capulli, AP225 Fall 2011

Reference

King and Jene Golovchenko, Probing nanotube-nanopore interactions, Physical Review Letters 95, 216103 (2005).

Key Words

Nanotubes, Transmission Electron Microscopy, Ion Blockage, DNA, Disjoining Pressure, Nanopore

Introduction: Motivation

The investigation into the properties of nanopore channels in biological membranes is not well characterized in their purest form; this is to say that high electrophoretically driven molecular speeds are required for the translocation of molecules through these biological nanopores (such as proteins, DNA, etc). With the semi-recent advancement in nanotechnology of scanning tunneling microscopy (STM) and atomic force microscopy (ATM) for example, as noted by the authors, there is a new interest in the physics of molecules at this size scale and the interactions thereof; in particular, at this size scale, the investigation into single molecule systems and characterization of the molecule is of interest. However, as noted, much of the study into these nanopore systems requires electrical charge of molecule in question to 'drive' its translocation through the nanopore. This addition of a charge can be thought of as slightly modifying the molecule thus resulting in study of an inexact system (not necessarily the molecule in its purest, uncharged form). This drives the need for a system of trans-nanopore delivery of molecules in such studies and is what Golovchenko et al present in this methods paper.

Nanopore-Nanotube System Construct

Using the technique of ion sculpting [J. Li et al., Nature (London) 412, 166 (2001)] nanopores of the desired diameter were constructed. The nanopore was fixed into the system (as shown below in FIG 1, separating two reservoirs a uniform ionic solution (1 M KCl, 10 mM TRIS-HCl,1 mM EDTA) which allowed current to flow between the silver (Ag/AgCl) electrodes of the system present in each reservoir (seen in black in the figure FIG 1 below). To summarize, the nanopore provides the only connection between the charged solution in the top and bottom reservoirs. An AFM cantilever with a carbon nanotube affixed to the tip of the cantilever is positioned above the nanopore and can be moved translationally (across the x-y plane the nanopore is in) and vertically (the 'z' direction through the nanopore) via the the AFM cantilever control system. Golovchenko et al refer to the movement in the z direction through the pore as being controlled by Zpiezo; this will appear in figures below and is just the vertical controlling movement of the AFM unit. Figure 1 below shows the construct:

JG48 FIG 1.jpg

Carbon nanotubes were fixed to the silicon AFM tips via iron catalyzation and can be seen in FIG 2 (b) below. Also in the figure are transmission electron microscopy (TEM) images of the nanopore (a) viewed along the previously discussed 'z' dirction (above the pore) as well as 'in fluid', meaning in reservoir, images of the nanopore (c) and the ionic current (d):


JG48 FIG 2and3.jpg

Nanopore-Nanotube System Current Testing

FIG 3 above graphically summarizes the testing results performed by Golovchenko et al. A simple test of the of the current (created by the electrodes described in the previous section) and resulting current blockage due to the insertion of the carbon nanotube into the nanopore repeatedly was performed. As can can be seen, an inverse relationship develops: as the nanotube is inserted into the nanopore (decreasing displacement of the dotted line) there is an increase in current blockage. As the nanotube acts as an isolating material reducing current flow through the pore as it enters; similarly, current increases (blockage decreases) as the nanotube is withdrawn. There is an observable plateau on the graph where the nanotube continues to be driven through the nanopore but current blockage remains the same: this suggest the point where the nanotube is fully through the nanopore and further insertion does not cause any increase in blockage. Using an assigned conductivity of .1(S/cm) to the ionic solution in the reservoir and the dimensions of nanopore (12nm diameter, 5nm depth) Ohm's law for the 200mV voltage applied at the electrodes, a current of 8.3nA was calculated for the system and was achieved (within 5%). Maximum current blockage was found to be around 7nA which is curious considering the nanotube has a diameter of 5nm as compared to the pore which has a diameter of 12nm; a smaller blockage was expected (7x smaller!). This leads to the interesting point of the article (the relates the methodology to the study of soft matter).

Nanopore-Nanotube: Connection to Soft Matter

As previously mentioned, given the size of the nanopore and nanotube, current blockage due to the insertion of the nanotube into the nanopore was expected to be significantly less. While Golovchenko et al discuss kinking of the nanotubes as a potential source of increased current blockage (their logic being a bent tube in a hole blocks more than a perfectly straight tube), there may be more to the story. As the paper reports, there may have been at this level, a layer of non-conducting water around the tube in the pore among other suggestions such as a contamination layer acquired on the nanotube during set up or bound ions within the nanotube. The interesting suggestion is the layer of non-conducting water around the tube within the pore. This very thin water layer would have a high disjoining pressure meaning high interaction of the water with the tube and the pore. This high interaction between the substances would result in lower conductivity and thus the increased current blockage. While the (insulating) carbon nanotube blocks the current via its insertion, it also 'brings with it' a thin layer of water that, due to its high disjoining pressure and lack of ion content, results in even more current blockage through the nanopore.


More Thoughts: While this interesting soft matter interaction of the water-nanotube-nanopore system potentially results in current blockage (insulating properties) the nanotube technique presented in this paper may provide an apparatus for future studies of biological single molecule systems without the need to charge molecules being studied. The authors mention that DNA has been shown to naturally bind to carbon nanotubes (M. Zheng et al., Science 302, 1545 (2003)) and via this insertion technique , DNA molecules may be able to be translocated into biological systems for study of in their pure form (as described in the introduction). If specific DNA pieces can be manipulated and delivered via this technique into biological systems, a more accurate and full investigation into their encoding and translation may be done.