Researchers create novel nanotechnique to sequence human genome

April 15, 2009
In this illustration, a DNA strand is leashed to a magnetized, iron-oxide bead, with a magnet hovering over it. As the bead moves toward the magnet, the DNA strand passes through nano-sized opening slowly enough that its base pairs can be read. Credit: Hongbo Peng/IBM Research

Since the human genome was sequenced six years ago, the cost of producing a high-quality genome sequence has dropped precipitously. More recently, the National Institutes of Health called for cutting the cost to $1,000 or less, which may enable sequencing as part of routine medical care.

The obstacles to reaching that goal have been primarily technological: Scientists have struggled to figure out how to accurately read the 3 billion base pairs - the amount of DNA found in humans and other mammals - without time-consuming, inefficient methods.

Physicists at Brown University may have an answer. They introduce a novel procedure to vastly slow the DNA's movement through openings that are used to read the code. In the journal Nanotechnology, the physicists report the first experiment to move DNA through a solid-state nanopore using magnets. The approach is promising because it allows multiple segments of a DNA strand to be threaded simultaneously through numerous tiny pores and for each fragment to move slowly enough through the opening so that the base pairs can be accurately read.

"When it comes to sequencing anyone's genome, you need to do it cheaply, and you need to do it quickly," explained Xinsheng Sean Ling, professor of physics, who joined the Brown faculty in 1996. "This is a step in that direction."

The idea of reading DNA by threading strands through tiny openings is not new. Scientists have shown that an applied electric field can drive the DNA molecules through a nanopore, a tiny hole in a membrane. But in those experiments, the base pairs moved too quickly through the openings for the code to be read accurately. So, while a large electric field is needed to draw the into the pore, Ling explained, the same field moves the DNA too quickly, a classic scientific Catch-22.

The trick is to figure out how to slow the strands' movement through the opening so the base pairs (A, T, C, and G) can be read. To solve that, Ling and Hongbo Peng, the lead author who performed the work as a graduate student at Brown and who now works at IBM, attached the DNA strand to a bead using a streptavidin-biotin bond. Like previous researchers, they used an electric field to drive the DNA strand toward the pore. But while the strand could pass through the pore, the bead, with a 2.8-micron diameter, was too large for the pore, which has a diameter of only 10 nanometers. So the bead was stuck in the hole with the attached DNA strand suspended on the other side of the membrane.

The Brown researchers then used magnets — they call them "magnetic tweezers" — to draw the iron-oxide bead away from the pore. As the bead moves toward the magnets, the attached DNA strand moves through the — slowly enough so that the base pairs can be read.

The scientists named their process "reverse DNA translocation" because, as Ling explained, "the DNA is essentially caught in a tug-of-war. And the speed of translocation will be controlled not solely by the but by striking some balance between the magnetic and the electric fields. From there, we can tune it to dictate the speed."

The scientists report their technique reduces the average speed of the DNA strand's passage by more than 2,000-fold. "It can be slower even. There is no limit," Ling said.

A similar experiment has been done using optical tweezers, Ling said, but it involves only one DNA strand at a time. The Brown method sends multiple strands through the nanopores simultaneously. "It is scalable," Ling said.

The researchers expect to test their technique in experiments using bacterial DNA.

Source: Brown University (news : web)

Explore further: Nanoscopic gold spheres can be reversibly bound to DNA strands reversibly bound to DNA strands

Related Stories

Genetic Material under a Magnifying Glass

January 28, 2008

The genetic alphabet contains four letters. Although our cells can readily decipher our genetic molecules, it isn’t so easy for us to read a DNA sequence in the laboratory. Scientists require complex, highly sophisticated ...

Nanopore Sequencing Could Slash DNA Analysis Costs

March 27, 2009

( -- Over the past 5 years, researchers have been exploring the use of nanoscale pores as nucleic acid sequencing tools. In theory, such pores should generate a unique response characteristic of each of the four ...

Recommended for you

Physicists develop new technique to fathom 'smart' materials

November 26, 2015

Physicists from the FOM Foundation and Leiden University have found a way to better understand the properties of manmade 'smart' materials. Their method reveals how stacked layers in such a material work together to bring ...

Mathematicians identify limits to heat flow at the nanoscale

November 24, 2015

How much heat can two bodies exchange without touching? For over a century, scientists have been able to answer this question for virtually any pair of objects in the macroscopic world, from the rate at which a campfire can ...

New sensor sends electronic signal when estrogen is detected

November 24, 2015

Estrogen is a tiny molecule, but it can have big effects on humans and other animals. Estrogen is one of the main hormones that regulates the female reproductive system - it can be monitored to track human fertility and is ...


Adjust slider to filter visible comments by rank

Display comments: newest first

1 / 5 (1) Apr 26, 2009
Geeez. Magnetism to mess with the flow and motion of DNA.

Who'da thunk it?

I wonder what other aspects of electrical function mess with the proper motion and behavior of DNA?

Cell phones?

Power lines?

Dr. Royal Raymond Rife?

How big of a list does there have to be before people willingly take note of such important things in a meaningful way?

Hmmm..DNA...electrochemical activity, anyone? And on the near quantum level. Yet, in another article here, we have 'extraordinarily sensitive' quantum organized structures that are EXCRUCIATINGLY sensitive to any magnetic field.

Now, what is DNA?

It is a quantum level organized electrochemical organic structure.

Now go read about DR. Royal Raymond Rife.
not rated yet Apr 26, 2009
Here be the sensitivity/entanglement article. DNA has many similar aspects:


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.