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April 24, 2012

ORNL, Yale take steps toward fast, low-cost DNA sequencing device

Oak Ridge National Lab - Researchers at Oak Ridge National Laboratory and Yale University have developed a new concept for use in a high-speed genomic sequencing device that may have the potential to substantially drive down costs.

"The low cost--if it can be achieved--would enable genomic sequencing to be used in everyday clinical practice for medical treatments and preventions," said Predrag Krstic, project director and former ORNL physicist now at the University of Tennessee-ORNL Joint Institute for Computational Sciences.

ORNL and Yale University researchers have created nanopores, or extremely narrow channels of water, with a radio-frequency electric field capable of trapping segments of DNA and other biomolecules.

Small journal - Tunable Aqueous Virtual Micropore




A charged microparticle can be trapped in an aqueous environment by forming a narrow virtual pore—a cylindrical space region in which the particle motion in the radial direction is limited by forces emerging from dynamical interactions of the particle charge and dipole moment with an external radiofrequency quadrupole electric field. If the particle satisfies the trap stability criteria, its mean motion is reduced exponentially with time due to the viscosity of the aqueous environment; thereafter the long-time motion of particle is subject only to random, Brownian fluctuations, whose magnitude, influenced by the electrophoretic and dielectrophoretic effects and added to the particle size, determines the radius of the virtual pore, which is demonstrated by comparison of computer simulations and experiment. The measured size of the virtual nanopore could be utilized to estimate the charge of a trapped micro-object.

ORNL and Yale University researchers used theory and computation, validated by experiments, to prove that a charged micro or nano particle, such as a DNA segment, can be confined in an "aqueous virtual pore." The water provides a stable environment for DNA integrity while the virtual "walls" allow DNA to move through the nanopore without interacting with physical walls.

As an added advantage, scientists can control the size and stability of a virtual nanopore by external electric fields, something they cannot do with a physical nanopore.

"As a single DNA polymer is translocated through a synthetic nanopore, we use the physical detection of single molecules to read electric signals that identify DNA bases," Krstic said.

To help control and localize DNA, ORNL and Yale scientists created the aqueous nanopore embedded in water based on a linear Paul trap - a device that traps particles in an oscillating electric field - and experimentally proved its trapping functionality. There were some doubts that a charged micro or nano particle could be confined by the quadrupole oscillating electric field of the Paul trap when filled by aqueous solvent, but ORNL computation and Yale experiments prove that water actually helps stabilize trapping mechanisms, making sequencing methods more feasible.


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