DNA gripped in nanopores

May 14, 2009

Molecular biologists, including the cool dudes from CSI, use gel electrophoresis to separate DNA fragments from each other in order to analyze the DNA. A team of researchers under the leadership of Vici winner Serge Lemay, has now shown for the first time how the gel influences the movement of the DNA. The researchers drove a single DNA molecule through a nanopore in order to analyze the forces on the DNA. The results of the research were published on March 29 in Nature Physics.

The movement of DNA under the influence of an electric field, electrophoresis, is caused by negatively charged groups in the basic structure of the DNA. These negative charges are shielded by positive ions, that accumulate in a layer around the DNA. These ions retard the movement of DNA under the influence of an electric field. The electrostatic forces and counteracting of the gel are inextricably linked to each other. Therefore up until now it seemed impossible to investigate these two factors independently.

Combination of technologies

The researchers developed nanopores with different dimensions in order to vary the spatial confinement of the DNA. They then used an optical pincet to grab a Perspex ball to which the DNA was linked. In this way they pulled the DNA molecule through a nanopore. The various dimensions of the holes offered them a direct look at the hydrodynamic linkage between DNA and the nanopore.

The measurements revealed that the retarding forces exerted by the , slowly decreased if the DNA moved through a larger nanopore. The bigger the pore the smaller the . Calculations based solely on electrostatic forces had yielded other expectations. The hydrodynamic environment was found to exert a greater influence than had been expected.

The team used a unique combination of different techniques. This combination formed a good basis for highly promising developments in single molecule techniques based on nanopores. For example, such techniques render the detailed detection of the interaction between proteins and DNA possible.

More information: Origin of the electrophoretic force on DNA in solid-state nanopores. Nature Physics, Stijn van Dorp, Ulrich F. Keyser, Nynke H. Dekker, Cees Dekker, Serge G. Lemay.

Source: Netherlands Organization for Scientific Research

Explore further: New technique could dramatically lower costs of DNA sequencing

Related Stories

New technique could dramatically lower costs of DNA sequencing

December 12, 2007

Using computer simulations, researchers at the University of Illinois have demonstrated a strategy for sequencing DNA by driving the molecule back and forth through a nanopore capacitor in a semiconductor chip. The technique ...

Crammed with charged DNA, pressure rises inside virus

June 5, 2007

It could be an artist’s depiction of someone’s stomach before and after a rather decadent meal. But it is a 3-D cryoelectron microscope reconstruction of the cross-section of a virus, before and after cramming itself ...

Real-time observation of the DNA-repair mechanism

May 22, 2008

For the first time, researchers at Delft University of Technology have witnessed the spontaneous repair of damage to DNA molecules in real time. They observed this at the level of a single DNA molecule. Insight into this ...

Researchers use 'nanopore channels' to precisely detect DNA

April 5, 2007

Researchers at Purdue's Birck Nanotechnology Center have shown how "nanopore channels" can be used to rapidly and precisely detect specific sequences of DNA as a potential tool for genomic applications in medicine, environmental ...

Recommended for you

Particles self-assemble into Archimedean tilings

December 8, 2016

(Phys.org)—For the first time, researchers have simulated particles that can spontaneously self-assemble into networks that form geometrical arrangements called Archimedean tilings. The key to realizing these structures ...

Nano-calligraphy on graphene

December 8, 2016

Scientists at The University of Manchester and Karlsruhe Institute of Technology have demonstrated a method to chemically modify small regions of graphene with high precision, leading to extreme miniaturisation of chemical ...

ANU invention to inspire new night-vision specs

December 7, 2016

Scientists at The Australian National University (ANU) have designed a nano crystal around 500 times smaller than a human hair that turns darkness into visible light and can be used to create light-weight night-vision glasses.

0 comments

Please sign in to add a comment. Registration is free, and takes less than a minute. Read more

Click here to reset your password.
Sign in to get notified via email when new comments are made.