X-Message-Number: 15713
From: "Mark Plus" <>
Subject: "Tiny Silicon Devices Measure, Count And Sort Biomolecules"
Date: Wed, 21 Feb 2001 19:59:20 -0800



Source:   Cornell University News Service (http://www.news.cornell.edu/)

Date:   Posted 2/21/2001

Tiny Silicon Devices Measure, Count And Sort Biomolecules

San Francisco -- Up to now, most biologists have studied the molecules of 
life in test tubes, watching how large numbers of them behave.
But now researchers at Cornell University in Ithaca, N.Y., are using 
nanotechnology to build microscopic silicon devices with features comparable 
in size to DNA, proteins and other biological molecules -- to count 
molecules, analyze them, separate them, perhaps even work with them one at a 
time. The work is called "nanofluidics."

"This will expand the methods for analyzing very small amounts of 
biochemicals, and create new abilities unanticipated by the test-tube 
methods," says Harold Craighead, Cornell professor of applied and 
engineering physics and director of the Cornell Nanobiotechnology Center 

Craighead described some of his laboratory's work in a talk, "Separation and 
Analysis of DNA in Nanofluidic Systems," at the annual meeting of the 
American Association for the Advancement of Science (AAAS) in San Francisco 
on Feb. 15. The talk is part of a two-day seminar on nanotechnology.

Craighead's work began with a quest for an "artificial gel" that would 
replace the organic gels used to separate fragments of DNA for analysis. 
Traditionally this has been done by a process called gel electrophoresis. 
Enzymes are used to chop DNA strands into many short pieces of varying 
length. The sample is placed at one end of a column of organic gel and an 
electric field is applied to force the DNA to move through the gel. As they 
slowly snake their way through the tiny pores of the material, DNA fragments 
of different lengths move at different speeds and eventually collect in a 
series of bands as a ladder-like structure that can be photographed using 
fluorescent or radioactive tags. The resulting image, Craighead explains, is 
just a list of the lengths of the fragments, from which scientists can read 
out genetic information. So he looked for other ways to sort DNA fragments 
by length that would allow scientists to work rapidly with small amounts of 
material. Craig! ! head and his colleagues manufactured a variety of 
silicon-based nanostructures with pores comparable to the size of a large 
DNA molecule.

They have explored three approaches to DNA separation:

o Devices with openings that are less than the "radius of gyration" of the 
DNA fragments -- When suspended in water, a DNA chain quickly coils into a 
roughly spherical blob. When pressed against a barrier with openings smaller 
than the radius of this form it must uncoil to pass through. Paradoxically, 
larger molecules do this more quickly, because they press a broader area 
against the obstacle, offering more places where a bit of the chain can be 
drawn in to start the uncoiling. When an electric field is used to drive a 
mix of DNA fragments along a channel with several such barriers, fragments 
of different lengths will move at different speeds, arriving at the far end 
in a series of bands not unlike those seen in gel electrophoresis.

o Sorting by physical length -- A DNA sample is placed just outside a 
"forest" of tiny pillars arranged in a square grid, and an electric field 
applied to force the molecules to move into the grid. (Imagine pulling a 
coiled watch spring into a long, straight alley.) If the electric field is 
turned on just briefly and turned off before the molecule gets all the way 
in, the uncoiled portion will snap back out, just as the watch spring will 
pull back into its coil. But once the entire molecule is inside the grid, 
there is nothing to pull it back out. By varying the length of the electric 
field pulse, the researchers can control the length of the DNA strands that 
are collected in the grid. In addition to providing a way to measure strand 
length, Craighead says, this tool could be used to separate DNA for other 
work. If two molecules of different length are present at the start, the 
shorter molecules could be moved into the grid, leaving a pure sample of the 
longer strands outs! ! ide.

oLateral diffusion by length -- When moving through a grid of tiny pillars, 
DNA chains are constantly buffeted by moving water molecules that can knock 
them off-track, a process called "Brownian motion." If the pillars are flat 
vanes, all angled in the same direction, movement of all the chains will be 
skewed to one particular side. Shorter, lighter molecules will be pushed 
farther, so molecules can be sorted or measured based on the distance they 
are moved across the track when they emerge from the grid. Craighead calls 
these devices "Brownian ratchets." These techniques all work with molecules 
en masse, but Craighead's group is also studying ways to work with single 
molecules, or at least to work with molecules one at a time. They have built 
microscopic tunnels just large enough for DNA molecules to run through in 
single file. Nanofabricated light pipes are placed on either side of the 
tunnel. Although very large, DNA molecules are still too small to be seen 
directly by v! ! isible light, but they can be tagged with other molecules 
that fluoresce when exposed to an ultraviolet laser, and the fluorescence 
can be detected, with larger molecules giving off longer pulses of light. In 
addition to counting the number of molecules of a given size in a sample, 
these devices could incorporate switches that could shunt molecules of 
different sizes into different channels, Craighead says.

While most of the work up to now has been with DNA, Craighead says, these 
methods could also be applied to the study of other large organic molecules, 
including proteins, carbohydrates and lipids.


Related Web site -- The Craighead Research Group: http://www.hgc.cornell.edu


Note: This story has been adapted from a news release issued by Cornell 
University News Service for journalists and other members of the public. If 
you wish to quote from any part of this story, please credit Cornell 
University News Service as the original source. You may also wish to include 
the following link in any citation:


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