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Oak Ridge National Lab’s Predrag Krstic on Exploring Nano-Ion Traps for DNA Sequencing

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Predrag Krstic
Senior Staff Scientist, Physics Division
Oak Ridge National Laboratory
Name: Predrag Krstic
 
Position: Senior staff scientist, Physics Division, Oak Ridge National Laboratory, since 1995
 
Experience and Education:
— Postdoctoral fellow, Oak Ridge National Laboratory, 1995-1998
— Postdoctoral fellow, University of Connecticut, 1992-1995
— Staff scientist, senior staff scientist, and professor; Institute of Physics, Belgrade University, Yugoslavia, 1976-1992
— PhD in physics, City College of New York, 1981
— MS in plasma physics, Belgrade University, 1979
— BS in technical physics, Belgrade University, 1975
 
Last month, Predrag Krstic from Oak Ridge National Laboratory won a two-year, $720,000 grant under the National Human Genome Research Institute’s Advanced Sequencing Technology program.
 
He and collaborator Mark Reed at Yale University will explore how a nanoscale ion trap for DNA sequencing can be fabricated and used.
 
In Sequence spoke with Krstic last week to find out about his research plans.
 

 
Can you explain what a Paul trap is, and what its advantages might be for sequencing?
 
In the so-called Paul trap, a special combination of DC and AC electric fields creates a quadrupole field, which efficiently traps the charged particles in a dynamic equilibrium. While its 3D version is used to study atomic and molecular ions trapped in a small volume, the 2D quadrupole trap is extensively applied in mass spectrometry. For this invention, Wolfgang Paul received the Nobel Prize in 1989.
 
The tunneling nanopore approach to DNA sequencing relies on the change of a transversal electrical conductance readout across a DNA as it translocates through a nanopore or nanogap by electrophoresis. The relevant electric current is strongly dependent on the geometry conformations of the DNA in the gap, which is difficult to control. Thus, the fundamental problem in this approach is the control of localization and motion of DNA in the gap, and this is what we hope to improve here by developing and applying a new, nanoscale version of the Paul trap.
 
A standard Paul trap ranges in size from hundreds of micrometers to centimeters. Its functions and its parameters, such as kilohertz-range AC frequency and voltages of hundreds of volts, are adapted to these dimensions. In collaboration with Mark Reed, a distinguished experimental physicist at Yale, we are planning to fabricate and test a Paul-type trap in the range of 50 nanometers and less that would provide virtual electric potential walls for confining a DNA molecule within required limits.
 
So this trap would be better at controlling the motion and localization of DNA than a nanopore alone?
 
We hope so. Being multidimensional in character, a Paul nanotrap will provide additional degrees of freedom of DNA motion control, on top of the usual electrophoresis and nanopore confining forces. However, the main advantage of the Paul trap is relaxation of critical dimension control, which simplifies the device fabrication. Critical dimension control becomes very problematic at dimensions below 10 nanometers due to resist resolution and pattern transfer limits of electron-beam lithography. This approach avoids these fabrication difficulties, since the electrostatic trapping volume is significantly smaller than the fabricated dimensions, which are in the range of 20 to 100 nanometers.
 
What have you already shown experimentally or in simulations?
 
So far, we have developed the lead idea, the concept. What we have shown by model computational simulations is that the Paul trap functions are preserved when the trap dimensions are reduced to the nanometer range, both in vacuum and in an aqueous environment. Theoretical predictions say that van der Waals forces from the trap walls, as well as micro-inhomogeneities in the dielectric constant and in the temperature of the water do not destroy the 2D or 3D confinement of an ion in the trap.
 
Of course, this is a theoretical model, and the main goal of this grant is the experimental proof of principle of the concepts, which we want to achieve by fabricating and testing the functions of the quadrupole nanotrap. This is where our main focus will be.
 
What do you regard as the greatest challenge in this project?
 
The greatest challenges of the main milestones of this project are the fabrication of the quadrupole nanotrap and testing its ion confinement, in particular its DNA confinement functions. While fabrication of the trap may be achieved by reactive ion etching through a dielectric and metal stack, higher resolution spatial information is needed to verify detailed trapping of DNA. We envision [using] total internal reflection fluorescent microscopy, or TIRFM, to achieve this. These techniques are either already available or are currently being developed in the group of Mark Reed at Yale.
 
What is your timeline for fabricating and testing the device?
 
In the first year, we will fabricate scaled designs at the level of a few micrometers, allowing for easy-to-fabricated center electrodes and recessed quadrupole electrodes. We will test their validity with ion species and fluorescently tagged particles, both in vacuum and in solution, to verify the quadrupole field shape. Then we can test variants of the electrode design. In the second year, we will fabricate at the 30- to 50-nanometer level for the DNA localization experiments. 
 
To characterize the trap, we will first employ vacuum ion trapping and air or solution nanoparticles to check the expected potential distributions, measured with optical microscopy. Next, we will move to liquid, with the use of fluorescently tagged molecules or colloidal quantum dots to image and understand trapping. Finally, we will use a fluorophore-tagged DNA strand to assess and visualize its localization. However, high-resolution spatial information is needed for the final verification of detailed trapping by TIRFM in the second year of the project.
 
Would the ultimate performance of this device be similar to what is expected from other nanopore sequencing approaches?
 
What distinguishes this approach from others is that the trap provides a localized central minimum for the target DNA structure, which is defined by the electrostatic potentials and electrode shapes, and not by the physical dimensions, which can be significantly larger than the 1- to 2-nanometer dimensions required by other approaches. This will allow for easier fabrication of an array of the devices on a chip. If successful, this may provide a faster and cheaper device that would share the common goal with other nanopore sequencing devices.
 
When do you think this could be used by researchers? Have you taken any steps in pursuing this commercially?
 
Concerning the main as well as the long-term goal of the project, which is DNA sequencing, we expect that not only us, but the efforts of other researchers will result in the $1,000 genome in five to seven years, probably by 2015. We also hope that our trap will become part of a DNA sequencing device soon after the project ends successfully. This idea is already protected by a patent. 
 
What do you think is the most immediate application for the nanotrap?
 
Obviously, the main targeted application is DNA sequencing. But it can be used for any application where control of localization and motion of a single molecule are important, such as single-molecule sensing and recognition, or for chemical identification of biological and environmental analytes at the single-molecule level.

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